Arete

In post #29 and #32 you cite only your own article and your own commentary on a video. Stating that other papers, which you don't cite have been peer reviewed is rather irrelevant to my point.

I especially enjoy the bit where your sources are your own article in a non peer reviewed source and links to your own commentary of videos.

I did my PhD in a herpetology lab, so worked a lot with snakes. The snake in Moontanman's post is a roadkill, so it's difficult to really tell what it is, but I'm pretty certain it's not a Sisturus - I'm not super good at US snakes so I might well be wrong however. For reference, here's a photo of Sistrurus miliarius, which is commonly referred to as a pygmy rattlesnake in the Southeastern US. The tail morphology of the flatsnake in the OP doesn't really look right - I'd guess that it's a member of the genus Thamnophis - or the garter snakes, as the morphology is a better match and the coloration of garter snakes is extremely variable - see the second photo. I also agree that people go a little crazy about snakes - I've heard countless stories of people being "chased" by snakes, whereas everything we know about snake behavior strongly indicates that the last thing a snake wants to do is chase a non-prey animal which can potentially squash them. The news report in which the two boys died describes the snake variably as a boa, and then a rock python. As boas only generally get to about 10 feet and 60ish pounds at their largest, it's hard to imagine it would see a human, even a child of 5 as a potential prey item and be able to kill them without anyone else in the house being alerted. They're generally also fairly docile and sedentary - which is why they're so popular in the pet trade. A rock python on the other had is a significantly different animal. These guys can exceed 20ft and weigh over 200lb. In the wild they can take on nile crocodiles, water buffalo and are known to have killed people. It's not impossible that such a snake could have constricted two children to death - but found them too large to swallow, or at least the act of doing so would have taken several hours. I agree with Dr Krysko in that a potentially 200lb snake isn't really a "pet" in the same sense as a tiger isn't really a pet. Incidentally, while I was in South Australia a professional keeper was potentially killed by his "pet" scrub python http://hkras.org/eng/herpnews/?record=184 He's a picture of me holding one we caught in the field:

To clarify, a lot of related fields will have a lot of the same fundamental theory and similar technical approaches. Having a demonstrably solid foundation in good basic theory and approaches is often more important than having experience in a precise, sub-sub field of study. For example, you could do a MSc on say, the developmental genetics of eyespots in butterflies, and a lot of the theory and skills would transfer if you wanted to do, for example, functional genomics of thermotolerance in cholera. You could then thread a common theme of trait evolution through your studies and generate a picture of a comprehensive, but diverse program of study. However, it all depends on where you want to end up. In many senses a PhD is a starting point, rather than an end point, so how you approach what you study might be influenced by whether you want to go into government, academia, private industry, etc. While a basic research PhD with a strong theoretical focus might help more in an academic setting, a more applied course of research might be more attractive to industry, etc.

Google reveals that you've been peddling your article extensively across many forums for some time - why must you self promote so extensively if the excessive rebuttals and critiques of your article are false and you do have the "ultimate" proof? A skeptic might suspect flagrant self promotion by a crackpot is afoot - and that repeating discussions that have proven to have had no effect on your position again would prove to be an exercise in futility.

My MSc was more population genetics, my PhD was more macro-scale evolutionary biology. However, I've worked on fish, lizards, insects, protozoans and viruses. The bench techniques and many of the analyses and theory are very similar once something has been turned into a tube of DNA - so I second CharonY's advice at least in regards to life sciences. Experience in a breadth of systems with a common theoretical theme is actually probably better in terms of career prospects than intense experience in a very narrow field. Depending on where you want to end up, being in an interview and being able to say "Here is/are the core question/s I am interested in and here is the variety of angles I have explored it/them from" is in many way preferable to "Explored X problem in system Y for all of my studies." You're more likely to have common ground with other researchers, allowing collaboration and more likely to be able to teach courses to a broader range of students.

That is precisely why you need a citation. All we have is your words, and no facts. All we have to verify your "problem" is your word, and now an anecdotal news article. If it happens "so often" as you assert, it should be relatively easy to provide some facts and figures to support the assertion. If you can't provide any facts or figures, then it is legitimate to question whether or not your anecdotal experience is representative and thus whether or not a problem to be resolved in the broader community actually exists.

Editorial rejection is a part of peer review - 7+ editors have reviewed your paper and found it too deeply flawed to warrant in depth review, or too far removed from the standard content of the journal to ever be considered for publication. While rejection is a part of scientific publishing and you should expect to have more papers bounced the first time than accepted, 7+ editorial rejections is excessive and suggests a manuscript is being submitted to grossly inappropriate venues, or is so fundamentally flawed a cursory glance over the manuscript reveals it to be irredeemable. If I had been canned by over 7 editors I'd be looking very closely at why the editors weren't interested in my work, rather than dismissing their comments.

a) 23andme sequences using an Illumina BeadChip array - https://www.23andme.com/more/genotyping/ They claim a million SNPs, but that doesn't match with any of Illumina's off the shelf chips, so either they've done some judicious rounding, or they use a custom chip. b) If someone, in the future discovers a point mutation associated with a disease that is not present on the chip used by 23andme, you won't have that information. In order to future-proof your data like that, you'd need a whole genome analysis. The reason microarrays exist is because generating such an analysis is time consuming, expensive and requires specialist knowledge and high powered computational resources. Thus, to generate useful, but efficient analyses that can scale up, certain studies subsample the genome using microarrays. This is the approach 23andme takes. It's a compromise - as producing an exhaustive, whole genome variation map with high confidence is a non-trivial task. Ergo, in answer to your original question, there is no easy way to deliver a confident, exhaustive variable call analysis of a whole human genome.There are however compromises like the microarray offered by 23andme which if you're a layperson without specialized skills in bioinformatics would appear to be adequate for most conceivable applications.

Having attended a seminar on the topic at a globally recognized meeting, I feel qualified to comment without sitting through a youtube video. BTW Darryl88 - is that you? Keyword - both. We gained additional information about epigenetically acquired, as well as inherited characteristics some time ago. Keyword - both. We gained additional information about variability in rates of evolutionary change some time ago. Sometimes the rate is slow, as previously thought, now we know that sometimes the rate of evolutionary change is fast. Keyword - both. We gained additional information about variability in stochasticity of mutations some time ago. Some mutations are relatively random, as we thought, some are less so. Ringer said it perfectly. The information provided by these new discoveries is a) Additional to existing theory not contrary to. None of the processes discovered in the substantial period of time since the 1940's dramatically disproves previous theory. They happen IN ADDITION to previously known mechanisms. b) It isn't exactly new information - evolutionary biology has taken on board and incorporated many new aspects of evolutionary theory as they've been discovered. c) No one in the field is denying that any of these processes exist, or play a role in evolution. As I've previously argued, as Ringer seems to argue and PZ Meyers argues the whole "synthesis" is a fluctuating beast. it's a synthesis of new, old and embryonic ideas as to how organisms evolve. You seem to be playing semantics with names.

One of the dangers of presenting the discussion as "rocking the world of biology" or a "paradigm shift" or *insert hyper-exaggerated tagline here* is that, for those who want to hear it as such, it may sound like the theory of evolution is being ditched by science - when that is unequivocally NOT happening. This is exactly what happened after the "Alternberg 16" meeting in 2008. http://pandasthumb.org/archives/2008/07/luskin-has-lost.html There was some discussion of what the result of the whole debacle was 5 years on at this year's joint Evolution meetings. The resultant conclusion was that, as has been noted above and in the previous thread - evolutionary theory has been gradually accruing new information and mechanisms for decades. There hasn't been a "eureka" addition of game changing information - like for example, plate tectonics was to geology. Cynics/skeptics in the evolutionary biology community would even suggest that the whole "new synthesis" of evolutionary theory was a profile building exercise undertaken by a few scientists in the field looking to generate high impact review papers as their tenure clocks ran out.

Not really. The topic was thoroughly discussed in a previous thread. As I posted there, the expansion of evolutionary theory to encompass novel mechanisms has been ongoing for decades. It should come as no surpise to anyone even tangentially involved in evolutionary biology that we've discovered that the mechanisms involved are more complicated than Mayr and Dobzhansky understood. PZ Meyers comment on the Arlenberg 16 sums up the whole "new synthesis" hype succinctly: "There are no grand reformulations of the neo-Darwinian synthesis in there, nor is anyone proposing to overturn our understanding of evolution — but that’s what I expected. It’s saying that there are a lot of exciting ideas and new observations that increase our understanding of the power of evolution, and promise to lead research in interesting new directions." http://scienceblogs.com/pharyngula/2008/07/19/altenberg-2008-is-over/

OK, so I'm going to guess what you mean by "whole genome sequenced for $10,000" is that you can get a DNA sample extracted, library prepped and run on a single lane of Illumina for around $10,000. The data you will get from such an undertaking would be 150 - 220 million short read sequences either 50, 75 or 100 base pairs in length. The term "whole genome sequencing" is a bit of a misnomer, as they "should" - dependent on your library prep, be randomly sampled from the genome and as such you'll have higher than average coverage from some parts of the genome, and none from others. De novo assembly is not possible from Illumina data alone, so the method you'd need to use would be a referenced alignment to an assembled genome, followed by SNP calling. By my back of the envelope, sketchy calculations, you'd be looking at around 3-8x average coverage from one lane of sequencing over the human genome, which isn't really enough to confidently SNP call - you'd want to get more like 20x. So your results would be fairly low quality in terms of confidence. Second, while the alignment and SNP calling software is largely free (I like GATK, SAMtools and VCFtools) you need a fair bit of computing power to run the analyses efficiently, and some relatively basic programming skills in pipelining and big data. I currently use a high performance cluster which runs 48 processors and 512GB per node, and I'd get that type of alignment done in an hour or two. A much, much better option if you simply want to know your allelic state at a bunch of important coding loci is a microarray approach. Affymetrix, Illumina, Fluidigm etc all have relatively cost effective, off the shelf SNP microarrays for humans which research scientists use all the time. As YodaPs points out, 23andme have a commercial service to run a variety of these chips for a lot less than 10 grand.

At the risk of sounding like a broken record, the scientific method has an explicit framework for dealing with hypotheses for which no evidence is found. If you are unable to reject a null hypothesis it is retained. In the instance of the supernatural, lack of evidence dictates that they cannot upheld as scientific explanations, and must be rejected as not significant. As such, retention of a positive result (in this particular case the existence of deity) is unscientific. That is to say it is distinctly not "beyond science" as you keep asserting - but unscientific, as in a violation of the scientific method. That's not to say that all belief that violates the scientific method is bad (e.g. my belief that my train will turn up on time may be unscientific) but if you're going to condemn Dawkins for a valid application of the method to religion, base it on something other than ad hom and logical fallacy. Aside from "you can't prove me wrong" (which has been repeatedly explained to be a logical fallacy and thus an invalid position, at least here) what are they?

Probably has nothing to do with it. It's logic. The burden of proof is on the side of the positive claim. Science (and law, and logical discourse) formalize this. Shifting the burden of proof is not a valid argument - and it seems to be the foundation of your entire argument. Repeating a fallacy doesn't make it become a valid argument. No there aren't. Religion doesn't get a special pass from the rules of logic because you say so - that's another logical fallacy known as special pleading. http://en.wikipedia.org/wiki/Special_pleading Sure it does - that's why "God did it" isn't a valid conclusion for an experiment or observation. The retention of a null hypothesis on God renders the concept unscientific. Religion, by affirming the supernatural is unscientific, not an exception to science.

Which is a logical fallacy, known as "shifting the burden of proof." http://www.nizkor.org/features/fallacies/burden-of-proof.html If you make a positive assertion that X exists, it is up to you to provide evidence that it does. Trying to shift the burden of proof and claim that the other party has to prove X doesn't exist and that the default position is to assume X exists is logically fallacious. This is why the scientific method relies on the use of test and null hypothesis. In the absence of evidence for the test hypothesis, the null is retained pending further evidence. Therefore, without repeatable observation demonstrating the existence of a deity, the scientifically correct position is to assume one does not exist until evidence to the contrary arises. Not, as you're suggesting to refuse to accept one "for no reason".

You also keep asserting that Islamic scientists "discovered" evolution centuries before Darwin - which is false. Plenty of groups of people were observing evolution in nature and thinking about it - including the ancient Greeks - well before your supposed Islamic discoverers of evolution were around: http://www.aboutdarwin.com/literature/Pre_Dar.html What Darwin contributed was a working theory of evolution by natural selection. http://www.darwins-theory-of-evolution.com/ Claiming that the Islamic world presented this working theory 6 centuries before Darwin did is false, and if we're going to get down to who observed that organisms changed over time first, the ancient Greeks beat the Arabs.

I would especially call into question Pasteur as being a " crackpot". Not only was he not the first proponent of germ theory, he was a dean at the University of Lille at the time, and the Pasteur Institute was developed while he was still alive. Pasteur was extremely celebrated for his scientific discoveries. To try and depict that he was marginalized would be extremely dishonest. http://en.wikipedia.org/wiki/Louis_Pasteur

BY making such a statement I believe you are now claiming to have knowledge of the intimate religious leanings of the entire Royal Society and AAAS. That's slightly ludicrous. Honestly, no. Dawkins, Christopher Hitchens, Daniel Dennett and Sam Harris are all atheists. So is the majority of the Royal Society and the AAS, going by survey results. The difference at least as far as I can see is one group publicly comment on their beliefs and the other don't. Again, no, I don't see. Dawkins, Christopher Hitchens, Daniel Dennett and Sam Harris are all atheists. So is the majority of the Royal Society and the AAAS. Why are the former "extremists" and the latter not?

Evidence suggests strongly that most scientists agree with them. To pull a quote of myself from an old thread: 97% of Royal society members and 93% of National academy of sciences members answer "No" to the question "Do you believe in a personal god?" http://www.humanreli...telligence.html www.stephenjaygould.org/ctrl/news/file002.html. This is in two nations (the UK and the USA) where 65% and 93% of the respective populations believe in some form of God. http://en.wikipedia....#United_Kingdom

One thing to remember about Dawkins is that at least one of his primary motivations is to sell books, and controversy generates publicity. A lot of the controversy Dawkins whips up around him is essentially for the purposes of entertainment - in the form of TV appearances, etc and so on. I believe the vigor and vitriolic nature of a lot of what he says in such appearances is unnecessary "preaching to the choir" and damages the actual persuasiveness of the arguments he puts forth, but it moves people like the OP to post about it, generating publicity. It kind of annoys me, as offending potential rational thinkers who happen to be theists by ridiculing their position ultimately pushes them away and results in more supporters for the anti-science lobby.

Any change in relative frequency of alleles over time would be considered "evolution". It comes down to what is practicable/ measurable. To offer an analogy - if the temperature in the room I am sitting in varies whatsoever, it could be said to have gotten warmer/colder. However, if that change was 0.001 degree, it would be unmeasurable - and probably not practical to refer to as a change, athough in absolute/theoretical terms, it would be a change. In the same sense, if I have a plate of 1x106 bacteria with alleles A and B in equal proportions, and a single A individual replicates whist no B individuals replicate, there has been a frequency change, however for all intents and purposes it would remain undetectable/appreciable. Is that clearer?

I think there's a few basic definitions missing from the discussion: allele: a particular genetic state at a particular locus or genome - or in other words, a specific genotype. frequency: the relative proportion of a given allele/alleles in a population of organisms. population: a group of organisms which share the same pool of alleles. The process of biological evolution happens at the scale of the population, or the meta-population, and can be defined as a change in frequency of alleles over time. The rate of evolution is generally scaled by effective population size (i.e. the number of individuals in your population), the rate of mutation (i.e. how often mutations happen) and the generation time (how ofter individuals within a population are replaced). As mutations occur randomly for the main, even in the absence of any selection, stochastic changes in allele frequency will occur. As such, all populations of organisms will evolve over time. Differential ability of particular alleles to replicate, and thus contribute to the next generation will determine the direction of evolution.

I have both a 9 pound propane cylinder here, and a pressure cooker. Similar size. However, the point is that "Don't mix x and y. It will explode and be bad" is the same information as "Mix x and y and leave it somewhere near lots of people".

Well, genetic mutation and germ line mutation are two distinct things. The inital post suggested there was limited research into the genetic mutations caused by alcohol and tobacco. There isn't. here are some studies which address germline mutation in relation to alcohol and tobacco, including a paper entitled "Mainstream Tobacco Smoke Causes Paternal Germ-Line DNA Mutation" http://cancerres.aacrjournals.org/content/67/11/5103.short http://www.sciencedirect.com/science/article/pii/S0006322312003551 http://europepmc.org/abstract/MED/12134623 http://carcin.oxfordjournals.org/content/17/2/261.short