chadn737

So it was a simulation and not an actual case? While its certainly possible for these things to work in simulation, the real question is whether this plays out in reality. In animals, the typical epigenetic mechanisms, namely DNA methylation, is reset every generation. In plants this works somewhat differently resulting in more known cases of true epigenetic inheritance in plants.

How was it determined to be "epigenetic"?

Selective breeding, aka "artificial selection", refers specifically to selective changes imposed by humans. Evolution has proceeded for millions of years without this (aka "natural selection") and certainly does not need selective breeding to continue as nature already does this constantly. Stress and the environment can induce various effects through gene-environment interactions, but these are typically not heritable and therefore its long term effects on the evolution of species is questionable. That being said, the concept of gene-environmental interactions is not new....it goes back at least to one of the fathers of populations genetics, R. A. Fisher, in the early 20th century. For some reason in the last few years the effects of the environment on modulating the phenotypic outcome of the gene has been rebranded as some brand new discovery. Typically when you see this, it is not coming from geneticists, but rather other fields of biology that seem to have not paid much attention to the history of genetics....that and people wanting to jump on the epigenetics bandwagon. Is it possible to adapt without some sort of "selection", whether natural or artificial? Thats kind of a complicated and vague question. First, what is meant by adaptation? Are we referring specifically to a positive adaptive response to some sort of external factor that negatively impacts the reproduction of a species? Then by that definition, all such adaptations will be the result of "selection" by that factor and hence either natural or artificial selection. Its rather tautological. On the other hand if we define "adapt" purely in a sense of changes in phenotype or allele frequency...which really isn't an adaptation per se....then there are three other mechanisms: mutation, genetic drift, and gene flow. In evolutionary and population genetics, four mechanisms driving changes in allele frequency are recognized: natural/artificial selection, mutation, genetic drift, and gene flow.

There ARE other genetic differences between populations. Enough so that we can trace ancestry and many of these genetic differences have phenotypic consequences of evolutionary importance. Some of the better studied would be lactose persistence, adaptations to altitude, various traits giving malaria tolerance/resistance (think sickle cell), etc. The caveats being that these trait differences do not break down along traditional/historical racial categorizations like asian/black/white and that while some of these traits may be present or more prevalent in one population than another, that does not mean that it is fixed within that population. Human genetic differences tend to exist in gradients spread geographically, so that if you take individuals that have been geographically isolated (like Iceland versus New Guinea) you will find a lot of differences, but there will exist a gradient of these differences over the numerous peoples that live between. Racism is a mindset based on prejudice and an incorrect understanding of biology and genetics, however, in the counter-reaction to racism, there has been a general rejection of the notion of phenotypic and genetic differences between humans that has reached an equally absurd level of "anti-scientism". This has profound implications for the advancement of healthcare. Disease alleles and other differences affecting drug reactions, etc exist in different proportions in different populations. A drug tested primarily in populations of European descent may have very adverse effects in populations of largely African descent or vice versus. Rational individuals can accept this fact without it inducing any prejudice. Unfortunately many cannot accept that such relevant differences do exist without it implying some sort of malice, much to the detriment of us all.

What is a "processed food"? Really any modification to food, whether it be grinding, cooking, etc is processing of some sort. Man hasn't ate "raw" food on a regular basis for a long long time.

There are also some noted open access journals, namely the PLoS journals and eLife, which are of high quality. You can also find occasional open access papers in many journals.

Then do the calculations. If your plant is heterozygous and you self it, 1/4 will be homozygous for the first mutation. It all depends on what generation of your mutagensis you are talking about. Are you working with the M1 or the M2?

viXra exists because arXiv has standards. Anything published on viXra is suspect.

The environment is in constant interaction with an organisms genetics and does shape responses, however, these responses occur with in a range of possible phenotypes are determined genetically. Through alteration of gene expression levels, timing or location of gene expression, protein modification, etc; there will be an altered response. The thing about such a response is that it is rarely ever heritable, meaning that rarely will it be passed on to the next generation. In the few true cases of epigenetics, where a response is passed on to the next generation, it rarely persists for more than a couple of generations. Such short term alterations means that these non-genetic responses do not have the permanence to be of long term evolutionary consequence. Because of the stability and reproducibility of DNA, this is ultimately the substrate upon which evolution acts over long term. The environment does have the effect through Natural Selection of eliminating deleterious alleles and promoting the spread of beneficial alleles, however, the environment did not induce these specific changes. One way to think about it is in terms of what is called the fitness landscape. Here peaks are viewed as variants underlying beneficial traits, the higher the peak, the higher the fitness of that allele. In contrast, valleys represent deleterious alleles. The landscape represents all the possible phenotypes. If mutation were non-random and environmentally induced, we would expect an organism to maximize its fitness and so adapt by developing phenotypes with the highest peak. That is not the case however, as organisms often get trapped on the smaller peaks. While these peaks still represent beneficial phenotypes, they are not the maximally fit phenotype. Once trapped on one of these lesser peaks, the organism would typically have to have cross one of the valleys to the next highest peak, a process which requires accumulating multiple deleterious mutations.

The transgenerational effects of low birth weight I think may be one of the few cases of actual transgenerational epigenetics in mammals that has held up to any degree. Although its very hard to rule out the effects of genetics. Even in homozygous selfing plants, many assumed "epigenetic" effects have turned out to be in reality genetic. It becomes much harder to rule this possibility out with mammals where selfing is impossible, making maintaining homozygosity very difficult. The other problem I have is that the transgenerational effects of low birth rate is not really adaptive as far as I can tell....at least its not beneficial in any sense. Not trying to debate with you on this, the point I'm trying to make is that while these would be non-random, they are not beneficial in the sense that natural selection would favor these effects and therefore maintain them.

Can you provide an actual paper or data that supports the claim "nutritionally abetted larger size human babies tend to make larger size babies in their turn, regardless of genetics". I find this highly suspect, especially the assertion that they have eliminated genetics as a root cause. If it is simply a matter that "nutritionally abetted" babies happen to live in an environment that provides such conditions and that that subsequent generations also live under such advantageous conditions, then this neither heritable nor adaptive. Its simply a result of positive environmental factors enabling a population to achieve its full genetic potential. The same can be said of clutch sizes. Furthermore, physiological/biochemical changes are in no small part genetically determined. Some people tan easily, some do not tan at all given the same environmental exposure. This variation is genetic. When discussing gene x environment interactions, we must be careful not to confuse the effects of alleles as being static. Rather, particular alleles determine a range of potential phenotypes. No matter how much some people work out and diet, they will have an upper limit in their ability to develop muscle mass. The genetics of another person, however, may enable them to achieve greater muscle mass than someone else, a potential that is genetic, but realized only under certain environmental conditions.

I can't read spanish, but I think this is simply a mistranslation or confusion over an analogy. Non-disjunction, i.e. the failure for disjunction to occur during cell division is when two sister chromatids fail to separate. They are "sticky" in the sense that the two chromosomes remain attached when they are supposed to separate. However, there is no "sticky gene" or "sticky genes". There can be multiple causes for non-disjunction to occur.

Then she is wrong.

There are lots of causes of genetic disease and this makes no sense. Either you have misunderstood her or she has no clue what she is talking about.

A "sticky gene"? Your teacher is full of nonsense sounds like.

The word "gene" was originally coined long before we even knew that DNA existed and even longer before we knew DNA was the molecular basis of heredity. Originally, it was simply a term for a "unit of heredity". Because no known physical basis of heredity was known at the time, "genes" were abstract concepts and not referring to an actual physical stretch of DNA. The first geneticists would look at how traits, whether physical or behavioral, segregated and estimate the number of genes, the dominance/recessiveness of alleles, and the linkage of genes. This was all done in abstract, so at the time, it was valid to say that there is a "gene for X". After the discovery of DNA as the basis of heredity, after it was known that proteins were encoded in the DNA, there was added a molecular definition of the word "gene" to mean a stretch of DNA that encoded a protein. What is interesting is that these two definitions coexisted and continue to coexist....in no small part depending upon the specialty of the scientist. Population geneticists, theoretical geneticists, quantitative geneticists still tend to think of genes somewhat in the abstract as "units of heredity" and not necessarily as protein coding sequences. Molecular biologists and biochemists think almost exclusively of "genes" as protein-coding. With the discovery of non-coding RNAs with biological functions, the definition of a "gene" has been expanded somewhat to include those segments of DNA that code for non-coding RNAs. So if you want to get anal about the definition of a gene, learn some history of genetics first. Dan Graur....although he is more of an evolutionary biologist than a geneticist. Some great essays last couple of years attacking ENCODE. He makes a distinction between "junk" and "garbage" which has made me rather fond of the term "junk DNA". The way he and others describe it, junk is stuff you have lying around that may someday be of use, while garbage is...well...garbage. Its a very long term evolutionary view, where the "junk DNA" lying around right now may not have a function, someday through evolution it may obtain a function.

I would think so, but I know next to nothing about the development of artificial intelligence. Nor am I a computer scientist, however, in essence isn't this the concept behind evolutionary algorithms?

The Extended Phenotype argues that we cannot limit the definition of phenotype to the biology of an organism alone, but should extend it to include culture and how we influence our surroundings. However, that does not meant that this or even our biology is determined exclusively by genetics. There is always a dynamic interaction between genetics and environment. The way to think about it is to consider the effect of the gene as defining a range of possibilities. Typically when people think about the effect of a gene variant they think in regards to simple traits, where the effects are binary. For example, if a pea has the allele for a yellow color, the pea will be yellow, otherwise it will be green. For some simple traits, that is true. However, for most traits, it is more appropriate to think of an allele as defining a range of values. For example, lets say you have a particular allele that influences height. It is more appropriate to think that this particular allele will allow you to grow to a height within a range of 5.0 ft to 5.7 ft. If you are malnourished, then you will not reach the full potential that this allele will allow you to grow to, so you may only be 5.0 ft tall. If you grew up without disease and are properly nourished, you may achieve 5.7 ft. When you think of it in terms of a range of values, then that gives room for environmental factors to also shape the final outcome. Someone else with a different allele may be able to achieve a maximum height of 6.1, but if environmental influences are such, they may not reach the full potential. Gene variants for many, maybe most traits are potentialities. Does that help clear things up?

DNA does not "alter itself". Maybe this is simply a confusion of words, but the DNA is not in directing in any fashion its own evolution. While organisms may alter their environment, shifting selection pressures, this does not mean that the DNA is driving the selection. For one, phenotypes are not determined wholly by DNA. It is a complex interaction between Genetics and Environment. While some traits are very heritable, others are less so, and some exhibit almost no heritability. Perhaps the most relevant kind of traits, behavioral, are often the most variable and exhibit some of the lowest degrees of heritability. Humans alter their environment more than any other and often how we alter our environment is driven by cultural factors. But culture is not genetic. Yet it shapes our environment and ultimately the selective pressures on us.

What you have described is standard Darwinian evolution. Just because you use different terminology does not mean that your idea is novel or different. I think one of the terms that best emphasizes this point is "coevolution", particularly since the example of a hummingbirds beak is a perfect example of this. Here you have a situation where two species evolve alongside each other, where the changes in one drive changes in the other. This can develop into a "loop" as the two species become increasingly specialized as they coevolve. Its not just that a hummingbird's beak fits certain flowers so well, but also that the flowers have evolved to fit the hummingbird in a loop of coevolution. The idea of coevolution dates back too Darwin himself, who really expounded upon it in Fertilization of Orchids. Sexual selection, particularly when it drives species to possess ever more grandiose traits, such as the peacocks tail, would be another example. We also have long known examples as it pertains to humans. Namely, as we have domesticated animals and plants, this has shaped our own evolution as it relates to our ability to consume and tolerate certain foods. The point being that the idea that natural selection can act in a circular loop, often driving traits towards extremities, is not novel. Its been present in evolution since the beginning and expanded since. One thing I learned quite a while ago is that there are a lot of smart people who have been working in biology for decades and typically, if you think you have a brand new idea, you probably don't.

Most of the genome of a typical organism is not under selection, but evolving neutrally. Dependent upon factors such as genetic hitchhiking and genetic drift, deleterious alleles can actually increase in frequency. This says that DNA does not direct selection on itself.

I find this confusing. Either you are simply reiterating the concept of Natural Selection on the genome or you are proposing that DNA is directing selection on itself in some fashion.

The information you want may not be available because its possible nobody has done the research. Otherwise.....google scholar + pubmed and just start digging deep.

Yes, he could, but it is unlikely. Furthermore, the father will not be exactly 1/16th Cherokee. Because of recombination he could be more, but more likely it is less.

The evidence against it has been building for a while after many failures to replicate. There was even a website where other labs would post their attempts to replicate it. Not to mention the duplicated images she has used....