chadn737

You must be using a different definition of "ridicule" then. Pointing out through simple math that such rapid speciation is not possible is what I call an argument and logic. Ridicule is the use of mockery and derision, which will only serve to inflict resentment and anger.

SO.....the entire point of this thread is that because humans evolved under a certain set of conditions that those conditions are therefore optimal to a long and healthy life. At this point I really don't know what you are arguing, it seems to flip back and forth between "yes there is an optimal environment for humans" to "this is how humans evolved". The former is an appeal to nature, the latter might be correct, but thats not the point. Sure, exercise is good, sun is good....this doesn't mean that there is an optimal environment or that such an environment is the same as which we evolved under, and thats the entire point. Humans evolved under many conditions and most of those conditions entailed disease, starvation, extreme environments, and violence. Exercise could be achieved by being chased down by a lion....it could also be achieved by running on a concrete track with an ipod. You can pull the latter off anywhere in the world, making the need for a specific environment irrelevant. Read the opening post. This is not merely a discussion of "healthy living", which I agree is shaped by our evolution, but about whether we should be living in a very specific environment, the one which we evolved under. It is this latter claim that I disagree with. What you are describing is not really the same as what I think the OP asks. I don't think one is going to live a healthier life for living in east central Africa as opposed to southern Sweden or Florida. We have evolved a certain set of requirements, but those need not be met by specific environments. Furthermore, the specific environment may not be the optimal. If we can achieve longer lives through artificial environments, then what does that say? Death by violence is a natural part of the environment and how we evolved. In fact, it is selective pressures, like violent death, that help drive evolution. When you start factoring out all the nasty bits and start cherry picking the few lucky humans that managed to escape violence, disease, starvation, etc you are left with an overwhelming exception, not the norm. The age of 70 seems entirely arbitrary. Why not 60? Why not 80? Why not 90? Why not 100? We have lots of people living in their 100s. The reason we rely on averages in discussions like this is because there are always exceptions, but exceptions do not prove the rule. If anything, the fact that the average age is now well above 70, despite how "unnatural" our life is, is evidence that taken away from our "natural habitat" we actually do quite well. If we as humans evolved specifically to live to an age of 70, then how do we explain the existence of people in their hundreds? The idea that we evolved to live to a certain age seems to me completely unrealistic, especially when there exists such a wide range. Menopause suggests that we did evolve to live past that point to a degree...at least women evolved that way, but to 70? I just don't buy that claim unless there is some other evidence that suggests as much. A few? Only because our ability to test such assumptions are limited and have limited us to previously easily testable traits like lactase persistence or sickle cell anemia. However, we are finding increasing numbers of other examples with next generation sequencing and large population studies, such as the aforementioned adaptations to high altitudes. Certainly such adaptations are recent....agriculture is recent....that doesn't make them insignificant. Isolated....if you consider hundreds of millions of people (lactase persistence probably has billions) to be an isolated example, then I suppose you are right, but that is not what I would call isolated.

The likely truth is that the first life resembled nothing like what we call bacteria or archaea.

I wouldn't even call such views unconventional, not anymore. I think ridicule serves no real purpose other than to bolster the satisfaction of the side doing the ridicule. Does the ridicule of creationists cause you to ever take a new look at your stance? Have you ever found yourself questioning the validity of evolution because of ridicule? If anything, ridicule invites resentment and entrenchment. If the goal is to generate genuine reconsideration and contemplation, then ridicule is the worst strategy to use.

Richard Dawkins has publicly called for people to ridicule and mock religion in all respects and does so himself...I would not call that "polite", "reasonable", or "sensible". Just last week I reread "The Selfish Gene", a book I consider to be on the excellent and a great introduction to a host of historically obscure theories. Even in this book written long before Dawkins stopped being a scientist and became the poster-boy for atheism, there is outright disdain and mockery for religion. If you are a dedicated atheist, I can understand how you might not view these actions as adding to the animosity, but rather simply refusing to "go out of his way to grant public deference to charlatans and con artists." However, it is adding to the animosity. When you stand up before a crowd, mock a belief that has no relevancy to acceptance of evolution and held by a billion people....when you publicly call for ridicule of religious people....you have just closed off their willingness to listen to what you have to say on anything else, no matter how reasonable. I have respect for Richard Dawkins' early works, The Selfish Gene and The Extended Phenotype, but he long ago abandoned any pretense of being a scientist and has since become the equivalent of a religious leader for radical atheism. And granting some respect can get you somewhere. I am not talking about people like Ken Ham, but nobody I think has any expectation of convincing Ken Ham. We are talking about your average creationist. They can be convinced, but not when you start off by mocking God, mocking Christ, mocking everything else they hold dear. I have no idea what you believe, but I suspect that you are not someone who frequents churches. Its surprisingly easy to strike up dialogue and to get people who never have reason to think about evolution anyhow, to think about it and concede on point, but to get there, you first have to show them that you are not a complete dick who is out to evangelize atheism...because thats often what happens. People like Richard Dawkins and Lawrence Krauss, they conflate their atheism with the science and they mix the two in such a way that they cannot be separated. I have seen a lot of average people discuss evolution with creationists, only to turn it also into an attack on religion as well because they don't know how to separate their atheism from the science. They also don't know how to show respect for differing views. I have convinced people, non-scientist Christians, that evolution is fact. I have convinced many more, that even if they do not accept evolution, that there is at least not a necessary conflict between evolution and Christianity....thats big in its own right. The influence of Francis Collins is far more sweeping than you realize, but its also more subtle and quiet. I have seen his books take hold and be talked about in churches. I have seen them mentioned and read by religious leaders. You may not hear about it in the news or on youtube videos, but its there. But then that really speaks to the difference between approaches. Richard Dawkins spends much of his time writing books and actively promoting atheism. He is an evangelical atheist. When was the last time he published a real scientific paper? I've looked, its been decades. He has a base of devoted followers, so he can always remain in the spotlight. Francis Collins is still a working scientist, not to mention head of the NIH. Amazingly enough, the guy actually responds personally to emails. I once emailed him three years ago. His influence is more subtle and that is why he will convince many more people of evolution than Dawkins at the end of the day. I read your hit piece on Francis Collins. Where does it challenge his claim of having been an atheist into professional adulthood? I see nothing there that questions that fact. Or do you not consider being a practicing physician "professional adulthood"? You may not like his reasons for believing in God, so what, you wouldn't like mine either. But you really aren't who Francis Collins is writing to. He is writing to the myraid of Christians out there who do not believe in evolution. The fact of the matter is, that the conflation of "evolution = atheism" a view promoted by individuals like Richard Dawkins does a vast amount of harm towards the acceptance of evolution. When people like Richard Dawkins call for ridicule of the religious...this is a problem.

1) There are many extremophile bacteria. 2) Archaea are not all extremophiles, they are found in all the same places as bacteria. 3) This presumes a certain directionality in evolution from extreme environments to relatively benign ones and the impossibility of adaptation to extremes after the fact.

The example set by outspoken scientists like Richard Dawkins, Lawrence Krauss, and others only entrenches these views. "Mockery" is played from both sides and the statements of a Richard Dawkins only creates more animosity and throws fuel on the flames. Contrast that to the efforts of someone like Francis Collins, who seeks genuine peace and communicates these concepts in a manner that does not imply hostility. Sometimes scientists are their own worst enemy, especially when atheist scientists allow their atheism to drive the communication of science.

Patient professors.

The United States.

I am a Christian and I am a geneticist with a phd. I also fully accept evolution, but come from a creationist background where I was a young earth creationist up until probably the age of 17. I honestly don't think Creationism is spreading. Perhaps it is more vocal, as all views have been made more vocal with modern communications, but we should not confuse the vocality of it with its acceptance. I increasingly meet young Christians who are open or accepting of Evolution in part or in whole. More so than I did ten years ago. I increasingly find people in positions of leadership within Churches who are accepting of such views and encouraging of it.

I didn't consider them "irrelevant". On the contrary, I am taking into consideration the full conditions under which man evolved, not just the ones that support such blatant romanticizations of prehistoric man. Just because we evolved under certain conditions does not mean that this is what is "optimal" for us. Its the classic appeal to nature fallacy. Many species evolved to run away from predators. That doesn't mean they will live to their full potential under constant threat of predators. On the contrary, remove them, place them in an environment where there are no predators and their life expectancy will go up. Whole populations of humans have evolved means of tolerating debilitating diseases like malaria, ironically with the effect of having other horrible diseases. That doesn't mean that they will survive optimally under malaria rich environments. On the contrary, remove them from that and their life expectancy will go up. Evolution cares about long life only as far as it ensures reproductive success and no further. The age of 70 is rather exceptional when the average age of prehistoric man was 54 (assuming they made it even past 15, otherwise the average was 33). There are many who live well over 100. This does not mean it is evolved, but rather under optimal conditions, which typically are not the ones we evolved under, man can extend his life. The effect of Natural Selection actually declines past the ages most relevant to reproductive success, pretty rapidly in fact. I am well aware of the "grandmother effect", but again, that does not mean we evolved to live to 70, especially when the average age of menopause is 51. You are talking about rather exceptional circumstances...that given the rare condition of not facing disease, starvation, etc...that somebody might live to 70. Furthermore, in many populations there is clear selection for many of the environmental factors you said we are not evolved for. One reason why European populations may have lower incidence of diabetes is that early adoption of agriculture may have relaxed the pressure on low-carbohydrate intake which drives insulin resistance. Lactose tolerance is the canonical example of human evolution towards agricultural dependence.

Factor out the trauma and disease deaths and you have an environment nothing like what ancient man lived in or evolved under. In fact, this only proves my point, that man's ancient and "natural" habitat is not that which is most conducive to a long and healthy life. More to come....but I have meetings and grants due.

It is an error to presume that I meant humans should live to the same length as other apes. What I meant by that statement is what the average age relative to what is possible. Of course humans do not age at the same rate as apes, that should be so obvious as to not need specifying. However, modern humans, live far longer today, even when we factor out the overwhelming number that died in childhood in ancient times. Apes in captivity can live far longer on average than those in the wild. However, that does not eliminate the fact that man evolved to live long enough to see successful reproduction and survival of their offspring and not much longer. Notice the key word survival. Human children have a rather long period of dependence upon their parents...many years in fact...before they even reach puberty. So yes, humans will have to live longer normal, but compared to modern standards, the average age of man through the majority of prehistory was still very short. Assuming they were even so lucky to survive past the age of 15, paleolithic man might live to be around 54. The average in modern times, world wide, is over 67. Even higher if we were to consider only westernized nations with all the features of modern life. In the US, that age is well into its 70s. It is highly unlikely that Evolution selected for such long lives, which would explain why our health typically declines so rapidly at such ages. This is supported by the fact that age associated diseases have shown signs of POSiTIVE selection. Most notable of these are alleles associated with Alzheimer's disease, many loci of which appear to have been selected for. Its is likely that through human evolution, people never even lived to an age where alzheimer's would have been a hinderance to fitness. What evidence is there that dietary regimes or environmental circumstances we evolved to are any better at promoting a long and healthy life compared to some modern alternative?

Again, I would just like to point out the fallacious reasoning at work that this is any way what is best or optimal for our health. Paleolithic man lived rather short brutal lives. The same is true of other apes. We did not evolve to live long healthy lives and our habitats certainly are not the secret to healthy living and there is no habitat best suited to us. Really, this is the fallacy known as the "appeal to nature"....the idea that what is natural is good and what is unnatural is bad. It is actually due to the unnatural that we live long healthy lives, rather than dying in infancy from disease.

Its complex and depends on a variety of factors. If the mutation rate is constant, as it is often assumed to be, then its going to be largely a factor of population growth. Non-African groups have lower genetic diversity because of founder effects. Only a subset of the original human population in Africa left to settle Asia, Europe, and eventually the Americas. This can have a similar effect to a population bottleneck, because you are starting again from a much smaller founding population. So with a constant mutation rate, the faster the population growth, the more often new mutations will arise, adding to the genetic diversity. A fascinating result of recent genome sequencing studies has been that with the rapid population growth of the last couple of centuries, many new genetic variants have popped up that did not exist for most of human history. http://www.sciencema...nt/336/6082/740 http://www.sciencema...ent/337/6090/64 http://www.nature.co...ature11690.html

One needs to be careful not to fall into the Genetic fallacy. Showing how something arose does not necessarily show that it is true or false. Consider science. All our theories arise from human thought and receive positive reinforcement through experimentation and observation. One could easily argue that a caveman, with his increasing intelligence, stumbled upon the idea of God and it was true.

In a large population with random mating (i.e. not incestuous pairings, etc) the frequency of a disease causing allele will not increase unless there is some other factor at work. This is a basic premise of population genetics, part of Hardy-Weinberg Equilibrium. There are other factors that play into this, but lets not worry about those for the moment. Now as the population increases, the total number of individuals with Huntington's will increase, but as a percentage of the population, this will remain relatively stable. That's because as the population increases, you increase the number of non-Huntington's causing alleles as well as the number of alleles that cause it. Now the percentage of the population carrying Huntington's causing alleles can shift if you have non-random mating or there is natural selection at work (we will ignore the effects of migration and mutation as that makes it far more complicated). Humans have a fairly large population, so its less likely that genetic drift will randomly drive up the prevalence of Huntington's, especially as this is such a horrible disease. Now we don't have totally random mating, but there are strong taboos against incestuous relationships in the Western world at least and for all intents and purposes, random mating is a relatively safe assumption in this context. So no, its really rather complicated and it is not likely that Huntington's will increase as a percentage of the population, even as the total number of individuals with the disease increases.

You really don't need a kit for site directed mutagenesis. The basic principle in both is the same....amplication of the entire plasmid by a high fidelity polymerase with the mutagenic primers followed by digestion with dpn1 to remove the original template. The Q5 system does the ligation before transformation, whereas the quickchange relies on the bacteria's on ability to repair. You could spend over $250 on a 10 rxn quickchange kit, or you could buy a high fidelity polymerase, like pfu ultra for ~$100 bucks (and much more than 10 rxns...good for other applications) and a tube of dpn1 for ~$60, also good for more than 10 rxns.

We really don't even need convergent evolution to explain this. The simplest explanation is that these biochemical pathways arose before the angiosperm/gymnosperm split in lineages that were the ancestors of the angiosperms. It really is that simple.

It depends on what you used for an entry vector. In some cases you should add 1-2bps to your primers to put the clone in frame. What are you using for an entry vector?

Traits evolve at different points and times. There is no reason that biochemical pathways involved in one process had to arise simultaneously to or after another trait like flowering. There is absolutely nothing unreasonable or unconventional about the explanation given by the researchers. This is just another argument from incredulity from creationists.

In a sense there is reproductive isolation....generational reproductive isolation. Our present day population is isolated from our ancestral populations 200,000 years ago, so there is no gene flow between modern humans and ancient humans. Time is the factor driving reproductive isolation.

How is such a population going to diverge unless gene flow is prevented. New mutations may arise, but in general, with gene flow, this recombination will break up any association and accumulation of mutations within a subpopulation. The one exception to this would be particularly large scale mutations that present potential reproductive barriers, such as chromosomal inversions...even in these circumstances, however, there may still be gene flow that counteracts the possibility of speciation.

It all depends upon gene flow between populations. If gene flow is limited enough, as in parapatric speciation what happens is that you get a continuous gradient along a population range, where there is a clear distinction between populations at two ends of a geographic range, but gradients in-between. A great example of this is the Ensatina salamanders in California. Subspecies at either end of the range cannot interbreed, but subspecies inbetween can.

Some adaptations can evolve relatively rapidly. Consider the evolution of lactose tolerance, which arose multiple times with the advent of animal domestication. There are population differences with different frequencies of lactose tolerance and intolerance and these differences coincide with the consumption of milk from domestic animals. Humans have been migrating for many tens of thousands of years. We are true omnivores, whereas many apes have much more specialized or restricted diets. Rather than having evolved to fit a specific niche, you could view humans as having evolved to be generalists, with the ability to adapt to new and changing environments. This is a speculative statement, but humans may have evolved to be adaptable to any environment. It is not the specific environment that drives our health, but our choices. As I stated earlier, man did not evolve to live long healthy lives in harmony with nature. We evolved to survive long enough to ensure reproduction and survival of the next generation. If they did not die in childhood, ancient man died relatively early. If you survived past 15, it is estimated that paleolithic man would live to maybe ~54. We live long healthy lives in part by defying our ancient roots. A steady food supply from agriculture, the specialization of occupation and accumulation of knowledge that enables modern medicine, access to clean water, reduction of violence, etc. In fact, much of the genetic basis of modern disease is probably evolved. Beyond the obvious example of something like sickle cell anemia, consider Type 1 diabetes, which has been hypothesized to be an adaptation in early man to cold.