chadn737

Genetic differences. Just because we can match sequence from two different species does not mean they are identical.

The questions you are asking assume modern statistics and research practices at a time when modern science was still in its infancy and statistics didn't really exist as a field. Darwin's arguments were in large part anecdotal and not based on actual probability, but rather field observations. However, he drew on many sources of data from not only his travels, but also the burgeoning field of plant and animal breeding at the time. That is really irrelevant however, because in the 150 or so since Darwin, thousands of scientists have conducted thousands of experiments in numerous organisms testing all aspects of Darwin's theories. After 150 years of rigorous research, Darwin's central ideas have held and so we accredit him with them.

The center of domestication appears to be Peru. Always some debate about exact locations. That is also the center of diversity for the crop.

Seriously is this debate still going on? I've long ago accepted that Overtone considers demands that he actually support a claim to be tantamount to personal attacks. ..... Culture is as much a part of biological evolution as physical phenotypes. Humans evolved to be generalists with great adaptive abilities and the idea that there is a singular sort of environment that humankind is adapted too is nonsense. As for specific adaptations, we can't make any negative claims regarding adaptation to North America, we are only recently able to identify strong signatures of adaptation to more extreme environments like the Himalayas. Who knows how much subtle adaptation there has been to less extreme environments. For that matter, the Inuit have very high metabolic rates, which results in higher body temperatures facilitated by high fat diets. The Inuit are amongst the most recent of peoples to inhabit North America, so who knows what other subtle phenotypes other groups have evolved.

There are many hormones involved with human growth. Nobody should talk in terms of single binary traits for multigenic quantitative traits.

The data is still discrete. In population and evolutionary genetics, typically you model evolution in terms of generations. Generations are discrete units. If you go from T0 to T1, there is not point intermediate point in the data because the data is discontinuous, being discrete generations. Mutations are also discrete. The DNA molecule is not a "continuous", but consists of discrete bases. Furthermore, demand that he define information in terms that can actually be measured. The term "information" in the context of genetics is poorly defined and is nothing more than handwaving when coming from creationists. They speak abstractly about it as if they have actually quantified it in some means, but they have done no such thing. One does not model evolution in terms of increases or decreases in "information" over time in a continuous manner. We typically model it based on the change in frequency of alleles over generations. This guy is bullshitting you.

I find the premise flawed. Define a "visible mutation". For one thing, many mutations/alleles are probably quantitative in effect, thus altering a phenotype in a subtle way. For instance, a mutation that would say reduce or increase height by 2% would not be so noticeable or selected on strongly. As such, there can be many "mutants" walking around that go unnoticed due to the subtlety of difference. There actually substantial numbers of de novo mutations in every individual human,

No such thing as a "growth gene". Genetics and biology does not work in this way.

I am still not certain if "baffling bullshit" is honest in that the people who spout it actually believe they know what they are talking about or if they are aware that they are simply making stuff up. Regardless, I find that it is very revealing to challenge the baffling bullshitter to explain and backup their arguments with substance. It has the advantage of exposing them.

Evolution deals with life. Which means it occurs in the context of populations of individuals. Individual organisms, individual cells, individual DNA molecules. Throughout evolutionary time there has been a finite number of all of these and each one is a discrete individual data point, not continuous. That being said, its really hard for me to be specific about nonsense. How the heck can somebody counter a nonsensical claim about the "mathematical formulation of the evolutionary process" with specifics? While different aspects of evolution can be modeled mathematically, there is no singular "mathematical formulation" of it. How can I be specific about something that doesn't even make sense? You can't. So challenge him to describe in detail what the mathematical formulation of evolution is, if he can't or refuses to do so, then call him out on it. Openly state that he is making stuff up if he is unable to present specifics on it or at least link to what this magical mathematical formulation is.

What he is saying really makes no sense. For instance, what is the "mathematical formulation of the evolutionary process"?

Yeah, he's full of bullshit and making stuff up.

I worked with cholera toxin many years ago. There are actually two subunits encoded by two separate genes. One subunit....the A subunit if I remember correctly, is the actual toxin. The B subunit on the other hand is actually the part that binds to the receptor and facilitates the endocytosis of the complex. You can use the B subunit to induce immune responses without the presence of the A subunit. When I worked with it, we were expressing the B subunit in corn and feeding it to mice to see if we could develop edible vaccines in this way. Its probable that they are using only the B subunit in these experiments to induce a response without the actual toxicity of the A subunit.

Well you lack replicates.....

Actually it looks like they just came out with a fourth edition in paper. For a while there it looked like they were moving everything online, but I haven't looked for copies since probably ~2011 and this came out in 2012. Illumina has so dominated the sequencing market the last 3-4 years that nearly all real advancements in library prep have been made for Illumina. There was a ton of excitement about Ion Torrent challenging Illumina, but they overplayed the output and quality. Meanwhile Illumina has been holding back updates and releasing them as new competitors arise to completely swamp them out. It really is amazing the pace of development when I started with next-gen back in 2008 and 454 and Solid was still competitive. With a chemistry background, I think you will find much of the benchwork behind molecular biology to be relatively easy. If you've worked with RNA, then you've already worked with the most sensitive of the three (DNA, Protein, RNA)....although certain proteins can be a huge pain in the ass. By the way, it looks like for a limited time they have knocked 30% off of the 3 volume set of the new Molecular Cloning....still expensive as hell, but much better at $255 than $365

I don't think we know that answer in terms of what the extent of introgression of Homo sapiens into these populations were. Currently we have a limited number of sequenced genomes from these other hominid species, which does not lend itself well to such a question that requires population level data.

Molecular Cloning is fully online now as part of CSHL protocols I believe. Not sure if they are releasing print editions anymore, but the print editions were great at explaining basic concepts. Still expensive for all three, but you can usually find second hand copies.

Agreed, sometimes your background may give you a distinct advantage. My undergraduate degree was in Agronomy. About half-way through when I was more certain I wanted to do basic research in plant molecular biology and genetics, I considered switching, but didn't. As a result, I have taken a lot of classes in soil science or agricultural management. This actually has been advantageous because I understand agriculture at a level many of my colleagues do not. As plant geneticists, our ultimate end user is typically the farmer. So this often plays out nicely. By the way, biomedical engineering is often more along the lines of creating devices and other things with application to human health. If you are interested in genetic engineering and biotech, then genetics is perfectly suited to that career choice.

Sometimes a reductionist approach goes too far and leaves you with fewer answers. I don't think it makes any sense to try to understand life in general from the quantum level.

Neanderthals and Denisovans were quite divergent, both anatomically and genetically. The concept of a species is a loose one and ill-defined, but the fact that we interbred is not proof that they were not a different species. Besides evolution by geographic isolation is a common means of speciation.

Scurvy was a recognized disease in numerous cultures throughout the old world, being recorded as far back as ancient Egypt. If they knew about scurvy and were writing about it in a time when writing was difficult and rare, then surely mankind has known about it for even longer. This proves that it is not something unique to North America or even Europe. You are trying to argue that the existence of knowledge of a disease in one location that has long plagued humankind world wide and in all populations is indicative that this one location is not suitable for human life. You are cherry picking your evidence. First off that is false, you are confusing a treatment of the disease as normal diet. First off, we can't even arrive at a universal diet for North America, so broad and diverse are the environments. The Inuit living in the far North survived off a diet of almost entirely fish and meat and had such abundant access to sources of Vitamin D that they never had the selective pressure of skin color that existed in Europe. Ironically, that would indicate that Alaska is very suited to human life using your line of argumentation regarding the availability of nutrients. There are an abundance of traditionally grown plants and wild plants rich in vitamin C available to Native Americans dependent upon locale. blackberries, raspberries, blueberries, and even wild species of strawberry are native to North America, were a standard part of the diet, and are rich in Vitamin C. Overtone, it is common knowledge that "Red" is offensive language. Right now there is national outcry over the Washington Redskins, much of it coming from various Native American groups. "Reds" is simply another version of the racist redskin. You can make anecdotal claims about knowing Native Americans who consider it acceptable and the other offensive. This is the classical defense I hear many white people make regarding the use of racist jokes. They say things like "Its ok, I have black friends". However, we all know that its offensive and unacceptable and that such statements are simply excuses. You can excuse yourself all you want, but to continue to use offensive terminology is to simply dig the hole deeper. Exactly. North America spans the frozen North to the tropics. It has climates of every type, abundance of different game species, plant species, etc. If man evolved to live in tropical forests, we can find tropical forests. If man evolved to live in temperate zones chasing big game, we can find that too. Our biological adaptation has been shaped in part by our cultural and technological adaptation. Preceding hominid species were using tools long before modern man evolved and when modern man did evolve, he did so in the context of a complex social and tool using environment. The evolution of our brain, our hands, and other physical aspects is driven by culture and technology. Even as recent as the development of lactose tolerance, a trait driven by one of the greatest cultural and technological adaptations of all, agriculture and the domestication of animals. You can't make such simplistic divisions and ignore them. Nor can you ignore how they have allowed us to adapt to a variety of environments.

This is not a simple question and there is no perfect way to do this. Its actually very difficult. In the past I have worked on signaling pathways and used numerous approaches with varying degrees of success. For instance, you can try to do an immunoprecipitation of your kinase. If it forms any stable complexes or if you can successfully crosslink it with interacting proteins, then you can pull those down with your kinase and identify them by mass spec. You could use a 2D gel to try and identify phosphorylated proteins in the presence or absence of your kinase and try to identify these by mass spec. If you work in a system that is easily mutable, you can always do mutant screens like suppressor screens, enhancer screens, etc.

The first recorded instance of scurvy is in papyrus from Egypt dating back to ~1500 BC. The disease was common and known throughout human populations across the globe. Treatment of scurvy was discovered and lost many times in this period. Same with all these diseases. You're acting like these were something new to Europeans and thus symptomatic of North American lacking resources. In reality, the problems suffered by many settlers and explores can be attributed to ignorance and not a lack of resources. Thats three times now that you have used a term for Native Americans that is considered offensive.

Since when did "Reds" become an acceptable term and not an offensive one? Thats at least twice now that you have used it.

No such thing as a population without mutations. We all carry mutations.