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Much of the literature for laypeople seems to consider (and to spread the idea) that an animal (or a plant, I guess) is characterised by its genome. I do not know whether the same goes for more professional literature. Even on this site, the tag is defined as The entirety of an organism's hereditary information, which seems to imply that it contains a description of all that can be be inherited.

It seems to me that attempting to define an animal with the sole knowledge of its genome (let alone recreate it as envisioned by some people) does not really make sense, without the complementary knowledge of the cell structure of the ovum that has to interpret this genome.

This question seems never to be seriously addressed in lay literature.

Is it the case that this decoding machinery evolves much less than the genome itself? This could be expected, since changing the decoder has usually more important, global and drastic effects than changing the genome, which may result in a very localized effect. Hence, changes to this machinery are less likely to give a viable being.

To refine that question (unless the moderator prefers this to be a separate question):

Is there any study of the diachronic evolution of that genome decoding machinery in a given species, or of the synchronic differences between species, which would probably give a measure of the speed of diachronic evolution of that machinery?

When two close species cannot mate, is it analysed (for some cases) whether it is due to difficulties in combining the two genomes, or to the fact that the ovum of one cannot properly interpret the genome of the other?

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  • $\begingroup$ Don't forget that the initial cell machinery provided in the ovum is quickly replaced by that of the newly-formed zygote. (e.g. ribosome half-life is about 5 days). Also, and perhaps this analogy does not hold, but kickstarting a bike might be very different from driving down a road, but the engine itself defines the properties of the vehicle, not the way in which the engine was started. $\endgroup$ – MBever Nov 18 '16 at 12:34
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    $\begingroup$ You might want to rephrase the question to ask about the general case of converting genotype to phenotype, because "the ovum" has nothing to do with it -- obviously, since the vast majority of living things do not have ova. Moreover as you suspect you have two unrelated questions here -- genotype to phenotype, and speciation, which have very little to do with each other. $\endgroup$ – iayork Nov 18 '16 at 13:48
  • $\begingroup$ @iayork I cannot well rephrase my question because I am not competent enough to use most words and concepts with precision. I am rather naive on all this, but shocked by presentations I found too simplistic. I refer to ovum as the only way I know to specify the context that initially interprets the genome - assuming there is such a specific initial phase, which I am note sure of. Also I first considered the issue for animals. Actually I wonder whether reproduction can always be separated from cellular differentiation (same genome, but machinery uses it differently) $\endgroup$ – babou Nov 18 '16 at 14:48
  • $\begingroup$ The short answer is that there is elaborate machinery needed to convert genetic information into a phenotype; that's nothing to do with the ovum; and it's hardly ignored in biology as it's the topic of intense research. It's difficult to answer your question any more than that since it seems to rest on so many incorrect assumptions. $\endgroup$ – iayork Nov 18 '16 at 14:54
  • $\begingroup$ @iayork Actually I am not assuming more than what you just said: I meant to say that genetic information is meaningless without knowledge of the machinery that will convert it to a phenotype (I did not know to express it that way). The rest (ovum included) is just my failed incompetent attempt at expressing it in a more concrete way. My question is only why most presentations for non specialist are ignoring that fact. I do expect biologist to deal with it, but is there a reason this is not explicited for the wider public, to avoid misconceptions. Maybe I should indeed rephrase. $\endgroup$ – babou Nov 18 '16 at 15:57
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Nice question! Let's start by talking about different forms of heritability.

What is heritable?

Here is a list of things that can be inherited. Some of them are only ('mainly' would be more correct that 'only') transmitted to the offspring while others can also be transmitted to any individual in the population.

The term epigenetics is used with several meaning. In its narrowest sense it refers only to modifications (typically methylation) on top of the DNA sequence or on top of histones (histones are proteins around which the DNA is wrapped). In its broadest sense, it refers to any element of hererdity that is not caused by the DNA sequence. In the below list, I will avoid using the term epigenetics.

What can be inherited:

  • DNA (obviously)
    • Modification of the sequence of DNA
  • Methylation on DNA
    • Modification of (typically) methyl group added on nucleobasis
  • Methylation on histone
    • Modification of (typically) methyl group added on (typically) the tails of the histones.
  • Environment (or rather macro-environment)
    • The term environment can be used with different definitions. Histone modification is generally considered as being the environment of the genome typically. I will however make a (somewhat) arbitrary distinction between this micro-environment and the more intuitive macro-environment
    • Individuals affect their environment and therefore can shape the environment for their descendents. An obvious example is a beaver dam which last longer the the life of a single beaver. Two key concepts here are niche construction and Ecosystem engineering. You should have a look at the post Does modern theory of evolution include modification of physical environment?
  • Memetics (See wikipedia > meme)
    • A meme is any idea or element of culture that can be transmitted. This type of inheritence is particularly important is species that have high cognitive abilites such as humans.

In this kind of discussion, there is often someone who stand up to talk about plasticity, developmental noise and mutational noise to mess things up. I will just consider them as phenotypic trait and will not much attention to them for the moment (even though part of my research is focused on these three concepts).

Consideration of the non-genetic inheritence in the literature

I like that you noticed that "the tag is defined as The entirety of an organism's hereditary information". Such definitions are common and grounded in an old view of inheritance. As listed above, there are other things than the DNA sequence that is inherited by the offspring. While all biologists know that, it is true that few really acknowledge the existence of these other forms of inheritence in their daily thoughts.

Some authors have argued that these other types of inheritence must not be neglected. Odling-Smee and colleagues wrote a whole book on the subject (Niche Construction: The Neglected Process in Evolution). Some have even argued that we should rename our theory of evolution to the light of the existence of non-genetic inheritence (see Laland et al. 2015). My feeling is the vast majority of biologist recognize the existence of these types of inheritence but do not consider that it is worth a renaming of the theory of evolution (current named modern evolutionary synthesis). Some would not consider this renaming necessary either because they neglect the important of these other forms of inheritence or because they just don't think it is worth renaming our theory even in the recognition of the importance of these other processes.

Viewing the cell as a decoder can be misleading

In your question, you are suggesting to view the cell as a decoder of DNA. IMO, this is misleading. In this discussion, I will exit science and enter in the realm of philosophy (identity).

What is generally considered as the mechanism of decoding DNA is actually part of our geome itself (consider typically the importance of tRNA and rRNA). If uneasy with basic concept of gene expression you might want to have a look at an intro course such as Khan Academy from the section Classical and molecular genetics to the section Gene regulation.

Also, I would argue that all the elements that are being transmitted to the offspring shall be considered as being the offspring. If it turns out (which we actually pretty much know is wrong) that histone modification explains more in the phenotypic variance than genetic variance, it would intuitively be unfair to see histone modification as just being a decoder of the genome. We would rather be tempting to see histone modification as central and the DNA sequence as a side-effect.

Layman literature

You say "This question seems never to be seriously addressed in lay literature". Richard Dawkins book called the extended phenotype, while maybe not directly addressing your question does a good job at playing out with thee concept of environment vs gene separation. You might want to have a look at it.

Note that the laland et al. 2015 cited above is easy to read and would be a good source of information for a layman.

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I think the reason for the simplification in many contexts is that the machinery that converts genotype to phenotype is ALSO specified in the genome; yes, it is necessary to have that machinery present for cells of all types to function and to create new cells (whether single-cellular or multi-cellular), but this machinery itself is not really inherited; the machinery (proteins and functional RNA) that exists in a founder cell cannot be inherited except in a very unusual and extreme cases.

There can be differences in translational machinery, for example see wikipedia, but precisely because as you write, "changes to this machinery are less likely to give a viable being" - that means that changes to this machinery are most likely to be lethal and therefore do not persist in a population.

Failures of fertility between species are due to simpler factors, and the transcription machinery is highly conserved across many species that are not cross-fertile.

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Craig Venter made his first synthetic bacteria by first making a synthetic genome containing all the genes required to run a bacteria (Mycoplasma. mycoides). His team then inserted this synthetic genome into related species of bacteria (Mycoplasma capricolum). The synthetic genome than took over the cell and over time turned the cell from one species to another. http://www.nature.com/news/2010/100520/full/news.2010.253.html

So... just because it does not make sense to your gut, does not make it wrong. Gut feelings are great... it is how we think the world should work. A short hand. But just because we think the world should work one way, does not make it so. The world and biology has many antigut concepts.

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