Arete

Ha - you (and my adviser) don't want to know what our monthly data storage bill just got to, but yes, it's nothing like the library prep cost for a 96 sample Illumina run. Data mining is much cheaper than generating novel data. The high performance computing department do want to know how I just crashed a 512GB node on the cluster. In their exact words "We're not upset, we just want to know what you were trying to do... [pairwise r2 calcs on a 6 x 105 SNP dataset from 108 individuals - forgot to auto delete non significant results from the out file]. So I guess we also break expensive toys, but usually not catastrophically.

How about Britain? "In December 2012 it was estimated that since the start of the year, over 200,000 Britons will have needed provisions from food banks" http://en.wikipedia.org/wiki/Hunger_in_the_United_Kingdom

Do you generally call strangers you meet "bro"? It's a slang term, that most people would find overly familiar and irritating, if not a bit condescending. I gave you a couple of neg rep points, but it's not because I don't "like" you - I don't know you - hence the irritating nature of the "bro" thing. The reason I gave you neg rep points was because you haven't been putting much effort into your posts. If a simple google search would answer your question, it's frustrating and annoying to ask other people to do it for you. A better way to approach the forum is to do some research yourself, and if you have trouble understanding what you are finding, ask for help once you've made an effort on your own. That way the discussion is more likely to be interesting and enjoyable for everyone and not just people telling you what 30 seconds on wikipedia might have told you. Also, I would avoid the one liner responses, and the text speak, as it tends to fill up a thread with posts that don't add anything to a discussion.

To quote Professor Jody Hey: "Very little in evolution make sense except in the light of genetics" The problem is that the fields of evolutionary biology and genetics are fundamentally entwined, such that not much of one makes sense without the other. I doubt whether anyone could claim to be both a strict, "6,000 year earth, no species has ever evolved, no genetic material is ever added" type creationist and have a particularly sound understanding of genetics. As such, it requires some apologetics just to work around the basics, such as the "macro - micro" arbitrary split - most of which require some level of deviation from strict logic to rationalize the two positions. Despite this, it is extremely difficult to find a practicing geneticist who openly rejects evolutionary theory. Most famous Christian biologists - like Francis Collins, Theodosius Dobzhansky (Who wrote the famous "Nothing in Biology Makes Sense Except in the Light of Evolution" essay) etc. accept evolutionary theory in its entirely and have written books documenting how they rationalize their beliefs with evolution.

As CharonY points out, the usually quoted figure for genomic homology between Homo sapiens and Drosophila melanogaster is around 50-60%. The fact that higher Eukaryota shares a good portion of genetic material *should* be unsurprising, as a majority of intracellular structure and metabolic pathways are common across the group. Most scientists would consider the presence of shared genes, encoding shared proteins, which have shared function across an organismal group to be strong evidence of (you probably guessed it) shared ancestry. The level of convergence required to achieve the level of commonality in coding, structure and function is shown relatively simply to be statistically near infinitely improbable. Evolution from a common ancestor is clearly the most parsimonious explanation for observed genetic and functional similarity. As such, I'd probably be confused if someone were to argue that "Humans and bananas share 50% of their genes. Therefore evolution is wrong and Creation is right." because to me, it strongly supports the opposite, but then most creationist arguments tend to rely on logical fallacy or misrepresenting/misinterpreting scientific results and thus shouldn't make sense to an educated, rational thinker. It also goes against almost all known examples of phenotypic convergence, which generally arises through completely different genetic pathways. It's also far from the only piece of evidence for evolution we have. It's tough to find many threads where the topic is discussed without descending into logical fallacy and subsequently locked, but here's a couple of links which might help give you some info. http://www.talkorigins.org/origins/faqs-evolution.html http://www.scienceforums.net/topic/79338-christian-vs-atheists/ http://www.talkorigins.org/indexcc/ http://www.scienceforums.net/topic/68167-how-did-evolution-get-it-right/

Glofish (Trademark etc) are GMO aquarium fish which are on the market today.

After the many threads in which it had been explained at length why it would be a bad thing for humans to decimate the world's biodiversity, I am somewhat astounded by the fact you still seem to think it would be beneficial to do so. Furthermore, one of the reasons that farmers in rainforest reasons have adopted slash and burn methods - which relocate the farm site to a new location on a regular basis is because in a rainforest, the nutrients are largely in the biomass rather than the soil, leaving it quite unproductive, such that yields decrease rapidly and the farms become nonviable in only a few growing seasons. And a second furthermore - global production already produces enough food for all the humans in the world - more production would be surplus to requirements and not resolve world hunger (which as been point out already is a connected but distinct issue from world poverty). Issues like a lack of infrastructure for disribituion of food in the developing world, conflict, natural disasters, unstable economic markets and wastage/spoilage are more of a concern.

This statement makes me fear that you have a fundamental lack of understanding of what evolutionary theory actually is. In biological terms, fitness is the average contribution to the gene pool of the next generation for individuals of a given genotype or phenotype. As for evolution in humans, a comprehensive study of human evolutionary trajectories was undertaken as a part of the Framingham heart study. This study showed that women in the Framingham population had evolved to be slightly shorter and stouter, to have lower total cholesterol levels and systolic blood pressure, to have their first child earlier, and to reach menopause later - thus unequivocally showing that certain human phenotypes have higher biological fitness than others, contrary to your statement. Only there are a multitude of independent lines of evidence for common ancestry across the tree of life, as has been said by multiple posters ad nauseum, with a significant body of supporting material, and none for different organisms having independent origins. Choosing to ignore evidence (or claim there is none despite being presented with it) in favor of an option you happen to ideologically prefer is rather unscientific. I'm not sure where this "cell" idea came from, as replicating "proto - life" molecules are extremely unlikely to have looked anything like what we generally consider to be modern organismal cells. In addition, you seem to be repeating the logical fallacy that one must understand abiogenesis to understand evolution. The basic premises of evolution have been directly observed in things like the Lenski experiment which I cited previously. Is it possible for you to start supporting some of your claims with references?

And you have another case of special pleading for 6.7m (22ft) 2,000kg (4,400lb) crocodiles (no penis, hipbones) and 2.8m (9.2ft) 156kg (345lb) ostriches (no penis, can't fly, hipbones)? Or Why do a bunch of invertebrates with penises as cited before not require hipbones? In fact, the organism with the longest penis relative to body size is the barnacle (no hipbones, in fact no endo-skeleton at all). According to your speculation, wouldn't it logically have the greatest requirement for a stabilizing hip bone? Why do salamanders, who don't jump have hip bones? Why do comparative anatomists say that hipbones evolved once in the fish and carried on throughout the vertebrates? What evidence do you have for multiple independent evolution of the hipbone in organisms with and without external genitalia? Also, would it be possible for you to back up the assertion that the primary role of hipbones in organisms with penises is reproductive - as Ringer points out this defies basic anatomy, that in Aves it's flight stabilization and in Anura for jumping? I hate to have to say it but it kind of does sound like you're making it up as you go along, and contradicting yourself as you do it -

This post seems highly contradictory, and also at odds with scientific observation. There is no logical reason that knowledge of abiogenesis is required in order to understand how organisms diversify. There are many multiple lines of independent evidence which corroborate evolutionary theory. Apologies for the copypasta, but it saves retyping: Also this comment is rather comprehensively false. There is a substantial diversity of organisms which do not have vaginal or penile reproductive organs, but do have hipbones, such as birds and amphibians. Also, a phenomenal diversity of organisms which do, but have no hipbones (in fact some with no skeletal structures at all) including, flatworms, sea slugs, orb spiders and barnacles to name a few. The recognized primary anatomical function of hip bones was to articulate the pelvic fin in fishes (which do not generally have penises), and subsequently the lower limbs in tetrapods. http://people.eku.edu/ritchisong/342notes5.htm http://link.springer.com/chapter/10.1007/978-1-4615-1847-1_2#page-1

It's much better to get red flags at the start and avoid a bad situation than end up in one - e.g. having done all the data collection only to find yourself missing from the author list of the resultant publication. I know charonY and I (and most other people who have done postdocs I know) have a horror story of how either through bad circumstance or deliberate dishonesty we've been exploited by PI's. Unfortunately as an undergrad, without knowing what sort of institution you're at (R1 vs LAC vs undergrad only, etc) you're probably barely a blip on the PI's radar and they are unlikely to care much whether you hang around or leave. If it sounds like the situation is starting poorly - which it definitely sounds like it is, you're probably better off getting out before you have much invested than sticking it out in the hope it turns out ok. At the very least I'd definitely advise you to have a look around the department and talk to a few other PI's about opportunities in other labs. As an undergrad volunteer, you are certainly replaceable, so try to make sure you have other options too. All of the paid undergrad interns in our lab get paid by an internal university grant. If you haven't already, I would see if your institution offers something similar. Having your own independent cash is a game changer.

Ahh the joys of exploitative science. The reality of working in science on soft (i.e. grant) is that there is a fair bit of uncertainty, and whether deliberate or not, young vulnerable people often get the raw end of poor financial management and/or tight budgets. As in all other forms of employment, if all you have is verbal promises, your recourse is very limited. Until you sign on the dotted line, consider all promises to be withdrawable - I've seen this happen up to an including the offer of tenured positions being cancelled after negotiations the day before a contract was to be signed. If you have signed a contract, the university should be able to enforce the terms on the PI. If not, you probably don't have much of an option other than to demand it, and quit if its not forthcoming. Personally, if I had gone into a situation under the expectation I would be paid and had that re-negged on after I started in the lab, I would leave, as it doesn't bode well for future good will (like promises of authorship, etc). If you can't get another paid internship and would settle for a letter and experience, I would personally go to another lab and start over with all the expectations out in the open.

A) I would argue the opposite - there is an exceptionally extensive body of research on genetic variation in humans, some of which is cited previously. This research has demonstrated that, by and large, the major "races" of humans represent cultural groups, which have undergone a considerable level of admixture throughout time, such that they do not reflect distinct genetic clusters. As a result, it is not possible for one to speculate about "outbreeding depression" between races, as to do so requires that races are distinct genetic entities - which they aren't. B) The study you cite investigates the psychological impact of identifying as mixed race. It makes no explicit or implicit link to any sort of heritable causation at all - in fact the opposite - citing environmental factors to do with identity crises as the most likely (albeit speculative) explanation for their observations. C) The (now banned) OP was trying to evidence some rather absurdly flawed notions regarding the validity of draconian eugenics and compulsory sterilization, so this was never really a good faith discussion. Ultimately, if your aim is to look at humans through the lens of population genetics (rather than try and push a controversial political agenda) starting with traditional "races" as your a priori grouping is not sensible. e.g. http://www.nature.com/nrg/journal/v10/n4/full/nrg2554.html http://europepmc.org/articles/PMC3042601/reload=0;jsessionid=PzMGvMBeHtlH8XC1Jo0A.2 etc

The results you posted in post #3 demonstrate that except in the case of twins, most (i.e. greater than 50%) of the observed variation in IQ is NOT explained by genetic components. This is in line with other studies I have seen on the subject which demonstrate that whilst heritability of measurable intelligence is significant, the majority of variation is due to differences in environmental factors.

The essential flaw in your argument is that science attempts to arrive at an "Absolute Truth" of some kind. Scientific investigation simply seeks to observe and describe the natural world. "Absolute truths" tend to lie in the realm of religion and the supernatural, which is outside the purview of science - which is ambivalent to the supernatural. As a demonstration of this in practice, most scientific results will be presented with a probability (or p) value - a statistical measure of how likely an answer is to be correct. P values can approach, but never reach 1 - so no scientific result could ever be said to be absolute. In fact, in the field I work in (evolutionary biology) I would say most if not all of our model based research is wrong, to an extent. We simply aim to provide the least wrong interpretation of the available data in order to answer our hypotheses - which is quite different from trying to provide any "absolute truth". On the other hand, if a concept that is religious in nature begins to make claims about the natural world - (e.g. the world is 6,000 years old) I personally would expect such an assertion to live up the same expectations of empirical evidence and mechanistic explanation I expect of a scientific explanation before I would entertain accepting it. Making a fundamental false assumption about the scientific method, and then using that false assumption as a basis to start slinging insults at scientists doesn't seem like a very rational, sensible or logical position. Such positions are not very well tolerated in the sciences, or on this board, so if you're motivation is to have some sort of constructive debate rather than to soapbox, I'd politely suggest changing your approach to a more engaged and polite one. Also, your word processor's bold function appears to be activating at random.

Now, now, only a handful of members here would know what an AFLP is, let alone be able to give you advice on them, so you'll need a little patience. One issue is that species delimitation is something of a small niche in evolutionary biology, and another is that AFLPs are a somewhat antiquated molecular marker that few people in that small niche are actively using. One of the main reasons for that is that AFLPs are notoriously difficult to optimize - a set of protocols that work for one study almost never work well for another, so a lot of tweaking and fiddling are usually required to generate consistent results. If I were advising someone embarking on a species delimitation study, I'd be strongly advising against AFLPs and pushing for a RAD tag approach instead. The reason would be threefold ). It's a newer method using next gen sequencing technology, so you get a lot more markers per dollar. 2) It's "sexier" so it will make for a more topical publication at the end - if you're aiming for Molecular Ecology or something similar. 3) The approach in terms of bench work is a lot more cookie cutter, so you'd have better data, easier and sooner. What's the reason for leaving them on the bench? No incubator? R/L at non optimal temperature is likely to reduce yields and give smeary banding on your gels is what I would guess.

"Thanks" for the condescending welcome. I am able to read past posts, you realize, right? It's an analogy, demonstrating that prediction based on observations and mechanistic explanation such as physical evidence of a crime implicating a suspect, or the sun rising is generally considered distinct from predictions based on faith, like a "hunch" or belief in a supernatural phenomenon.

Would you consider legal defense 1: "We found his DNA at the scene, and the weapon with his prints on it in his car" And legal defense 2: "We just have absolute faith that he did it." to have equivalent veracity?

Allow me. China announces emissions trading scheme to lower emissions India announces emissions trading scheme

People have been using antibacterial soap for a long time - which acts as a preventative for bacterial infection, however has little application as a cure. A colleague of mine is working on phage therapy treatment for antibiotic resistant bacteria; i.e. using bacteriophages (viruses which attack bacteria) to treat infections of resistant bacteria, in conjunction with traditional antibiotics. The idea is that one of the ways in which bacteria become resistant is to generate more active efflux pumps to excrete antibiotics - thus driving bacteria to evolve more efflux pumps. Some bacteriophages bind to efflux pumps, using them to enter the cell - thus driving bacteria to evolve fewer efflux pumps. As such, you can drive an evolutionary trade off where combinatorial therapy prevents resistance to either treatment - at least until the bacteria evolve a novel trait which allows them to escape both treatments, that is. Unfortunately, one of the biggest hurdles is also one of the major benefits of phage therapy - in that phages, being RNA viruses have very high mutation rates, and thus evolutionary potential, so the phage could evolve alongside the bacteria, preventing resistance. However this makes phages very specific to particular infectious agents, and also makes them very hard to keep stable, and thus patent - and therefore apply FDA approval etc to.

You seem to be fixated on whether or not you are "right" as opposed to whether or not your argument is sensible, which unfortunately it doesn't really appear to be. Definitions of life can be as specific or vague as one wishes.The difficultly arises not because the various definitions of life are vague, but because biological systems are complex and thus tend to obfuscate arbitrary categorization. An analogy would be colors. We can define our colors very specifically, e.g. "true" blue light has a wavelength of 475nm and "true" green light has a wavelength of 510nm. What's light with a wavelength of 492.5nm? It's exactly halfway between green and blue - so calling it blue would be equally correct (or incorrect) as calling it green. Our definitions aren't vague - on the contrary, they are very precise. Light itself isn't vague, as calling an object vague is nonsensical. The inconsistency arises through the existence of intermediate states between our precise definitions. It depends. A virus, per se is usually made up of nucleic acids and proteins, rather than randomly distributed strands of RNA - so a strand of RNA of any kind floating around an environment would generally not be a virus (or any other organism) at all. Then there are RNA viruses, ssDNA viruses, dsDNA viruses, those that contain their own polymerase, those that utilize a host's, etc etc etc. So dependent on the location of that strand of RNA that has viral origin (e.g. inside a capsid, incorporated into a host genome, randomly floating in the environment, etc) it may be a virus, a transposable element, a plasmid, an insertion, an intron, environmental DNA, mRNA, or any other number of components of biological systems. As a result, your question without context is not answerable.

A) The only person who's actually used the word "nonsense" at all in this thread is you. B) What we've been explaining to you is that this statement you made: Is inaccurate. Biological entities don't fall neatly into categories. A virus isn't "dead" outside of a cell and become "alive" inside of a cell. There's shades of grey between "alive" and "not-alive" which viruses fall into. There isn't a right and a wrong in the argument you're trying to make - as charonY and I have pointed out it's all dependent on context. "Alive" and "not alive" are in some respects, simply categories of convenience.

As a researcher in a virus lab, I feel qualified to comment. It seems that you and moontanman have stumbled into a semantic argument whereby through the beauty and complexity of biological systems, you're both wrong. Biological organisms - if particular viruses, don't separate neatly into "life" and "non-life", instead there is a gradient of grey between the two states. Under the convenient umbrella term "virus" you are describing an extremely diverse group of organisms which occupy a myriad of states that display a variety of traits that don't neatly split them into categories. Neither do they miraculously become alive upon entering a cell - for. e.g. some viruses rely on the host's polymerase to replicate, some have a gene encoding their own. To really throw a spanner in the definition of life with viruses, one of the viruses we work on are endogenous retroviruses (ERVs). The genes encoding ERVs have been integrated into the host's genome - and therefore are technically genes of the host. Once expressed, the proteins assemble into viruses, which the host immune system recognizes as foreign and can attack. So are these viruses part of the host (i.e. "alive")? are they "non-life" which has simply invaded the host genome? Like many things in biology, they don't fit into neat pigeon holes. For the purposes of my research in evolutionary theory, viruses evolve and therefore, we would consider them "alive" in the sense that they are useful to examine evolutionary processes which are extrapolatable to other organisms, but again that would be a categorization of convenience rather than a biological reality, which is much more complex.

The simple answer is you used two different methods to calculate inbreeding and got different results. positive Fis values indicate that individuals in a population are more related than you would expect under a model of random mating. negative Fis values indicate that individuals in a population are less related than you would expect under a model of random mating. You don't indicate if your Fis values significantly deviate from zero, and there will be some stochastic variation even in populations which are in Hardy-Weinberg equilibirum. Also from the Plink manual: Note With whole genome data, it is probably best to apply this analysis to a subset that are pruned to be in approximate linkage equilibrium, say on the order of 50,000 autosomal SNPs. Use the --indep-pairwise and --indep commands to achieve this, described here. Note The estimate of F can sometimes be negative. Often this will just reflect random sampling error, but a result that is strongly negative (i.e. an individual has fewer homozygotes than one would expect by chance at the genome-wide level) can reflect other factors, e.g. sample contamination events perhaps.

Unfortunately this thread plainly demonstrates that it is not nonsense, but a rather well substantiated assumption. For e.g. You've stated this: And then, later in post #178, you post this: A seemingly rather flippant and condescending use of the argument of irreducible complexity - an anti-evolution argument which has been thoroughly debunked. Unfortunately this argument, if used in the knowledge that it has been thoroughly addressed and dismissed through scientific investigation, it indeed presents you as a science denialist. So it would at least seem, prima facie, that despite lacking the requisite background knowledge, you are picking up refuted, anti science arguments as supposed ammunition against components of science which you personally find objectionable. This is indeed a denialist position. I may have interpreted your intentions incorrectly, but then it would appear others are misinterpreting you too, so it may behoove you rethink the way you are presenting your discussion points, if you wish to eliminate incorrect interpretations of what you intend to present.