Do you have a better way of measuring large scale genotype and phenotype difference?
-_- considering the fact that we can actually sequence genomes, I'd say yes. Heck, given that species of animals is partly determined by ability to reproduce, it entirely neglects the population of Triops I am working with, which reproduce via self-fertilization. Phenotype is not the best indication of the degree of difference in genotype, however, so I wouldn't consider phenotype in and of itself to be
That taxonomy is a human invention seems like a pretty trivial point when it still effectively communicates the fact that we're talking about large scale change.
Actually, from looking at taxonomy so much, I'd say genus is more a measure of the number of divergences that retain certain common traits we chose to focus on rather than a consistent measure of a specific degree of similarity/difference. For example, while all members of the genus Nepenthes seem to be capable of reproducing with each other, this is not the case with all members of the genus Drosera. These are both plant genera. Genus doesn't even have consistency on whether or not the members share the same number of chromosomes.
Yes, I am well aware that phenotype variation has to do with genes. Should I rephrase then? Changes to genotype and changes to phenotype aren't directly related. Happy?
-_- they are directly related. Rather, all changes in phenotype are not due to changes in the genome exclusively. But straight up, unless the mutation itself is neutral (like changing a codon to another codon that selects for the same amino acid), chances are the mutation will have some impact on phenotype. Assuming the cells actually use that gene to begin with, which is why mutations as an embryo cause so much more change than the mutations your cells acquire throughout adult life.
Yes I believe I mentioned that epigenetic changes have to do with the expression of genes.
I believe you're mistaken. There are epigenetic mechanisms that can alter what organisms have the potential to express. Take the bacterial SOS response for example.
The SOS Regulatory Network:
The SOS Regulatory Network
-_- note the list of regulatory genes in your source and that all of them are just as prone to being influenced by mutations as any other gene. Heck, cell specialization in and of itself is the result in only certain genes being expressed within the cell, but the process by which the excess genes are kept inactive is mediated by protein products of genes. Genes influenced by hormones and other signals given off by cells in close proximity. However, the process by which the cells do it is nevertheless a part of the genome just as much subject to mutation as anything else.
The issue with treating epigenetic influences as a major cause of evolutionary trends is that the ones not tied in some way to genes directly have practically no staying power. If epigenetic changes were the most prominent source of variation, the differences between humans and other members of the same species living in different environments would be far more extreme within a relatively short period of time.
In fact to go a little further on that, you might want to see Timescales of Genetic and Epigenetic Inheritance:
https://www.cell.com/cell/fulltext/S0092-8674(07)00121-3
-_- your source is over a decade old and incorrectly suggests that mutation rates in microbes (which I assume to be any single celled organisms, but most likely refer to prokaryotes) are higher than in human cells:
"Point mutation rates vary between organisms, and values range up to about 10^4 per base pair per generation for certain RNA viruses, around 10^6 to 10^8 for most microbes, and 10^9 per base pair per cellular generation for human cells."
-_- given that epigenetics is a new study in genetics, perhaps the most rapidly developing area of science within the past 20 years, why would you ever use a source more than a decade old (this source is from 2007)?
One of the few examples of multicellular organisms this paper actually refers to is the result of an injection of RNA into cells (not exactly something that would normally happen and could be expected to be a source of inherited changes in the wild). The other simply involves genes impacting the expression of each other to produce variable genotypes, and that since genes interact, methylation of one of these interacting genes will result in a different phenotype. That is, genetically identical individuals won't necessarily end up with identical phenotypes. True as this is, it isn't directed any more than mutations are. Here's the part of your source I am referring to:
"In multicellular organisms, a great deal of recent effort has focused on the role of transgenerational inheritance of RNA molecules. Most notably, microinjection of double-stranded RNAs into Caenorhabditis elegans is sufficient to produce a loss-of-function phenotype in a substantial fraction of F2 animals, and this effect persists for up to 80 generations after the injection (Fire et al., 1998, Vastenhouw et al., 2006). A small number of molecules were sufficient to initiate this heritable effect with thanks to amplification of the interfering RNAs by RNA-dependent RNA polymerase. In mammals, epigenetic inheritance of RNA molecules was recently described in which expression of unusual Kit RNAs in the germline of mice resulted in a phenotypic effect (on coat color) in the progeny of the affected mice such that two genetically identical mice might differ phenotypically based on their parents' genotypes (Rassoulzadegan et al., 2006). This last example mirrors the phenomenon of paramutation in plants, which was first discovered in maize in the 1950s by R. Brink (see also the Essay by V. Chandler, page 641 of this issue)."
To view changes in bacterial cells and the cells of other single celled organisms as being analogous to changes in multicellular organisms is a big mistake. In single celled organisms, daughter cells are composed of the cytoplasm, etc., of a parent cell, thus are invariably going to be directly influenced by any epigenetic factors which impacted that parent cell. However, in multicellular organisms such as humans, the sex cells are heavily protected from genetic change compared to somatic cells, thus they are not hit immediately with those epigenetic changes, only having some of the tendencies of the parent as a result of being somewhat exposed. As a result, epigenetic inheritance gradually increases influence as we age, and also changes as we age and are exposed to different environmental conditions. This makes epigenetic changes not factor in nearly as much in a 20 year old as it does in a 60 year old, yet those daughter cells would be impacted practically as much as the parent cell was. This also means that despite a degree of inheritance, the less similar of an environment you live in compared to your parents, the less of a shared epigenetic pattern can be observed. The changes are just too unstable and don't hit early enough to be as big of an evolutionary influence as you want to assert they are, and they aren't less random in a sense of selecting for beneficial traits in multicellular organisms. And all of the gene mediated ones obviously are subject to genetic mutation themselves, not independent of it.
Ok, the difficulty I have with this is that you're banking on the same or similar (allegedly random) mutations to occur universally.
How so? Very different gene combinations can result in extremely similar phenotype, so I see no reason I would need to rely on that. Mutations are not purely random, though, they are just the most random aspect of evolution. Random assumes that all mutations are equally probable, and that simply is not the case. Mutations that insert a large number of bases are far less common than ones that insert only 1, and certain regions of genomes are far more prone to mutations than others. Hence why mutations in eye color are so uncommon in humans yet more than 10% of hemophilia types A and B occur in individuals with no family history of the disease whatsoever.
Either nature isn't very creative and has to regularly wait on the correct type of variability, (which may or may not come) or it might be reasonable to think that there are programmed default responses.
You seem to be assuming that there are a ton of different traits that would be equally beneficial for a given environment, and that there aren't any traits so extremely beneficial that any environment of a given type would select for it very powerfully. For example, in all aquatic environments, having a streamlined body with very little drag is a beneficial trait to have, and there aren't many body shapes which optimize it. Thus dolphins and sharks end up with very similar body shapes despite extremely different evolutionary histories. Tons of different genomes result in similar body plans, though, so the same mutations don't have to occur to end up with this result.
However, in a cold environment, there are lots of very different ways for animals to adapt, from growing very thick fur to having blood that contains anti freezing agents to having thick layers of fat. Organisms which share those traits despite not sharing an ancestor with those traits may have similarities in their relevant genes, but the genes are not identical by any means. There are a lot of mutations that will result in fur becoming thicker, for example.
No. You are obviously very wrong about what I think.
Apparently so. But again, you just seem to be assuming that a lot of variation is more the result of epigenetics rather than the genes themselves changing, but this is demonstrably false (for multicellular organisms in particular). If, for example, the key differences between a polar bear and a grizzly bear were epigenetic, their genomes would be a lot more similar to each other than they actually are, to the point that they could potentially be confused for each other. Plus, there is a huge variety in epigenetic tendencies between humans, but it doesn't result in much phenotype variation, and any that does result doesn't persist for more than a few generations with any consistency. Significant and stable instances of epigenetic change resulting in changes in phenotype that are adaptive to the environment are extremely rare in multicellular organisms and they aren't stable traits that can be consistently passed on.
Even within individual multicellular organisms, the trait that is purely a result of gene expression changes alone can change back and forth for no really good reason. For example, I have a professor that grows day lilies. In day lilies, the trait of variegation is extremely unstable. Individual plants can go back and forth between producing leaves with and without variegation, and it is practically impossible to breed for this trait with any consistency. It also has no benefit to the plant whatsoever, which is why it is so rare in the wild. Yet, we observe plants that go back and forth between the more beneficial fully green leaves and the variegated ones, with no purpose to that change in gene expression. Your assumption that epigenetic changes are more centered on beneficial phenotypes in multicellular organisms doesn't have strong evidence supporting it. At best, the changes have a temporary benefit.
I don't buy the idea that *random* changes accumulate over enough generations. I think the weight of the evidence supports the idea that biology has a programmed path.
-_- you do know that epigenetic factors mainly turn genes off and that they aren't directly accomodating changes in environment, right? That is, people addicted to tanning that have kids aren't going to improve the ability of those kids to tan due to how tanning influences epigenetic tendencies. In fact, exposing yourself to anything that makes the process of methylation more prominent, such as smoking, decreases quality of health for oneself and the next two generations following you. The only way for methylation of a gene to be beneficial is if that gene is mutated in a very specific way and you have redundant copies of it. That is, the gene is mutated and competes with the functional variants for resources to such an extent that they can't function if it is active. And epigenetic factors aren't "pre-programmed" to target those.
-_- it's more along the lines of "that's a really great cell division regulation gene you got there. Wouldn't it be a shame if it was rendered inactive at age 55, despite being an entirely beneficial gene?"