Arete

Fish and chippocrites? If their reasons for a vegetarian diet are conservation/environmentally motivated, then more often than not seafood is a very poor choice. However most cephalopods are annual species - which means they recover from harvesting very rapidly and are likely to be much more sustainable than longer lived populations. Plus they are tasty - I did a few field seasons on Sepia apama in Spencer Gulf - delicious fields seasons they were.

From an evolutionary perspective, cancer is a result of somatic mutations which disrupt cell signalling, cell division and/or apoptosis. As somatic mutations accumulate over the lifespan of an individual, the longer you live the higher the probability that a somatic mutation will occur that causes malignant cell growth. In other words, it becomes a numbers game in game theory terms - the longer you "play", the higher the likelihood you'll "lose". As we've done a very good job of reducing mortality due to infectious disease, more individuals live long enough to get cancer.

Personally (I'm never usually worried about integrity, as I'm either going to PCR it or shear it up for a short read library) I hit it with the benchtop vortex for a minute or so, or I leave it a room temp on the bench for an hour or so. Another possibility is that the pellet you're observing is actually contaminants that the purification step failed to remove, rather than DNA. Depending on the tissue type, it's sometimes impossible to get all the contaminants out of an extraction with a standard protocol (I'm looking at you, jellyfish samples. Grrr.).

This isn't actually correct. The OP refers to teaching assistantships (TA's). I TA'ed throughout both my masters and PhD in Australia. Also, you do not need a PhD to be an adjunct professor or an associate lecturer in Australia. You do generally need a PhD to be a faculty member, but you can teach without being faculty or holding a PhD. blue89 - if you're currently an MSc student, is there a reason you can't TA at your current institution? A TA/RA position is not really a career path - they're more something you do whilst doing your research degree to get cash/experience - you'd generally be a TA at the same time as being a an MSc/PhD student.

One thing I'm a little baffled by is Trump's slogan: "Make America Great Again" and many of his supporters state a strong belief in American values, while at the same time many of his actions and policies seem to take direct aim at constitutionally protected freedoms. For e.g. Advocating the mistreatment and assualt of protesters at his rallies, and actually legally defending those arrested for said assaults, along with advocating the discrimination of migrants based on their religious views , would seem to show abject contempt for the freedom of speech and freedom of religion protected under the first amendment. I'm a non-resident in the US, so it may be a misunderstanding, but I'm confused as to how a political figure who is seemingly taking a massive, steaming figurative dump on constitutional rights could be considered in any way supportive of the values of the nation. As is the case in a number of other predominately white, western, Christian nations I've lived it seems that "traditional *insert country* values" is coded language for "the values of white, xenophobic, Christian, cis, citizens of *insert country* and the suppression of everyone else's rights". In other words, it seems that Trump and his supporters don't care about "American values" in the sense of constitutional freedoms, fair governance and judicial systems at all. Also, does anyone else find the incitement of violence towards detractors by a presidential candidate utterly terrifying? What will he do once he is president to those who don't support his policies? Can you imagine a Trump administration response to for e.g. past anti-war protests?

You are repeating the same intellectually fallacious argument from incredulity, but simply shifting the goalposts each time the justification you use to support it are shown to be flawed. If you bother to actually read and comprehend the evidence, that's precisely what the cited mechanisms do - generate novel protein coding sequences. This is documented all the time in the literature, and your repeated denial of it begs repetition ad nauseum which is tiresome. A great example comes from a system I've worked on - Trypanosoma brucei. T. brucei is an obligate parasite that evades the adaptive immune function of its host via antigenic switching. They have a variable library of ~1,500 pseudogenes encoding the protein coat on the outside of the cell surface (VSG genes). Only one of these is expressed at any given time, allowing the rest to accumulate neutral mutations due to their non-expression. Approximately once every 100 generations, the expression site is switched for a novel gene from the library via ectopic recombination. This allows a novel protein coat to be expressed, avoiding the host's evolved antibodies for the previous cell surface. Thus, the generation of new genes is not only routinely observed in T brucei, it is essential to its existence. http://mcb.asm.org/content/16/7/3615.short http://nar.oxfordjournals.org/content/early/2015/12/15/nar.gkv1459.abstract http://science.sciencemag.org/content/309/5733/416.short But wait I hear, they only ever mutate into other VSG genes, not genes with a novel function. Except when they do. Humans and some other great apes (funny that...) have innate as well as adaptive immunity to trypanosomes, allowing us to avoid infection by most Trypanosoma species. These trypanolytic factors (TLAs) cause lysis of T. brucei cells, preventing them from infecting people. The recent evolution of a truncated VSG gene, known as the serum resistance associated (SRA) gene, prevents the uptake of TLAs and thus allows a subspecies of T. brucei - T. b. rhodeseinse to infect humans with fatal consequences. The presence of the SRA gene is the only known distinction between the two forms. Ergo, the mutation of existing genetic material into a novel protein sequence confers a novel function. http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=324617&fileId=S0031182005007560 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147660 Edit to add: Funny you bring that one up... experimental exposure of the bacteriophage Phi 6 to heat shock causes fixation of a non-synonymous point mutation in the P5 protein - Valine to Phenlalanine at position 207. This mutation alters the protein's folding to fill a hydrophobic cavity, increasing the protein's thermostability. http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003102 Except in the multitude of cases where they are - like the evolution of novel cell membranes through chimeric interactions. Or novel exoskeletons in crabs. Or functionally novel proteins in frogs, etc. So, basically you're repeating the same, intellectually dishonest argument from personal incredulity, and when your justification for it is found to be false, you hand wave it away as "semantics" and shift the goalposts to a new faulty argument rather than actually learn biology.

A) Your initial supposition "[sic] novel genes cannot be created" is demonstrably false due to the above mechanisms. You now appear to be hand waving away this flawed argument by shifting the goalposts to say that the existence of these multiple mechanisms for the production of new genes as "semantics" doesn't explain the emergence of complex, multi-cellular structures in isolation. B) We almost have a "If we evolved from monkeys then how come there are monkeys?" argument here. The evolutionary claim is of shared ancestry, not that bacteria "turn into" vertebrates. This is a fundamental misconception in basic evolutionary theory. If a bacterium did suddenly wake up one day and discover it had binarilly divided an elephant, our current understanding of evolution would be thoroughly broken. It's not what evolutionary theory claims or predicts. C) We do have a good understanding of many of the evolutionary steps between unicellular and multi-cellular life. For example, the evolution of endosymbionts into organelles, the evolution of multicellularity, the evolution of stem cells and the origins of cell types, etc. To say that this extensive body of empirical and experimental research represents "unfalsifiable just so stories and semantic games" is just not correct. The point is that you accused me of not understanding the "problem". I understand what you think is the problem just fine. It's just that we don't agree with you that it is a legitimate problem. It's been thoroughly explained that the principle is NOT the same but to repeat: A) Codons are largely redundant, meaning that most mutations are neutral (i.e. synonymous), as they do not change the translation of the sequence. B) No codons are meaningless. 61 of the 64 possible combinations represent amino acids, the remaining 3 are stop codons. There are no "meaningless combinations of letters." let alone an infinite number of them. This means that when you randomly change the nucleotide sequence of a gene, you do not end up with gibberish, as you do with letters in regard to words. The analogy fails comprehensively. The answer to both consists of two parts: 1) Mutation via various mechanisms results in novel sequences of nucelotides. 2) Selection allows for the proliferation of those sequences which are advantageous (i.e. functional) and not those which are not. The combination of mutation and selection over generations leads to the emergence of biological entities. Again this is a goalpost shift. You initially claimed that "There is no knowledge in biology, based on facts learned through experiments and observation which shows that process of evolution can create new/de novo genes". Now that that's been proven to be false, you're shifting to a claim that it cannot explain the emergence of complex systems - which is a distinct claim with a different explanation. Please refrain from intellectually dishonest tactics - they prevent constructive discussion and are against the rules.

I would strongly disagree. Lateral gene transfer, ectopic recombination, exon shuffling, gene duplication and point mutations are all independent genetic mechanisms that refer to very different changes to the genetic architecture. Their roles in producing novel genes are also very different. I would go so far as to say that referring to the distinctions between them as "semantic" belies a fundamental lack of understanding of genetics. I, and the rest of the scientific community don't believe there IS a problem. There's multiple problems with the word analogy, as has been pointed out by other members. I'm not going to repeat what's already been said but will add that words and codons are quite different for two major reasons: 1) There are 64 codons, and only 21 meanings (20 amino acids plus stop) , leading to considerable redundancy in the genetic code (i.e. multiple codons encode for the same amino acid). 1) Of the possible 64 codons, 61 are "sense" codons, and 3 are stop codons. Therefore every possible combination of nucleotides results in a translatable "word" (following your example), in fact the removal or nonsynonymous mutation of a stop codon can produce a much longer, more complex "word" relatively straightforwardly. Therefore the analogy of words is of very limited relevance. The duplication and re-assortment of existing genetic material into novel sequences via a variety of different mechanisms has been directly observed many times. I thought this had been established.

Err, yeah they do. Exon shuffling brings together two or more exons to produce a new intron-exon structure. Ectopic recombination re-assorts genes into novel arrangements. Gene duplication followed by a point mutation/s results in a new gene. If the contention is that new genes don't simply "poof" into existence, fully functional and encoding a complex trait, well no, they don't, and you wouldn't expect them to using any assumptions based on evolutionary theory, making any argument that the duplication and re-assortment of existing genetic material into novel sequences doesn't represent the creation of new genes a strawman argument. A) The development of complex structures does not necessarily require the development of new genes. Existing structures have been co-opted for novel functions. For e.g. signalling pathways developing into photoreceptors. http://www.nature.com/nrn/journal/v8/n12/full/nrn2283.html http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001054 B) Now we're simply at the logical fallacy of irreducible complexity. Just because you don't understand how a complex trait can emerge from evolutionary processes in no way supports and argument that it can't. C) Bacterial transfer is by no means the only mechanism for the creation of novel protein coding sequences. No one is suggesting that horizontal gene transfer from prokaryotes explains the evolution of the heart, so this is a rather blatant strawman. D) Your claim was: "that [the] process of evolution are not able to create new/de novo genes" but now you're shifting the goalposts to state that the production of new genes doesn't explain the emergence of complex structures - which of course in isolation, it does not (throw in another strawman for good measure, hey). Any explanation of how a complex structure evolves is, by its nature, complex. We actually know a good deal about the evolutionary origins of the heart, and have extant examples of varying complexity ranging from a single peristaltic pump, two, three, four and more chambered hearts across the animal kingdom. http://www.tandfonline.com/doi/full/10.3109/07853890.2011.607468 http://genesdev.cshlp.org/content/20/19/2728.full To suggest we cannot explain its evolutionary origins and the process by which the regulatory, developmental and coding genetics underlay its evolution is false.

And neither are the publications cited. Edit to clarify - none of the publications cited are characterizing existing genes. They all document mechanisms by which novel genes are created or otherwise incorporated into a genome in which they previously were not present. Also, the Lenski experiment does nothing to "prove" that novel genes are unable to evolve. It simply has not been documented in that system. It has in others (as previously cited). Gene duplication, horizontal transfer, exon shuffling, etc. have all been demonstrated to occur, and to generate novel genetic material. The claim that "evolution cannot produce new genes" is demonstrably wrong. Would you like to move forward in a new direction acknowledging that fact?

"By comparative genomic analysis of 12 closely related Drosophila species (7), we identified 566 new genes in the D. melanogaster genome." http://science.sciencemag.org/content/330/6011/1682.full "Exon shuffling is an essential molecular mechanism for the formation of new genes. Many cases of exon shuffling have been reported in vertebrate genes...our experimental work, which revealed four new genes in Drosophila, plants, and humans" http://wweb.uta.edu/faculty/betran/pdfs/genetica2003.pdf "Several molecular mechanisms are known to be involved in the creation of new gene structures" http://www.nature.com/nrg/journal/v4/n11/full/nrg1204.html Given that we now all know that novel genes can and do originate via a variety of mechanisms, do you want to revisit your proposal?

What about animals used for medical research? With no model systems, a lot of biomedical research is not possible. Where do you draw the line for animals? Do insects count? What about parasites? Are we allowed to treat blood fluke and guinea worm infections? What about mice? On average, 55 mice are poisoned for every 100kg of grain produced. Do we need to stop protecting our vegetarian food from pests? what about insecticides?

What do you want someone to look at your work for? Publication suitability? Proof reading for assignments? Fun? Also, if you've worked with reputable scientists to do the work, are they unable to read your work? They would presumably be the best qualified to assess it.

I'm a white, native English speaking H1B visa holder, currently going though the green card process. I love it when I encounter the 'H1B visa holders are evil' argument. It's fun to gently scratch away until you hit the racism part...

Reliving stress and anxiety, and removing carcinogenic substances from the body are two entirely distinct phenomena. One is not a simplification of the other in any way, shape or form. As result, I see one example here as "actually reading the article and using an evidence based argument", and the other as "making stuff up." I think that being unable to distinguish between coming to a conclusion based on a preponderance of evidence, and simply making things up will seriously inhibit one's ability to discuss science. Are you sure you're clear on the distinction being made here?

Herein lies the problem. You just made this up and state that it "probably explains the study". You can't just throw out conjecture without any support. You need to back up that opinion, as you're contradicting the causative effect offered up by the authors: "That proposition is based on the theory that infrequent ejaculation increases the risk of prostate cancer because of retained carcinogenic secretions in the prostatic acini."

No you're not. No it's not science at all. If you can back up what you say using data and evidence, sure, of course. The more opinions the merrier. What I don't want is someone offering up their opinion as fact with no way to support it. When you present us with "I feel itchy/dirty after a hand shandy" we have an anecdote. A single anecdote does not evidence make. When I say "jerking it (or heading on down to towel town, if that's floats your boat) what 3-7 times a month can lower the risk of prostate cancer in men; here's a study". That's an evidence backed statement. Do you understand the distinction?

I just visited the local water treatment plant (phage discovery!) and found that they've switched from chlorinating effluent from the plant, to sterilizing using UV.

I think in the same sense that most people can play a violent video game and not become violent as a result, most ordinary people can separate sexual fantasy from reality. I once read a study which indicated that the industry switched from deliberately using men of lower attractiveness to using more adonis-like actors, because it fit better with the fantasy world men create when watching it - can't find the original study, sorry. Of course in both circumstances, a minority of people (seems like 2% of users in the case of online porn) suffer addiction, and some a warped perception of reality based on exposure to porn/video games, but it doesn't seem to be the case for the majority. Also, pretty much all men watch porn at some point in their lives. Seems that at about the age of 10, most males will seek out visually arousing material. While the technology of, and the media by which erotic material is delivered is changing rapidly, human behavior regarding erotic material has not dramatically altered in the face of increased access to it.

You haven't read rule 34 of the internet. If you can imagine a human phenotype, I'm willing to bet there's a porn star matching it.

It's now clear you do indeed have the wrong attitude, even if you do have the requisite experience, which is doubtful. Sorry.

I'm a PI who supervises graduate students, and recently served on a graduate admissions committee. In the case of our department, that standard requirement for entry into the program is a minimum undergraduate or master's GPA of 3.0, a minimum GRE quantitative score of 155, and a minimum GRE analytical score of 4. If someone does not meet those requirements, it is possible for a PI to grant an exception for a particular student, however they will not receive funding from the program for that student, and thus have to find external funds to both support them, and pay their tuition. As a result, it's a rare occurrence. Applications from qualified students usually outstrip the number of available places, so there would be no reason to take on a student that's going to potentially cost ~$40,000 a year, when you can take a less risky candidate who is supported by the program. As a PI, there's several things I look for in a potential student, and I mean this as positive criticism, but I already know from this thread that I would not consider a candidate such as yourself. 1) A functional lab group requires people who get along. A problematic individual can interfere with the productivity of the whole group and therefore I will overlook someone with good on paper credentials if it looks like they might cause interpersonal problems in the group. If you do not like people, you probably won't fit well into a research lab. 2) A PhD is a significant undertaking that represents the start of a journey, rather than the end. I generally take on students with some life experience and a clear understanding of why they wish to do a PhD, and what their medium to long term goals are. Someone just out of high school does not have that experience. 3) I generally consider students who have some research experience, and more often than not, a publication or two under their belt. This is because I have some demonstration that they know what it takes to produce research. You might find a PI willing to take you on as a graduate student with no undergraduate degree, sure. It would take a pretty compelling case for me to consider someone straight out of high school, and an exceedingly mature attitude. I have seen it happen once, however that student had published their first peer reviewed paper at 14, and had a solid publication record by the time they graduated high school. Unfortunately, it doesn't sound like you have either the experience or the attitude I would consider acceptable to consider skipping undergraduate studies. Best of luck with whichever path you choose.

I'd be interested as to how you feel about Japanese love pillows. (link is wikipedia and sfw). Is it OK to make love to linen, if the linen has porn on it?

and the scientists will let the data tell them the answer.

Or you could draw conclusions about someone's personality by interacting with them rather than forming superficial prejudices about their appearance. Yesterday I met with the provost, so I wore dress shoes, trousers, a dress shirt and a tie. Today, I have to crawl down a man hole to get a water sample, so I'm wearing sneakers, old jeans and a hoodie. I don't think my personality drastically changed overnight.