Arete

Virtually every major scientific development since the inception of the scientific method has been opposed by the church and the list of scientists who have suffered persecution at the hands of religious establishments reads like a who's who of significant contributors. Whilst many people use apologetics to try and reconcile the two philosophies, it's extremely difficult to find an example of religion aiding a scientific development and extremely easy to find many examples of the religious establishment directly impeding science. Harmony between the religious establishment and secular science is largely wishful thinking. http://www.jstor.org/pss/1027380 http://www.annclinlabsci.org/cgi/reprint/37/3/295.pdf http://cscs.umich.edu/~crshalizi/White/ http://www.huppi.com/kangaroo/L-sciencechristianity.htm http://www.sunclipse.org/?p=626

can you treat user actions as a continous variable or is it strictly categorical? I'd be leaning towards not involving any sequence data coding and using either a distance or dissimilarity matrix and a hierarchical clustering approach e.g. http://www.statmethods.net/advstats/cluster.html That way you don't run into all sorts of issues regarding erroneous assumptions you will have to make by trying to treat your data as sequence data.

The premise is fundamentally reliant on two equally supported hypotheses. You have no second hypothesis and no observations. In the absence of these, the premise is entirely nonsensical.

1) You have no observations or an alternative hypothesis. 2) You therefore have no equally well supported hypotheses or justification of how one hypothesis is simpler than the alternative (as no alternative is given). The invocation of Occam's Razor does not make sense or support your position.

Forgive me if I am missing something, but it seems like you've gone "Occams' Razor + reducibility = God axiomatically exists" Occam's Razor states that if observations support two hypotheses equally, the simpler of the two is more likely to be correct. To evaluate the above proof, we need to know what the observations are, what the two competing hypotheses are, how you tested significance and how the you've justified one to be simpler than the other. Otherwise the premise is nonsensical, at least in a scientific context, which is more or less what I think people are taking issue with.

It might be just me, but a sentient being capable of creating the universe is rather by definition more complex than the universe itself. Concluding that the most simple answer is God despite no supporting observational evidence of God's very existence is a rather disingenuous application of the concept.

Mitochondrial and chloroplast DNA is maternally inherited. They do not have independent evolutionary histories and are again, not equatable to bacteria under any existing system of biologically relevant terms.

We're moving from computing the realm of statistics but: I did a chapter of my PhD using continuous morphometric data, nucleotide sequence data and categorical allele frequency data, so I have some idea of the statistical tools for comparison of each data type and the assumptions that go along with them. Basically, you seem to have a string of either continuous integers or a very large suite of categorical states representing individuals. How you treat them will be somewhat dependent on what exactly you want you're using the data to answer. Are you trying to determine which individuals are more similar to each other? Number of clusters in your data? Where in the sequence individuals differ? Something else? It is really hard to determine the validity of a methodological approach without a clear idea of the actual hypothesis you're testing... You want to concatenate these data points into a string and then treat them as you would either a string of unlinked genetic loci or as a single linked gene to compare them, right? Having worked with these different data types, I'm seeing a lot more negatives than positives in trying to adapt your data to a sequence alignment software than treating it under a more realistic set of assumptions... how are you going to deal with issues like gap open penalties, repetitive regions, etc. Then what sort of downstream analysis do you intend to do? Phylogenetic analysis has a large suite of assumptions which it's almost certain you'll be violating many of. (ploidy, model of substitution, minimized deep coalescent events, clock like substitution rates, etc) Population genetic methods are even worse (no unsampled populations, neutral model of evolution, etc) There's suite of traditional statistical comparisons which at least to me would seem far more appropriate given your data. If you can let me know the hypothesis you're testing I can probably give you some suggestions on approaches to take e.g. converting categorical data to a dissilmilarity matrix, testing for clusters using PCA ordination and Bayesian cluster detection, Euclidean distance tree building, classification tree analysis, discriminant function analysis, distance based redundancy analysis etc. There's reasons why us biologists don't try and convert other data types into sequence data, and it's almost always because there's a far more appropriate method available to answer the question at hand with the data at hand A bit more information might help us to provide suggestions...

Noncoding DNA will generally not be translatable into AA. What does your numerical data represent and what are you attempting to do with it? There's probably a more appropriate method for analyzing it than translation into nucleotides...

While the wikipedia article outlining the concept explains its implications in a religious context, the concept in itself is an unequivocally scientific notion regarding the burden of scientific proof. Thus it's an example of ridicule being useful to science.

I'm not sure. Fairly often, in my experience, pointing out how a hypothesis or experimental design is ridiculous is an effective scientific tool is pointiong out flaws. We recently had a grant reviewer suggest common garden experiments be conducted in giant tortoises. We politely pointed out that if Darwin himself had of set up the suggested experiment, it would still be running and thus probably didn't fit in with the grant's 3 year time frame (i.e. the suggestion is clearly ridiculous). In this sense, ridicule can be a valid tool for scientists. The use of the celestial teapot http://en.wikipedia.org/wiki/Russell%27s_teapot is a long standing example of how a clearly ridiculous idea effectively conveys the concept of scientific burden of proof. Obviously ridiculing a group or person directly is unlikely to be constructive in any circumstance.

I'm sorry - but given the recent posts you've made in the biology section I feel it's necessary to call you on this one. For example in this thread: http://www.sciencefo...tween-bacteria/ You've challenged current scientific theory based on a complete misinterpretation of a popular science article - which you didn't reference leaving us to dig and assume we found the right one. You've then gone on to completely misunderstand the definition of many very basic biological terms in order to try and argue a point e.g. I mean absolutely no disrespect, but I've worked with year 9 high school students who can tell me without hesitation the difference between an organelle, a bacteria, a prokaryote and a microorganism. They are fundamental building blocks of knowledge, essential to the understanding of cellular biology. Despite being furnished with wikipedia links to explain the key differences you argued the point that in your opinion they were one and the same for over a page. It's not our or any scientist's fault that your basic scientific knowledge is this lacking - you need to do a bit more reading. This brings me to three major points: a) Scientific illiteracy is a problem, sure. Its got roots in science, in education systems and in the media. However - ALL of the scientific literature is internet based these days. With the advent of FOS journals like PLoS and BMC, the literature is more accessible to the general public than EVER before. b) If you're going to assert changes to a well supported scientific theory (i.e. evolution by natural selection - http://www.sciencefo...prey-mechanism/), you need to pose a legitimate problem with the theory and pose legitimate alternatives. If your problems with the theory stem from a poor or incomplete understanding of what the theory actually states, people politely and comprehensively try to explain how the theory doesn't work the way you're proposing it does and you react with snippy, sarcastic responses, it inevitably elicits frustration in the people trying to help you. c) Scientific language, terminology and nomenclature exists purely for clarification purposes. In the above thread you deliberately refused to acknowledge fundamental, learned in high school biology scientific definitions when presented with them because it didn't suit the point you were making. (i.e. you stated: mitochondrion = microorganism, I corrected: mitochondrion=organelle, you cited: that's your opinion) It's again, not science's fault that you refuse to acknowledge differences in definitions pointed out to you reflective of important biological differences because it doesn't suit you. It also makes it near impossible to have a meaningful discussion on a topic of science when you refuse to acknowledge these definitions. Again I mean no disrespect or dismissal of you or your posts, but please don't blame a lack of knowledge and education on science/scientists/this forum if you're capable of picking up a biology textbook and reading it.

Ok so for clarity - 1) You first made a preposition that an article posing widespread HGT between endosymbiotic bacteria and their human/animal hosts posed challenges for evolutionary theory. The forum demonstrated that even if this did occur, it didn't challenge current species concepts or evolutionary theory, the article was not actually proposing this at all. The article was actually citing high rates of HGT in endosymbotic bacteria within vertebrate hosts - this is a long known phenomenon, the results of the initial Nature publication not unexpected, posing no challenges to current species concepts or evolutionary theory. 2) It seems like you're now postulating that considering bacterial endosymbionts and their hosts to be separate entities in terms of taxonomic classification/evolutionary history somehow trivializes or ignores their co-dependence? Because this is simply wrong - the classification of evolutionarily distinct organisms as different is fundamental to further study characterizing co-evolution and co-dependence of organisms. I mean, every heterotrophic organism on earth is dependent on autotrophs for survival. If we called every co-dependent group of organisms the same thing it would severely hinder any study of the actual systems themselves and wouldn't make any logical sense under current species concepts.

Your interpretation of the facts appears to directly contradict observation on a number of fronts in this thread. 1) There is no documentation of widespread bacterial-human HGT in the article you alluded to. 2) There's no such thing as "The genome project" (It's the Human genome project, the 10k Genome project, the Honey Bee genome project....etc) and the Human microbiome project - which you were actually referring to - never stated that 90% of human DNA was microbial. 3) They actually stated that 90% of the cellular diversity of human body was bacterial. That's a very very different statistic in biological terms. By weight only about 10% of a human is symbionts. http://www.stephenja...d_bacteria.html 4) A considerable amount of scientific research is conducted into human symbiotic organisms, not none as you suggested. Spend 10 mins on google scholar and you'll get a feel for the quantity of literature on the subject. 5) Endosymbionts cannot be interpreted as being the same species as their host under any biological concept. 6) Mitochondria are hypothesized to have prokaryotic origins, but cannot be interpreted as actually being microbes under any biological concept, any more than my desk can still be considered to be a tree. It's not that you're interpreting observations or facts differently, it's that the observations you're making are actually incorrect.

The fact a microbe lives within a human does not make it part of the human nor it does make human DNA 90% microbial - I think Psycho's analogies are trying to convey this point. Hmm the source you seem to be citing - the Human Microbiome project, is a major NIH funded investigation into human endosymbionts.... which would rather strongly suggest that scientists are not ignoring them - see publication list below. A major component of their research is investigating the role of the human microbiome in human health. http://commonfund.nih.gov/hmp/sciencepub.aspx http://commonfund.nih.gov/hmp/initiatives.aspx#relationship The fact we have endosymbionts just simply doesn't pose any challenges to the theory of evolution or current best practice species concepts, which it seems to be what you started out arguing. No it's not, it's an organelle. http://en.wikipedia.org/wiki/Mitochondrion http://en.wikipedia.org/wiki/Organelle

living inside a human =/= being part of a human. Otherwise this is evidence that trees are actually part parrot.

Wow quadruple post.... A quick literature search fails to find this statistic reported anywhere. Care to link? Unless you're referring to the report from the Human microbiome project which reports that >90% of the cellular diversity of the human body is made up of microbial cells, once endosymbionts are included. http://discovermagazine.com/2007/jun/your-body-is-a-planet http://mpkb.org/home/pathogenesis/microbiota If this is the statistic you are referring to, it's a statement of the biodiversity of our symbionts and has nothing to do with humans having 90% microbial DNA.

And if someone with one of these things tells you diagnosis over an internet forum is not possible?

Diagnosing medical conditions over the internet is like giving a haircut over the phone.

It might be because I'm one of them mainstream science people but I really don't differentiate between flavours of intelligent design. If a concept can't provide a falsifiable hypothesis which can be validated by observation, it isn't science, belongs outside of the science classroom, natural history museum, science funding and science forums. I've mentioned elsewhere that I'm a strong secularist and support the right to formulate one's own beliefs but in the world of science a concept we can put a p-value on trumps one we can't every time. My personal view is if people have a problem with that, they have a problem with the scientific method, which while not perfect, has a considerable history of answering complicated questions. It's still a little unclear - are you saying you disagree that say, E. coli and humans are considered different species? If that's the case the answer is in the species concept issue I raised earlier. Size/scale is irrelevant to contemporary delimitation of species, which is based on evolutionary independence of metapopulations. E. coli is, by a number of genetic, phenotypic and physiological attributes, considered an organism in its own right, as are humans. They have independent evolutionary histories, thus they are considered independent species. The fact one is an endosymbiont of the other is not relevant to their status as species. If you're proposing that you use an entirely different system of classification to the Linnaean system, you'll need to describe it and how it works if you expect not just the scientific establishment, but anyone else to understand anything based on it - in order to have it adopted by others you'd need to demonstrate how it is superior to other systems - I can already see major issues with it if you're considering symbionts to be the same species, if it is indeed what you're proposing. There's a rather long list of genetic, phenotypic and physiological distinctions between eukaryotes and prokaryotes. The nucleus is but one. I'm still not sure what you mean by "OUr DNA is 90% microbial"... Scientific language doesn't "change all the time" in fact, quite the opposite. Scientific terms generally have succint, very clearly defined meanings. Any new terms need to be clearly defined. Public scientific illiteracy is a problem, but pointing blame solely at the media is unwarranted. Most scientific study and thus explanations require dedication, attention to detail and are difficult to integrate in a sound-byte ridden, 5-30 min entertaining story. Many scientists, including myself find it irritating that something which takes years to understand properly is expected to communicated in such a fashion and don't try hard enough to make our research understandable to the general public. The media need it be so, and often incorrectly interpret research in their communication of it to the public. The public attention span is often too short for the message to get across anyway. It's a problem which needs to be addressed by everyone in the chain. It was rather neatly demonstrated by your own misinterpretation of the article you started this thread about

It's not so much a facet of Bayesian stats as evolutionary theory. A common ancestor fossil represents a hard "at least" date - the presence of a common ancestor demarks a point at which you can infer that the split had to occur after. Due to the fact speciation is an ongoing process, happens over a considerable time and it's conceptually hard to call exactly when it has occurred by, the absolute minimum date of a speciation event is much more squishy. A lognormal distribution is a good way to reflect the hard maximum, squishy minimum nature of fossil calibrations If you're using a vicariant event e.g. closing of the isthmus of Panama (I generally don't like them because of the huuuuge confidence intervals they require to be in any way realistic) A uniform or normal distribution around the prior might be more suitable.

I'm not sure what the problem is... That endosymbionts are considered seperate species to the host? That bacteria which can exchange genes are considered separate species? Both these questions are dealt with under the discussion of species concepts. Are you trying to state that the DNA in a human cell nucleus can be considered 90% prokaryotic? Because that's simply not true. That intelligent design is not considered a scientific theory? Not for this thread/section of the forum, and has to to with how the scientific method works.

As a postdoc working in a phylogenetics lab, occasional lecturer and author of above-mentioned phylogenetic papers, I at least like to think that my basic knowledge of phylogenetic tree reconstruction methodology (I say methodology because at least, Bayesian tree reconstruction is founded on coalescent theory which I linked to in my last post) is reasonable. 1) We generally don't use entire genomes, as it is an assumption of most methods that loci are unlinked and accumulate mutations under a neutral model of selection. 2) Time calibrations for phylogenetic divergence estimation are generally based on fossils. What you do is identify a fossil/multiple fossils which undoubtedly represents a common ancestor of some or all of the terminal taxa you are interested in. The estimated date of that fossil's formation represents a hard lower bound for the relevant node in the phylogeny (i.e. we know that the group of organisms in question is at least this old). By applying a lognormal prior distribution to that node, and a relaxed clock model to mutation rates across the tree, we can generate probabilistic ranges of divergence around each node in the tree - giving us an idea of the dates certain species split from each other. Calibrated phylogenetic reconstruction is based on fossils, so the conundrum you seem to be posing cannot, by definition, exist - if the fossil evidence a tree is calibrated on is wrong so are the estimates of divergence. If you're interested in how it works, grab some free nucleotide sequence data from Genbank, use free web based clustal to align it and have a play with the Beast software (it's free and probably to most user friendly as it has a GUI) http://www.ncbi.nlm.nih.gov/genbank/ http://www.ebi.ac.uk.../msa/clustalw2/ http://beast.bio.ed.ac.uk/Main_Page

Brainteaserfan suggested (whether intentionally or unintentionally - just to be certain there's no implications) that evolutionary theory had humans evolving from chimps, which is does not. We actually have physical evidence of several common ancestors of extant hominids. http://www.talkorigins.org/faqs/homs/species.html http://www.science20.com/news_articles/meet_ardipithecus_ramidus_early_hominid_common_ancestor_was_neither_chimp_nor_human_says_study Evolution is a continuum. Expecting a magic discovery of a specific, pinpointed "common ancestor" is to completely misinterpret evolutionary theory regarding speciation - it's a piece of supposed "evidence" that is not expected under theoretically supported prediction. See coalescent theory, species trees and divergent selection. http://en.wikipedia.org/wiki/Coalescent_theory http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000501 en.wikipedia.org/wiki/Divergent_evolution

The very fact the basis of the variation is random would logically imply the opposite. Two forces acting to create an equilibrium doesn't imply or need intelligence to manifest either, given the countless examples of chemicals and physical objects in equilibrium between two forces. Estimated and observed rates of extinction suggest that equilibrium states such as the hypothetical I proposed are relatively rare and unstable - it's far removed from a "just so" story.