Until it was derailed, several people and I were having a fruitful discussion about evolution in a thread about the Abrahamic god. At the whims of a power mad mod, I have created this thread to discuss evolution, genetics and why life is the way it is. Many philosophers have attempted to come up with the meaning of life, and, now, finally, we have an answer to that question. It's not a very nice answer, but it is an answer that exhaustively applies to everything from pre-life self reproducing RNA molecules, to whales, dinosaurs, fungi and people. A little about me: I was a scientist in a lab studying the genetics of speciation and hybridization until recently. I discovered that, although I love science, I do not love doing science. It's tedious and it eats your life - one researcher I admire very much said that he only had two priorities in his life, his family and research, and research came first. What I hope to do with this thread is 1) Provide a history and background for evolution. Too often science is taught as a body of facts, rather than the story of discovery. 2) Do a general Q&A about topics in evolution. Any questions, I'll try to answer them or find a way to answer them. Finally 3) I want to persuade the doubters that, at the very least, it is the most supported and widely exhaustive theory for why life is the way it is.
First, let's start with some misconceptions from the previous thread. I want to first note that I am not writing about anyone as if they are stupid; evolution is a very complex, nonintuitive theory and there's a lot of misinformation out there. If I hold up one of your quotes as a misconception, please look at it as a learning opportunity and not as if I am mocking you. Many, if not all, misconceptions are ones that I have held myself. Goldshifter starts us off with the following: A very influential biologist, Lamarck, theorized that evolution could occur through the efforts of an individual organism. By craning its neck to the sky, a giraffe could influence its offspring in such a way that they would have longer necks. This explained much about the morphology of animals and the suitability of each organism's morphology (physical appearance and traits - do stop me if I get too caught up in the jargon) to its individual niche. This view has been, mostly (more on this later), discredited. Amputees do not have limbless children. Gaining strength by rebuilding muscles is an example of phenotypic plasticity, not of evolution. Say what? Ok, there are two aspects to an organism: their genotype and their phenotype. The genotype is the genetics of the critter, what genes they actually possess and are able to pass down to their offspring. The phenotype of an organism is formed through an interaction of its genes and the environment. You might have genes for great height, but if you don't receive the proper nutrition as a child you won't ever reach that height. Aspects of our phenotypes are fixed - without the aid of contacts or plastic surgery your eyes will stay the same color. Other aspects are plastic in that they are able to respond to the environment. The influence that phenotypic plasticity has on evolution is a hotly debated subject right now - one prominent biologist, Mary West Eberhard, has said that phenotypic plasticity leads and genotypic changes only occur after the fact, fixing what was initially an individual responding to the environment. After all, why spend the time learning to ride a bike if you can just have that knowledge innately? In any case though, it is not evolution. So what IS evolution? Evolution is the change in allele frequency over time. Alleles are variations of a particular gene, their frequency in an environment is the fraction of a population that has that individual allele. Different events can cause the perturbation of that frequency; perhaps one allele has a slightly significantly better reproductive rate than the other, perhaps a disease sweeps through a population killing off all individuals with one or the other allele, perhaps due to random luck an individual with a new, extremely beneficial mutation is hit by a sperm whale hurtling through the atmosphere. There's no telling! In any case, what's important to note is that evolution does not occur within individuals, it occurs among populations. More glossary terms: Adaptation - the dynamic evolutionary process by which a species becomes more adept at utilizing its niche. This does not refer to phenotypic plasticity, as when we workout and become stronger, but genetic changes that are passed down to our offspring. Fitness - the contribution that an individual makes to the next generation, or the benefit of having a particular gene or combination of genes. Survival of the fittest does not imply survival of the triathalon runners, but survival of the lazy son of a gun who had a hundred children.
This is much closer, but still has some errors! Phylogenesis =/= evolution, it is its own process by which new taxonomic groups are generated. Evolution can occur within a species, often called microevolution, or form new species, called speciation. Epigenetics is one form of phenotypic plasticity, one that can be passed down to your offspring. It involves alterations to your genes, or gene expression, that occur through your interaction with the environment. Gaining muscle is not an example of an epigenetic change, unless it leads to alterations of your DNA. Mutations are random with respect to fitness. Certain portions of the genetic code are more fixed than others - they have more robust repair programs, have less genetic variation and are less likely to mutate. Other regions, such as noncoding, nonsense regions, mutate freely. But these mutations do not occur to assist in the evolution of a trait. Evolution does not look forward, does not plan, it is forever looking back. Evolution does not only occur between generations - refer back to our definition of evolution as a change in allele frequency. If I have fifteen birds that are black and five that are white, then I fire a shotgun into the group and kill 7 black birds and 1 white bird, the ratio has changed from 3:1 to 2:1. Evolution has occurred without any time passing. Sneaks up on you like that.
Species are the only taxonomic classification based upon biological reality, but, the definition of what a species is precisely is difficult to nail down. Where does the difficulty arise? Well, to explain let's look at some pictures. Here is a phylogenetic tree: There's some cool things about it! It illustrates the evolutionary history of a group of organisms, it's fractal in nature, such that if you were to examine the evolutionary history of sharks it would also be a complex tree, but in some ways it neglects the reality on the ground so to speak. The delineations are complete. A more accurate depiction of evolution might look something like this: Notice the difference? Species are diffuse, diagnosed more as constellations of traits. Rather than being a sharp delineation, it's a gradient, but that doesn't mean it's not necessarily there. Ernst Mayr ventured forth the modern definition of species that is most commonly used by organismal researchers: a population of mutually interbreeding individuals. Already the astute will notice some problems - how do you diagnose a species of asexual organisms? How do you know if a fossil represents a species? What if two individuals will interbreed, but never get the opportunity to do so? What if they didn't interbreed, but due to environmental disturbance, they now do? All of these cases happen in the wild because speciation is not like flipping a switch, it is the slow accumulation of differences that make two individuals incompatible with each other. These differences can occur at different junctures of the reproductive effort. For example, in Lake Victoria (or maybe Lake Malawi, not sure) there is a diversity of cichlid fishes. The lakes of the Rift Valley in Africa were formed recently, I believe in the last 12 million years or so, and, after an individual cichlid species was introduced to each, they underwent an amazing adaptive radiation (when a founding species diversifies into many different species) with the fastest speciation rate of any vertebrate. They exploited different niches, developed different mating rituals and different colors to advertise who they were looking for. Diving in these lakes is like diving in an aquarium, there is just a panoply of fish at every turn of every possible species. Then humans started exploiting the lake and polluting it. Agricultural runoff released sediment into the water, clouding it, making it impossible for the fish to recognize these colors that they advertised to each other. Down is up, dogs are marrying cats and the fish started to hybridize. So were they separate species before? Have we lost species? Is the hybrid a new species? It depends upon which concept you're using for your study. They were isolated as species before the formation of a zygote, prezygotic isolation, but there's other forms of isolation. For example, the sterility of mules occurs after fertilization, post zygotic isolation. Theory suggests that initially species separate and become adapted to their microenvironment. Imagine two populations of rodent, one living in grass, the other in trees. Genes that facilitate life in the trees may be deleterious (bad) for organisms living in the grasses, and vice versa. Offspring between the species, even if fertile and viable, may not be adapted for either environment. This situation promotes advertising - if you are a female grass rodent, carrying tree rodent offspring may be extremely bad for your overall reproductive yield. Kids gotta eat yo. By advertising if you are a grass rodent or a tree rodent, you have made it more likely to find the appropriate mate and have gained fitness. Gradually, incompatibilities between your genetic codes will increase, leading to greater and greater isolation. Speciation, then, is a process, one that is ongoing in many, many populations, but that does not neglect the reality of the classifications. Honestly, can go on all day about this, some very cool situations arise. Hybridization, the transfer of genetic material between different species, is a huge thing. Here's how deep the rabbit hole goes:
And so we have some tunes: [ame="https://www.youtube.com/watch?v=aDaOgu2CQtI"]Pearl Jam - Do the Evolution - YouTube[/ame]
Is it true that there is some indication of epigenetics being able to pass down "true" inheritable changes in very simple organisms?
Good question! I'm honestly pretty poorly read with epigenetics, most of the papers I have read on the subject have to do with methylation and demethylation of DNA. This involves adding a very small molecule to a portion of DNA to turn it on or off. These changes can be passed down to subsequent generations and then mutation can solidify the change. After all, if you've turned off a gene, there's no selective pressure keeping it as an A, T, C or G. The evolutionary advantage of epimutations is that they can quickly be turned on, but just as quickly can be turned off.
Thanks for the explanation, Philosoraptor! You are, of course, right. I probably didn't consider all of the possibilities and details, only wrote a rough scenario. I'm quie surprised about the definition of phylogenesis. Yes, even from the name "phylogenesis", your explanation seems closer. I wrote it, or used to take is as the opposite of "onthogenesis" - what doesn't happen within an individual, but brings changes to the genetic code, genetic pool, etc. So I thought even microevolution can be said to be a part of phylogenesis, since it changes organisms, even within one species, but on a longer timescale or under certain events, it can lead to speciation (?). You are right about the mutations, I didn't think what I wrote through well enough. And the evolution between generations too. Of course, you can change it like that, but in my mind I kind of took this scenario that it is indeed an evolutionary change between generations, because something changed in comparison to the previous one. Just my logic, though, and probably not too accurate one.
If this is a thread to discuss and ask questions, I'd have one I've a bachelor degree in Ecological and Evolutionary biology, now I study Zoology. I used to have a great interest in evolution, but it's been a few years since I learned about these subjects and I tend to forget some things. When I was about 14, I started reading books about evolution etc. Some details of it, however, seemed a bit stange and some things didn't make too much sense to me. While some clever books on Creationism did and I was perfectly unsure about what to believe. When I came to uni, I learned about genetics and how things work in more detail, which made much more sense. But I still have one thing that kind of bothers me. It is the always mentioned missing links between species. Why do we only find fossils of some species of dinosaurs and why are there more from one species as opposed to many fossils of various types that show the slow evolution? Why are the fossilized species so well defined like that. Shouldn't there be much more "links"? I think I actually even found an answer in the hypothesis the professor at our university developed. It's called Frozen evolution. Again, I don't remember the details too well, but I have it all in a book on my shelf My question is if "Frozen evolution" is known generally or I'm just biased since we had to learn our professors opinions. If it is known, do you find it realistic? If it is not, how do you explain the missing links phenomenon?
At least one explanation is that, given the time scales involved, we're lucky to find any fossils at all. Since none of the organisms involved would have made any special effort to get themselves fossilised, the fact that some of them ended up with the exact set of circumstances at their point of death that led to their form being preserved is pretty remarkable. Asking for a full, incremental, fossil record is a pretty big ask!
Personally I think we're lucky to find any fossils at all let alone a nicely laid out hierarchy of evolutionary processes. Fossils are very rare snapshots of single organisms. They aren't rare in the sense of how many there are (you can find ammonites and shark teeth sold as kiddies gifts they are so common) but rare in the sense of how many organisms they represent compared to sheer number of animals that have existed and didn't become fossils (the VAST majority). If I travelled from London to Edinburgh on foot but you only took a picture of me in London and then another in Edinburgh you wouldn't get any idea of the transition that took place. But that transition still took place. You'd need photos of me leaving London, going up the M1, passing Nottingham etc. All the steps on the way. The fossil record is not a complete and nicely ordered inventory but rather a scatter shot sampling of whatever was "lucky" enough to die in circumstances conducive to becoming a fossil.
Yes, that's true, but what I thought is more about, hmmm, how to explain. Of course, we're lucky to have at least some fossils, but since evolution is supposed to be slow gradual proces, what is the probability of finding one specific type of organisms (like London ) in multiple copies? I mean when one species was found multiple times. The probability is lower that finding several quite similar fossils that show that the species underwent some changes. If you go from Edinburgh to London and do take pictures along the way, what is the chance you will only have pictures with towns on it and never take a photo of forest, farms and the landscape that's in between? Or to be more precise that you'll have several pictures from one town in the middle, but never take a picture of other towns or the landscape in between?
As I understand it we have a pretty good transitional fossils for horses, whales and humans? Not sure on other organisms. I think evolution moves at a highly variable rate (philo will know better)? Slow and steady was the standard view, then punctuated equilibrium made an appearance. These days i think the view is that some organisms stay pretty static while, in certain circumstances, populations can make fairly quick evolutionary change. Niches open up, mutations assist other mutations, a new pressure is applied, etc, etc.
