Arete

Kupiec's theory (for those reading along, the fundamental premise is that gene regulation is purely stochastic and local environmental pressures cause selection amongst cells in an embryo, ultimately leading to phenotypic differentiation in the resultant individual) has some fundamental flaws/gaps: A) There's an extraordinary body of evidence that regulatory genes constrain embryonic development: 668, 000 hits on Google Scholar, representing thousands of individual experiments empirically confirming that unlike as Kupiec claims, the expression of regulatory genes is not stochastic. e.g. http://www.nature.co...bs/nrg2781.html http://www.plantcell...12/8/1491.short http://www.jimmunol....46/6/1914.short etc. B) If, as Kupiec claims, regulatory genes are purely stochastic and the local enviroment is wholly responsible for embryonic development, what evolutionary purpose do the regulatory genes whose existence is experimentally confirmed (e.g. HOX genes: http://en.wikipedia.org/wiki/Hox_gene) serve? C) If the local enviroment drives diversification, why do all embryos pass through the same developmental stages? If the local enviroment is driving cellular selection, surely there would be variation in the process of embryonic development, in association with variation in selection pressure. This is not observed, even in widespread species living in vastly different environments. Differences in embryonic development appear to be related to divergent evolutionary history, not differences in environmental pressures. http://en.wikipedia....i/Embryogenesis D) If the genome is, as Kupiec assumes, purely a generator of proteins without regulatory functionality, how do organisms with very similar protein coding structures existing in very similar environments wind up being very different organisms? http://nook.cs.ucdav...ehl_COSB_01.pdf

Nope, some species display polyploidy: http://jhered.oxford.../9/379.full.pdf As I tried to explain above - the defining feature of a species, at least under the general lineage concept is that they are a species is a group of organisms, which through the process of sharing alleles with one another, share a common evolutionary history, which is distinct from other groups of organisms. The characteristics by which you decide that they have a distinct evolutionary history are secondary, and may be different depending on the particular species division you are considering, particularly when speciation is very recent. E.g. it could be fixed genetic, ecological, life history or morphological differences, evidence of either reproductive isolation or persistence of both species in the presence of hybridization through hybrids being at a selective disadvantage, etc. As speciation is a multifaceted process, there's no one, silver bullet way of delimiting species. Hope that helps

Indeed - reproductive isolation is not the be all and end all of species classification. Species are more rightly defined as "independently evolving metapopulations." http://sysbio.oxfordjournals.org/content/56/6/879.short That is to say a species is a group of organisms, which through the process of sharing alleles with one another, share a common evolutionary history, which is distinct from other groups of organisms. Despite rather seemingly convincing evidence for pre-mating isolation between a great dane and a chihuahua, they are only genetically distinct from one another at relatively very few genetic loci - that is to say most of their evolutionary history is very closely shared. Given most purebred dogs represent extreme selection on rare mutants in a population I'd personally suggest that they represent extreme outliers in a normal distribution of phenotypic variation - like a dwarf and a pro basketball player would in the human population. If the isolation was maintained for long enough, they may well end up being different species, but they're so recent in that they lie somewhere on the continuum from homogeneous population and distinct species, which is difficult to define.

Tip: If you're not aiming to eliminate all of the potential life forms in water, you're sanitizing rather than sterilizing it Putting water in the fridge will have a negligible effect on any microorganisms in it - as most of the kinds of organisms you'd wish to eliminate from it have thermal tolerances which well encompass what you can achieve in a home fridge/freezer. Heat (e.g. boiling) is much more effective. We have LN2 on hand in our lab and -80C freezers, but we still use the autoclave to sterilize equipment. Second what do you want it for? If you want to purify tap water for drinking, there's plenty of non-biological stuff you'd want to remove too, which heating will do nothing for such as heavy metals, nitrates, etc. Filtration is a much better way to make water more potable than boiling. If you want it for experimentation, simply purchasing RO or distilled water will probably be far more cost effective than achieving the same level of purity with any method you could implement at home.

If you are interested in Darwin's thoughts on the species problem, have a read through the first link in the post you quoted. It contains an exhaustive list of Darwin quotes on the topic, along with commentary from Ernst Mayr. If you look at the considerable amount of thought Darwin put into the species problem, it seems ignorant of these efforts of his to characterize his attitude on the paradox as in any way dismissive, and again, to insist on the abolishment of the Linnaean system of classification seems ignorant of the extensive body of work which has been undertaken to reconcile it with genetics and evolutionary biology. A quick literature search on Kupiec shows he has published extensively on intracellular mechanisms, but has not published broadly on speciation, population genetics or evolutionary biology - these don't appear to be his fields of expertise, yet his theory proposes the overthrow of many fundamental aspects of these fields without really offering an alternative explanation for much of the observed phenomena supporting current paradigms: A comprehensive critique beyond what could be conveyed in a forum post is here: http://www.nature.com/nature/journal/v460/n7251/full/460035a.html which I thoroughly agree with. This is also getting thoroughly off topic and is probably worth a thread split if you wish to discuss this specific example further.

Does he, as you claim, call the concept of species an "abstraction", compare it to the concept of races, call for its abolition and claim Darwin "scoffed" at it? If so it would seem as though he is fundamentally ignorant of the works of Darwin, state of the field evolutionary biology and comprehensively misses the point the concept of species (all cited in my previous post). There is always the possibility that you've misinterpreted his work, represented it poorly or I have misunderstood what you wrote - feel free to provide clarification. Given my limited familiarity with his cellular Darwinism theories is seems the latter is likely. Cellular Darwinism lacks a solid empirical foundation, while simultaneously contradicting many of the well-supported principles of population genetics - which is why it isn't mainstream science. He's never offered as an overthrow to species concepts and pop-gen principles in peer review to my knowledge. If he doe so in his book - he's probably wrong.

At least his comment on species concepts seems ignorant of A) The agonizing Darwin did over the species problem. Darwin did not "scoff at" the concept of species and wrote a considerable body of work on the issue. The actual writings of Darwin seem to suggest that he spent a great deal of time and energy trying to reconcile the species problem, and was in no way dismissive of it - http://www.ucl.ac.uk/taxome/jim/Mim/darwin_on_spp.html B) The fact that scientists know that species boundaries are arbitrary http://en.wikipedia.org/wiki/Species_problem. It is in fact mainstream science which defines organismal diversification as a continuous process and thus introduces the problem that classification of a hierarchical, ongoing process is, by definition, artificial. Being artificial is, however very different from being useless. C) The evolution of the concept in light of genetics to arrive at a more biologically informative, and therefore useful state. The work of people like Ernst Mayr and Theodosius Dobzhansky in the development of the modern concept of species: http://www.pnas.org/content/102/suppl.1/6600.full http://www.stephenjaygould.org/library/dobzhansky_organic-diversity.html and the current consensus that species define "independently evolving metapopulations." http://sysbio.oxfordjournals.org/content/56/6/879.short Compare this to the concept of races for which the same author as noted above (Dobzhansky) for contributions to solving the species problem, called for the abolition of due to the non-evidence of their existence: http://www.jstor.org/stable/10.2307/2739576 So at least in the area of the species problem, he seems to have gotten it rather comprehensively wrong.

Let me know how you go convincing Answers in Genesis that intelligent design is not a valid scientific concept. Some explanations to some people are wasted breath. Did you miss the first paragraph of my post? I spend a lot of my time reviewing new ideas in papers, hearing about them and discussing them at conferences, workshops and seminars, teaching students the critical thinking skills they need to come up with new ideas, etc and so on. In my experience, as a scientist, scientists are very open to new ideas. They aren't open to pages and pages of word salad. Why are you randomly capitalizing words? Actually, science is exactly what I'm paid to do. Scientists can, according to wikipedia be separated by either field of study or employer http://en.wikipedia....s_of_scientists More specifically, as my salary is funded by a federal grant, a panel of other scientists, representing the taxpayers of the USA employ me to investigate a specific question I proposed to answer in my grant proposal. If we really want to get antsy, I'm not paid in my capacity as a scientist to evaluate new ideas at all - I'm paid to investigate a specific idea I came up with and wrote a grant proposal to investigate. All that time I spend reviewing new ideas as outlined in the first paragraph of my first post is peripheral to my core responsibilities and part of my service to the scientific community. Ok, so to get more specific: there is a proper way, in science to convey your ideas and have them evaluated. I outlined those channels in my previous post. Spamming random academics with unsolicited emails is not amongst them. If your ideas are worth being considered, they are worth presenting in an accepted format. Novel ideas are extremely valuable in science. A career can and often is built on a single, novel idea and the investigation thereof. Exciting new hypotheses can be gold mines of knowledge and research. It is therefore unusual when someone starts throwing them at random strangers. I've never received an unsolicited email with an idea in it which wasn't either fundamentally flawed, unintelligible, or religiously motivated and unscientific. These ideas are being given away for free because they are worthless. I've already outlined the methods in which scientists routinely provide service to their communities by evaluating new ideas. Again, replying to wall-of-text emails is not amongst them. If you or anyone else wants their ideas evaluated by the scientific community, they're worth putting in the correct format. Read the first paragraph of my first post which you seem to have missed.

Here's a post I made in another thread on the issue. Homosexuality is consistent with evolutionary models of kin selection and homosexual individuals can have net positive impact of the evolutionary potential of the population they belong to:

What sort of biological samples (museum specimens, tissue samples, buccal swabs, cell cultures etc etc etc)? What do you want them for (Sequencing, collections, allozymes, etc etc etc)? There's dozens if not hundreds of potential answers, we will need more details to answer the question.

There's a fairly strong consensus in the literature that extinction rates are being increased by anthropogenic activities and that this increased extinction rate is a problem: "Recent extinction rates are 100 to 1000 times their pre-human levels in well-known, but taxonomically diverse groups from widely different environments." http://www.sciencemag.org/content/269/5222/347.short "The current rates of species extinction are 1000–10,000 times higher than the background rate of 10–7 species/species year inferred from fossil record." http://tejas.serc.iisc.ernet.in/~currsci/mar252002/638.pdf "There is no question that the loss of individual species is a cause of great concern to conservationists, but we can now appreciate that these extinctions are symptomatic of a global-scale ‘biome crisis’ that threatens biodiversity loss, ecological dysfunction and consequent impacts to human lives and economies." http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2004.00686.x/full "Assuming no radical transformation in human behavior, we can expect important changes in biodiversity and ecosystem services by 2050. A considerable number of species extinctions will have taken place." http://www.sciencemag.org/content/302/5648/1175.full

Given the video, could you point out exactly where anyone on this board has accused you of racism? I've tried before but I'll try again: Here's a summary of what both parties have had to say on gun control: http://www.ontheissu...gun_control.htm http://www.ontheissu...gun_control.htm Now, rather than presenting sensationalized, out of context quote mines, half made up Jefferson quotes or things that are just plain not true - could take a minute to look at what each party actually intends to do regarding gun control and tell us specifically, what about each parties' approach you object to or agree on and why? Or try with tax reform: http://www.ontheissu..._Tax_Reform.htm http://www.ontheissu..._Tax_Reform.htm Or any other issue?

Makes sense. I only had the public account to go on. Most scientists routinely do these - I participate in peer review of the work of other scientists through journal reviews, attending conferences, participating in seminars and workshops, mentoring both graduate and undergraduate research students enrolled at the institution which employs me, and participating in some community events. What I don't do is go through unsolicited, wall of text emails from non-experts and blow by blow explain how they don't add up. A) It rarely, if ever persuades the sender of the flaws in their pet idea B) It often incurs the ire of the sender, and result in more wall of text emails C) It's a waste of my time D) It's not what I'm paid to do. If non-experts want to participate in science, there's courses, there's community/citizen science projects etc. - volunteer at the museum, enroll in a science course, undertake an internship in a research lab, etc, etc, etc. If you want an idea scrutinized by the scientific community, there's peer reviewed journals and there's conferences. Like everything else in life, there's proper channels.

Swansont was specifically pointing out how your statement deviated from reality with specific examples of how "wackos" have purchased their firearms legally. I think we're all still waiting for you to support your statement: If you can't provide an example, it renders the statement baseless which puts a rather large hole in your credibility. What actions by the federal government are you referring to?

In addition, you're allowed to drive anywhere in the US for the first 3 months on your home country's license - so it's not actually preventing non-English speakers from driving anyway. I had more trouble adjusting to the fact that road rules are seemingly just mild suggestions in New England than I did to driving in non-English speaking countries like Costa Rica, China, Vietnam, Venezuela and Ecuador.

That isn't actually how it went down. Immediately after the NASA lab's experiment was reported on, a bunch of other labs launched their own experiments trying to replicate the result under the conditions of the original experiment. Skepticism arose when none of them could - it turned out that GFAJ-1 probably can't scavenge arsenic to replace phosphate in it's DNA, but is really really good at scavenging trace amounts of phosphate in harsh, arsenic rich environments. It's not an example of a scientific breakthrough being ridiculed by the community, it's an example of a result being broadly overstated, then retracted when it didn't stand up to scrutiny. http://www.sciencenews.org/view/generic/id/66953/title/Bacterium_grows_with_arsenic http://www.sciencemag.org/content/337/6093/470.abstract http://www.lefigaro.fr/assets/pdf/arsenic-edito.pdf

Janitors and theme park managers get a bad wrap on scooby doo, but I'm pretty sure most of them aren't pretending to be ghosts. Oh and psychology is a "soft" science. This is not meant to be a criticism as you seem to have taken it, but a description of the methodologies employed to test complex and often abstract hypotheses which do not lend themselves to experimentation, mathematical description and accurate modeling in many of the social sciences. http://bill.silvert.org/notions/ecology/hardsoft.htm http://medical-dictionary.thefreedictionary.com/Soft+Science "A field of study in which accrual of objective and reproducible—‘hard’—data is difficult as the field examines societal phenomena and dynamics susceptible to subjective interpretation. Examples Anthropology, economics, psychology, sociology, social medicine"

So, one of my jobs in undergrad involved landscape regeneration, we killed a lot of non-native trees. The easiest way to kill a tree is using glyphosate poison like Roundup. Drill holes around the trunk, as close to the ground as possible, about 10cm in and about 5-10cm apart, in a ring (see below). Basically you want to deliver poison into the vascular cambium all around the tree. As soon as a hole is drilled, pour in the glyphosate undiluted. Wait 4-8 weeks. As for not having it fall on a fence/house etc. I can't see any option being realistic apart from getting up on a ladder/rope and trimming it - it's usually how arborists go about taking down a tree. It should be easier once it's died off a little, but I wouldn't leave it so long that there's a danger of it dropping branches. If those things are beyond the scope of what you can manage (i.e. tree is too big to get up with your available gear), it's probably time to call in the professionals. No point risking falling out of a tree, or having a big dead branch squash someone.

A species is generally defined as a metapopulation of organisms sharing an evolutionary history. http://sysbio.oxford.../56/6/879.short Plenty of different species can hybridize to produce viable offspring. e.g. http://onlinelibrary...12.05571.x/full http://onlinelibrary...12.05571.x/full http://onlinelibrary...09.04471.x/full A vaccine or a chemotherapeutic treatment will be also affected by evolution in the host, pathogen or vector - if the host, pathogen or vector have different evolutionary populations, they may respond divergently to treatment. Partially effective treatments may lead to selective sweeps and rapid inffectivity of the treatment. A treatment for an autoimmune disease may only be partially effective if, for instance the causes of the disease have independent evolutionary pathways. None of these have anything to do with antibiotic resistance. Changes in allele prevalence between populations and over time are what evolution is. I'm not sure I understand. Genetics, particularly population genetics and phylogenetics, which I study, are subfields of evolutionary biology. Our lab is a genetics/genomics lab in the evolutionary biology department. The study of genetics and evolution, particularly at the level of the population or species, are intimately intertwined. Much of the theory which allows us to explain genetics is evolutionary theory. You can't have one without the other, at least in terms of modern science. Well, no, because the evolutionary history and processes of human populations will profoundly affect the dynamics of H1N1 epidemiology. If you don't understand the evolutionary dynamics of the host population, it is impossible to determine the dynamics of disease within that population. Well, one is focused on maintaining or maximising the genetic diversity of population for the purposes of maintaining the population in a natural state in perpetuity. The other is focused on maintaining a harvest without inducing a population crash. While some of the population parameters you would want to know about each population would be the same and thus many of the techniques would be similar, they are ultimately two distinct examples of how evolutionary theory is useful. Hopefully we've collectively demonstrated how it is and I hope you continue to find the field interesting

The point is rather this: If you built a business in the USA, you did so either due to the enviroment created by, or directly using resources that the government, and therefore taxpayers developed funded and maintained. You should not be exempt from contributing to that system simply based on the fact you decided to become a business owner. Sure, running a business involves financial risks. It often contributes to employment. A country like the USA benefits considerably from the development of private business and it should be encouraged. BUT and its a big but, to suggest, as some business owners do (see above) , that they did develop their business entirely without assistance and therefore should not have to contribute to taxation, and therefore the various infrastructure systems and services which are critical to the development and success of their business is false. Obama's point was and remains that US business owners are dependent on a number of publicly funded resources for the success of their businesses. In that sense, no, businesses do not actually exist is due wholly and solely to those who took the chance and made those businesses exist. They exist because a publicly infrastructure supported a person who decided to take a financial risk and invest capital in a private business venture. That's not in any way meant to belittle business owners, dismiss the benefits they have for society, but no man or business is an island.

If you re-read post #20 in this very thread, I posted evidence suggesting that outlawing abortion does not reduce the rate of abortion. Jews do not march themselves into gas chambers en masse on their own, but abortions happen whether or not they are condemned or permitted. Ergo, it is a false comparison.

Given that the poorest 40% of US residents have 0.2% of the financial wealth of the country, I'd be interested in the non-progressive taxation strategy you'd suggest that would raise an adequate budget whilst this section of the population contributed the same percentage of income tax as the richest 40%, who have 96% of the financial assets. I mean, even if you took every cent that the bottom 40% had, you'd still have to take a massive hit to your annual income with a flat income taxation rate.... http://en.wikipedia....e_United_States

All of these require a PCR step in them. 454 uses emulsion PCR, as does the Ion Torrent and Illumina uses bridged amplification. The newer PacBio machine is the only one to my knowledge that does not. Illumina is the only strictly short read technology in there. 454 typically produces fragments ~500bp in length. Ion Torrent is dependent on the chip set you are using. PacBio produces reads in the 2-3kb range, but as up to 15% error in base calling. Unless you're working on viruses/prokaryotes, it's highly unlikely that you'll get adequate coverage from a single lane of any of those technologies to produce a contig. There's numerous approaches to generate data specific to answer particular questions - reduced representation libraries, RNAseq, shotgun sequencing, etc.

DNA would be recoverable, but you'd be looking at aDNA techniques. http://en.wikipedia.org/wiki/Ancient_DNA I've had some cursory experience in ancient DNA from a purely research point of view. I'm not aware of any publicly available aDNA resources, but based on my experience, to recover the kind of loci you'd need for a paternity analysis you'd be looking at thousands of dollars in consumables before you even paid anyone for their time or equipment.... Your best bet would be to contact someone who specializes in aDNA (Google is your friend), and see if they would run your sample. Be aware that it will be expensive, and you will get zero guarantees as to it working. Good luck, and sorry if its not what you were hoping for.

I'll start with the fact that I am not eligible to vote in the US election, so don't have a dog in the fight, so to speak, but: You can believe a ladder is bucket all you like, but it doesn't make the ladder a bucket. communism has a definition: http://en.wikipedia.org/wiki/Communism http://dictionary.re...rowse/communism "a theory or system of social organization based on the holding of all property in common, actual ownership being ascribed to the community as a whole or to the state." As does socialism: http://en.wikipedia.org/wiki/Socialism http://dictionary.re...rowse/socialism "a theory or system of social organization that advocates the vesting of the ownership and control of the means of production and distribution, of capital, land, etc., in the community as a whole." The policies of the United States Democratic Party are not describable as either communist or socialist under standard definitions of those political ideologies. You can say that you disagree with their policies for reasons x, y and z, but to simply state you don't like the healthcare bill or the taxation policy simply because it is "socialistic" or "communistic" is incorrect, and to do so after repeated correction does make you appear ignorant. It would be more conducive to discussion to point out actual differences in policies between the two parties and explain why you prefer one to the other, or even point out why both are inadequate... E.g. http://www.ontheissues.org/celeb/Democratic_Party_Health_Care.htm http://www.ontheissues.org/celeb/republican_party_health_care.htm point out what you like and don't like about each, perhaps?