I will answer every question about evolution you have

originally posted by: PhotonEffect
Yes genes are very important in all if this, but epigenetics is showing that variation can occur without changes to the underlying nucleotide sequence. Hence no mutations required. And with new technologies to study the genome, researchers are finding evidence of epigenetic signatures more and more.

You may be mistaking me. I don't consider the mutation of genes to be the only cause of variation. However, it is the primary. Epigentics is a very interesting subject.

originally posted by: PhotonEffect
I'm asking specifically how a researcher, looking at an organism or a group of organisms, can determine whether those phenotypes came about due to natural selection or genetic drift?

The effects can be seen through the genetic diversity of a population, that's the point I was was trying to put across. Genetic drift leads to a smaller gene pool in one way or another (Bottlenecking/Founders), and thus significantly reduced genetic variety.

We can show that a species had gone through some sort of genetic drift in the past by testing populations of the same species and then comparing their DNA. One sign of genetic drift would be a detection of a significant number of haplotypes that spread across many, if not all of the tested populations.

There was a great article I read a while ago that went into details on how some researchers discovered a Bottlenecking within pandas that occurred around 43,000 years ago. It went into more detail on the methods they used. I can see if I can find it if you'd like?

originally posted by: PhotonEffect
My take way is that it's not at all an easy process, which I suspected. Yet much of how we verify certain evolutionary mechanisms in a population is based on it's size. Genetic drift, it's said, can't be measured in large populations. But since we can't easily determine what is sufficiently large (or not), it seems it must involve quite a bit of guesswork.

It can be measured in larger populations, at least if there was a time when the population had once gone through genetic drift (as mentioned above).

Nevertheless, in some areas in biology, there is a lot of guesswork. But again, no one is claiming there is none.

originally posted by: PhotonEffect
Taking your volcano example – if you were to observe those organisms which survived, how do you determine if it was due to some beneficial trait that allowed them to escape the inferno (natural selection), or that perhaps they just happened to be in the right place at the wrong time (genetic drift)?

You're viewing it in kind of the wrong way. Genetic drift only occurs after the fact that the volcano wiped out or separated the population. It could very well have been natural selection that had allowed parts of the population to develop some kind of more keen sense for seismic activity, or something far more mundane like part of the population enjoyed more sun than the others, and due to their basking they were out of the way of the lava that separated/killed the rest of the population.

It's not necessarily a matter of "did natural selection do it or did genetic drift do it" because they are on a different spectrum in this context.

originally posted by: PhotonEffect
Would a selectionist see it differently?

I have actually not heard of a 'selectionist' or a 'neutralist' before you've mentioned it.

originally posted by: PhotonEffect
Are you saying that traits are only the effect of mutation? If so, I will respectfully have to disagree.

No, I'm not claiming that.

originally posted by: PhotonEffect
Thanks, yes, I've read this one. I think it does well at explaining that there is not at all a linear relationship between genotype and phenotype. So a mutation is not generally going to cause meaningful effect on its own.

Correct!

originally posted by: PhotonEffect
Okay, so you do think mutations alone are responsible for trait expression.

I was just referring to the mechanisms that I listed, of which you asked me to choose from. Out of the one's I listed, Mutations would be the one.

a reply to: Barcs

originally posted by: Barcs
I don't think I've ever said that it's simply mutation and natural selection, and that's it. And no it's not antiquated because genetic mutation and natural selection are observed CONSTANTLY in ongoing experiments.

Well you did say that. And I have my doubts that genetic mutations represent the majority of all trait expression, especially in light of all the fascinating research over the last 20 years.

You have to consider this Barcs, only 2% (maybe less) of our genome actually codes for proteins. Think about that... Now don't red flags go up?

Evolution needs variation, yes. But I will argue that variation does not come predominately from genetic mutations. Most people assume that it does because frankly that's what we've been told since high school biology. Except when the Human Genome Project and ENCODE started revealing results from GWAS many began to wonder where had all the heritability gone? Turns out it's not all in the underlying genetic code where we'd expect.

In other news, I just read an interesting article about a geneticist who runs a lab at Washington State University and his team is finding that epimutations actually can influence genetic mutations. Now what?

From the article:

Washington State University researchers say environmental factors are having an underappreciated effect on the course of disease and evolution by prompting genetic mutations through epigenetics, a process by which genes are turned on and off independent of an organism’s DNA sequence.

Their assertion is a dramatic shift in how we might think of disease and evolution’s underlying biology and “changes how we think about where things come from,” said Michael Skinner, founding director of the Center for Reproductive Biology in WSU’s School of Biological Sciences.

“The ability of environmental factors to promote epigenetic inheritance that subsequently promotes genetic mutations is a significant advance in our understanding of how the environment impacts disease and evolution,” they write.

originally posted by: Barcs
It's great that you think other factors are involved, but can you please break down how many species are said to have evolved via epigenetic factors, that do not include genetic mutations?

It's great? I just want to be current on my understanding of evolution, don't you?

What I'll do is provide a basic list highlighting where epigenetics is known to play a role, because I think the number of species is too many to list:

Bacteria – from the abstract...

In contrast with the standard assumption, our model predicts that adaptive resistance cannot be explained by increased mutation rates. Our results identify the molecular mechanism of epigenetic inheritance as the main target for therapeutic treatments against the emergence of adaptive resistance

Plants
Insects
Mammals (pdf)
(Mice) –I never once thought genetic mutations had anything to do with instincts. This may be how it happens.
(Humans)
BRCA1 might actually be influenced by epimutations.
Invertebrates

There are many many more. In fact, I have a strong intuition that epigenetic factors play a significant role in the evolution of all organisms. And once the theory changes to accommodate this, you'll know exactly who told you first.

originally posted by: Barcs
Little is known about epigenetics, more work needs to be done before incorporating it into MS. Epigenetics has only been observed in a select few simple species and it is about gene EXPRESSION, not the development of new traits. If I'm wrong about this, please correct me,

Why do you keep saying that little is known? No offense, but that's where you're misguided, because a lot is known. Sure, more still needs to be studied. But heck, we've known about epigenetics for over 50 years now. I will say though, the value from the research that's been done has probably been realized more so in the last 15 years with the sequencing of full genomes.

Actually Epigenetics has been shown to influence not only development, but also the expression of new traits in all sorts of complex animals. Are you aware that locusts and grasshoppers are actually the same species? Locusts are actually morphs of grasshoppers when the environment changes (typically due to overcrowding, then they swarm like madmen!). What's crazy is they look and act very different from each other. And guess what they suspect could be the impetus of this Jekyll and Hyde phase change? Yep. And yep.

Okay, I think I've gotten carried away with this post, so I'll have to come back with a part two..

originally posted by: PhotonEffect
a reply to: Barcs
Are you aware that locusts and grasshoppers are actually the same species? Locusts are actually morphs of grasshoppers when the environment changes (typically due to overcrowding, then they swarm like madmen!). What's crazy is they look and act very different from each other. And guess what they suspect could be the impetus of this Jekyll and Hyde phase change? Yep. And yep.

Very cool. I'll have to look into it

Part two

originally posted by: Barcs
Can you explain to me how natural selection is ever not a factor, even in cases of genetic drift? I thought I questioned this in my last response.

GD and NS are two separate mechanisms that, by definition, operate differently on populations. It's either one or the other. So when drift is said to be working, allele distribution happens randomly which would be in lieu of natural selection, which is said to happen due to fitness effects (non-random), and vice versa. You'd have to familiarize yourself with the differences to understand what I'm asking.

So I guess my question still stands – how does any one decipher between the effects of GD vs NS in a natural setting?

I say it's mostly by guesswork and assumptions, when not based off of computer models.

originally posted by: Barcs
I was hoping you could provide a model of evolutionary diversity that does not include natural selection or at least explain how this would be possible. I'm only familiar with the standard model, I have not seen any others.

Neutral Theory of Molecular Evolution is at least one.

The neutral theory of molecular evolution holds that at the molecular level most evolutionary changes and most of the variation within and between species is not caused by natural selection but by genetic drift of mutant alleles that are neutral.

originally posted by: Barcs
I never said that it wasn't drift. You are looking at it like an either/or scenario. I think you missed my point in breaking up my post the way you did. I was trying to say that natural selection STILL plays a role in populations that experience genetic drift. How could it not?

Hey I did't make this stuff up, them's is the rules. They're considered two different mechanisms.

originally posted by: Barcs
Are beneficial mutations more rare than epigenetic factors in evolution?

Yes, I think so.

originally posted by: Barcs
Because genetic mutations are not just recombination of DNA. There are several different ways that genetic coding sequences can be changed.

Recombination is not considered to be a mutational event. They are two different things.

originally posted by: Barcs
I just don't understand the big fight here against genetic mutations and NS as if they aren't responsible for the vast majority of observed evolutionary changes even when epigenetics may apply.

The debate stems from the fact that you and many others think evolution predominantly works as a function of natural selection and genetic mutation. And I don't think it does. We know that there isn't a direct relationship between the genome and phenotype. In fact many phenotypes can come from the same genome (polyphenism). It's very plastic. The prevailing view is that natural selection shapes adaptation. Well I don't agree that NS is the predominant "force". It doesn't make any logical sense to me. Epigenetics does, very much so. And the more you read the more you'll realize that many other scientists agree.

You seem to think that epigenetics is some niche area of research. It's actually quite broad and is gaining more and more momentum. It's answering a lot of questions that the old view established by the MES can't answer.

You should look into it more.

Here's one for you. It was brought up in another thread.

What's your take on the recapitulation theory? Not just what it is, but if it's got any feasibility, in your opinion.

a reply to: Ghost147

Yeah pretty neat stuff.

originally posted by: TerryDon79
What's your take on the recapitulation theory? Not just what it is, but if it's got any feasibility, in your opinion.

I'm actually not too familiar with the details of the concept. I know of it, and I know it's been thoroughly debunked, but I have also heard that some scientists still feel that parts of it could still apply to some degree.

Unfortunately I'm not familiar enough with it to really state an opinion on the matter

originally posted by: Ghost147

originally posted by: TerryDon79
What's your take on the recapitulation theory? Not just what it is, but if it's got any feasibility, in your opinion.

I'm actually not too familiar with the details of the concept. I know of it, and I know it's been thoroughly debunked, but I have also heard that some scientists still feel that parts of it could still apply to some degree.

Unfortunately I'm not familiar enough with it to really state an opinion on the matter

I'd seriously have a read up about it (more than just a wiki read).

The idea is pretty good, imo, but the idea is too broad.

I just wondered what peoples opinion on it was (when I say people, I mean people who believe in evolution).

originally posted by: Ghost147
You may be mistaking me. I don't consider the mutation of genes to be the only cause of variation. However, it is the primary. Epigentics is a very interesting subject.

Right, okay, but is it at all possible that what was initially thought/assumed/inferred to have been [phenotypic] variation by genetic mutation was actually variation by some other means?

originally posted by: Ghost147
The effects can be seen through the genetic diversity of a population, that's the point I was was trying to put across. Genetic drift leads to a smaller gene pool in one way or another (Bottlenecking/Founders), and thus significantly reduced genetic variety.

Right, I understand all of that. My point is that natural selection can also reduce the variation of a population. GD doesn't just reduce variation, as the distribution can "drift" the other way. Same with NS.

Really, GD and NS are essentially the same thing, absent a human derived just so story for how the phenotype came to be. So if both do the same thing but by different means, how are we able to know which one is at play? From my understanding, it's not a straightforward determination. Yet the application of evolutionary theory rests on knowing these values. It seems flawed to me.

originally posted by: Ghost147
We can show that a species had gone through some sort of genetic drift in the past by testing populations of the same species and then comparing their DNA. One sign of genetic drift would be a detection of a significant number of haplotypes that spread across many, if not all of the tested populations.

Okay, I will look into this.

originally posted by: Ghost147
It can be measured in larger populations, at least if there was a time when the population had once gone through genetic drift (as mentioned above).

Nevertheless, in some areas in biology, there is a lot of guesswork. But again, no one is claiming there is none.

This is where I'm running into some issues, because the Theory of Evolution by Natural Selection is touted as one the most bedrock solid theories ever conceived. It's stood the test of time. Yet it seems that the underlying measurement and application of it is a bit shaky. My intent is to understand how we measure these values, and here you are admitting that guesswork is involved, which I've already suspected to be the case.

originally posted by: Ghost147
You're viewing it in kind of the wrong way. Genetic drift only occurs after the fact that the volcano wiped out or separated the population.

I don't think I'm viewing it the wrong way though. NS occurs after the fact too. You're telling me that after the volcano struck we have a population of survivors that is completely random and will lead to drift. I'm asking, how do you know it wasn't because of a keen ability to escape the lava? Which would be more along the lines of selection.

originally posted by: Ghost147
It's not necessarily a matter of "did natural selection do it or did genetic drift do it" because they are on a different spectrum in this context.

Sure it's a matter of that. People think they are seeing the effects NS everywhere in nature. That it's the cause of most if not all adaptations. I'm trying to undermine this by asking how can this be verified reliably and accurately? It can't most of the time. So the theory, it seems, rests on guesswork. That's what I'm saying.