DNA may not be life's instruction book, just a jumbled list of ingredients | Hacker News Reader

DNA may not be life's instruction book, just a jumbled list of ingredients

phys.org

58 pointsSCAQTony22 comments

In essence, the papers argue that DNA is microcode ROM, and for any particular cell the actual "user code" is contained in "the molecules that regulate the cell's DNA and other functioning systems."

>For example, the gene for eye color exists in every cell of the body, but the process that produces the protein for eye color only occurs during a specific stage of development and only in the cells that constitute the colored portion of the eyes. That information is not stored in the DNA.

How does the molecule arrangement and information get passed to offspring?

That varies a lot. Probably simpler to consider a single celled organism like a bacterium. Bacteria will only multiply by splitting themselves into two copies of themselves. When talking about heredity, most people focus on the DNA. But it pays to remember that each child cell is recieving half of the parent's proteins, RNA, salts, and other essential vitamins etc. So effectively we can think of each child cell as inheriting the parent's cell makeup as well as the DNA.

A quick concrete example in humans is the inheritance of antibodies between mother and child which is transfered via the placenta.

This is all the phys.org press release seems to be saying: heredity is DNA + all the other stuff. As far as I am aware, this is not controversial at all in biology. The actual substance of the two papers is a model for understanding that process, if it's a good model I am sure it would be a good contribution to evolutionary science.

Fair enough, but let's go beyond bacteria. In plants and animals, am I right in thinking that the contribution of these extra-chromosomal components is primarily from the female parent?

If I am not mistaken, there are several evolutionary explanations, such as for a 50-50 sex ratio being a stable equilibrium, and for the benefits of altruism, that assume an organism's fitness comes equally from the male and female parent. If, however, the female parent has significantly more contribution to the offspring's fitness, would that alter the calculus in these cases?

Sounds about right.

Humans inherit mitochondria only from the mother, and an egg cells is about 0.12mm vs a sperm cell at 50μm long.

Edit: fixed a word

Sharing the contents of a dividing cell is important. But unless both of the two resulting cells can produce more of the initially shared stuff, they are limited to the half-size of the original cell.

What controls this production?

AFAICT, only DNA and RNA fit the bill.

Well protein production is regulated by other proteins that are indeed made from instructions encoded in the DNA. But you could imagine that a given cell has produced certain proteins that turn some genes on and others off. This pattern of control can be passed onto both daughter cells. This process is also somewhat stochastic, so not every cell in the population behaves exactly the same, so their daughters wouldn't either.

> That information is not stored in the DNA.

“Information” here is not referring to the molecule for eye color. It is referring to the information about when and where the gene is to be expressed (ie the molecule is created).

I think this has been known for a while though. That deriving molecular folding and structure from DNA sequences is a tremendously hard problem, and that “command and control” of the entire apparatus is at least as hard or harder of a problem.

That's funny I thought experiments had been done where growth of an eye could be triggered in unusual places specified in the DNA. sorry, no reference.

It gets even better: teratomas. Fully formed teeth, hair, bones and organs can grow in "other" parts of the body. It's a kind of cancer, but it demonstrates that germ cells (undifferentiated cells that divide and differentiate to become specialized cells, like tooth tissue) contain everything necessary to form complex, accurate structures far from the original area.

Most people would say that's because everything required to make a tooth- the process of making a generic tooth, not the structure of a specific tooth- is encoded in DNA. Of course, it also requires that there be various proteins present in the cancerous germ cell- cellular components that themselves are encoded by DNA.

If I were to put this as succinctly as possible, I woudl say "there appears to be some amount of non-DNA cellular state which affects development, that cannot be traced back directly to expression of protein from DNA in the cell, that is heritable when cells divide". Good luck proving that! The experiments would be nearly impossible to run.

I thought what used to be called "junk DNA" was now thought to be regulatory instructions?

Parts of DNA contain regulatory instructions and other very vague signals. Vast regions of it are just repetitive sequence that probably does not have any functional effect. What hasn't been explained: why is there so much "unproductive RNA production"- that is, RNA that gets transcribed from DNA regions that appear to have no functional contribution. Also not explained: why is there functional selection on regions that seem not to produce anything "useful"?

People have proposed taking genomes and replacing all the parts that aren't under functional selection with random DNA, and showing the organism is still viable. Other folks have proposed cutting out those parts. Nobody has run a convincing experiment on a higher animal to show this is possible, or that the results are convincing in any way.

I’m no expert in biology, but I live with one. This statement is incorrect. The DNA is the blueprint. It’s like saying the information of a Mandelbrot set doesn’t exist in its expression. It’s not a perfect analogy, but in both cases, the information in question is emergent from the starting point and the rules. Both parts are defined in DNA.

Edit: I have a feeling that this article isn’t telling the researcher’s whole story. The implications of epigenetics are vast.

I am not a biologist but biologists have discussed the idea that phenotype changes can occur without genotype change, since a long time. Although genotype inarguably influences the development and expression of phenotype, selective forces ultimately operate on phenotypes.

The concept of genetic canalization addresses the extent to which an organism's phenotype allows conclusions about its genotype. A phenotype is said to be canalized if mutations (changes in the genome) do not noticeably affect the physical properties of the organism.

This means that a canalized phenotype may form from a large variety of different genotypes. If canalization is not present, small changes in the genome have an immediate effect on the phenotype that develops. [3]

Mary Jane West-Eberhard famously told "“The 20th century has been called the century of the gene, the 21st century promises to be the century of the environment.” ... ” Darwin, who didn’t even know genes existed, had it right, he left open the possibility that new traits could arise because of environmental influence." [1]

An example of such epigenetic and heritable trait changed in morphology without change in DNA is here [2]

[0] https://en.wikipedia.org/wiki/Mary_Jane_West-Eberhard

[1] https://www.smithsonianmag.com/science-nature/how-the-tree-f...

[2] https://www.ncbi.nlm.nih.gov/pubmed/12483213

[3] https://en.wikipedia.org/wiki/Genotype%E2%80%93phenotype_dis...

One would have though the recent developments in bringing extinct species back [0] would have made it plain. In that case they inject the DNA into some other species ovum. You don't end up with some hybrid - you get whatever the DNA programmed.

https://www.nationalgeographic.com/magazine/2013/04/species-...

Reminds me of a clever exploit. The code for the OS is backdoor free, but the running OS has a backdoor. Once the running OS compiles a new OS from code it installs the backdoor. This way, no matter how much the code is inspected, backdoor is never discovered. However, each fresh version of the OS still has the backdoor. The exploit is always part of the running system information even though it is never in the static codebase. No reason why our biological information system cannot have an analogous aspect if our vastly inferior human designed systems can. (Also makes me wonder about the claim that the bazaar improves security. Maybe it only provides the appearance of greater security.)

This is framed more classically in terms of the compiler and toolchain: https://www.cs.cmu.edu/~rdriley/487/papers/Thompson_1984_Ref... "Reflections on Trusting Trust"

The only way that analogy works is with some kind of self replicating prion disease, which would get selected out pretty quickly. The main fallacy that people tend to make drawing comparisons with biology and computers is the degree to which biology is in a stable equilibrium (occasionally punctuated).

There are lots of endogenous retro viruses (ERVs) in various states of genetic activity. However the only time this comes up is when considering ERVs from e.g. pigs for organ transplants. I remember reading some time ago about an effort to remove all the ERVs from a line of pigs to make that safe. I don't remember what happened of that.

You do see some unicellular organisms that will prioritise maintenance of proteins over DNA if the proteins have low copy number and are critical for survival.

Doesn't DNA encode proteins that both constitute, assemble, and perform the functions of the cell? It's not a list of ingredients, it's a library of blueprints for machinery and specialized components. The information necessary to operate these molecular machines is built into their structure, different outputs require different molecules not different instructions.

Incredibly complex structure can arise from simple rules, see Turing Patterns https://en.m.wikipedia.org/wiki/Turing_pattern and cellular automata.

Haven't there been nucleus swap experiments that showed transfer of major cell characteristics between species like e.g. different protists?

I vaguely recall reading something similar.

What does it prove though? We already know that cellular components are the same or similar across all life.

Here's an experiment: take two zygotes from each of two animals, and do a DNA swap. That's 2x2 combinations of environment-DNA pairings. Compare the 4 offsprings. If this can be done, it has been done a million times already, I presume. What's been observed?

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