CharonY

Hmm, do we normalize by individual or by biomass?

In cases like this (i.e. wildly misleading title in the news section) wouldn't it be appropriate to change the title?

I actually do think that most agree that the quality of education one receives pre-PhD is more dependent on the student rather than the school (if we disregard potential extremes, e.g. schools with no practical courses for natural sciences and suchalike). The training as a PhD student is far more specialized and highly lab-dependent in natural sciences. There the group is more relevant than the school. However, research-oriented studies will be funding-dependent and if you are a student in a teaching uni with no funds for high-end equipment, you will not receive technical training or expertise in them. As I mentioned earlier, one cannot conflate undergrad with grad training.

Actually, I am not even sure whether a pure meat diet would be bad per se (as in being toxic) just less healthy than a more balanced diet. The linked article does a bad job in interpreting the study they cite and even the the study itself is not without issues (the smoking is a gross exaggeration, for that matter, although effect size is a bit tricky to calculate). Just to make a point, the cited study also found that low-protein intake may be actually be hazerdous for older adults. They found for example that at least 10% of the calorie intake should be proteins for adults older than 65 to minimiz IGF-1 loss for example. In summary the associations are indicative for certain metabolic functions that we are still uncertain of and are somewhat age dependent. It would be hard to make the case for toxic effects as known for tobacco smoke. Edit: I overlooked that the the point was made earlier already.

You cannot simply dismiss numbers that you dislike. The trade volume (both ways) between China and the EU is about 433 billion euro, between Russia and EU 335.9 billion euros in 2012 (in goods only). The respective BRICS volume are lower (total volume of all trade within the same year was about 300 billion USD). Cutting off the European trade (US trade is much lower for Russia, but is much more significant for China and Brazil) would create a huge deficit that the BRIC countries would simply not be able to absorb, unless they suddenly triple or quadruple their trade with each other. And it does not really matter if the values are given in Yuen, USD, Euro or Pesos. You just use the thing called conversion factor (which incidentally put one Yuen at 0.15 USD).

Due to the fact that empathy and social behavior is found in other animals as well. As you may have noticed, the reference I presented earlier was about the evolution of empathy. It s not something exclusive to us humans. So unless you want to point out that animals are religious, I am pretty confident that empathy has a longer history with us.

Seems like a typical Venter project. Massive technological upscaling, but little in terms of hypothesis driven research (or in gaining fundamental insights, despite claims). I assume something will come out of it, but i would not be surprised if they face similar issues as other high-throughput database projects.

Nope, if you overcome these emotions it it will be due to mechanisms like habituation or conditioning, but not by merely applying logic. I f you go bungee jumping the first time your logic will tell you that the chances of accidents are low and you are nicely secured. Still, your adrenaline will speak. Similarly, if you see other someone getting harmed you will wince (or, if you have good self control, it will require a PET scan to reveal brain activities that emulate getting harmed yourself). Unless you are a psychopath, of course. Fears, empathy and similar emotions are deeply embedded in us and while we can overcome them e.g. by getting desensitized, it does require quite some efforts. As such indoctrination is a much more suitable mechanisms to overcome empathy. The overall point however, is that social behavior and empathy are much more deeply rooted than religion.

I am not sure how plasma is going to help. Greg's proposal makes more sense to me.

Yeh, and with sufficient training you may advance to: "why are the grad students so ignorant" and eventually graduate to, "why are the PhDs so bloody daft?".

Some official statements have been issued, it seems http://www.globaltimes.cn/content/845914.shtml#.UxSrlfldXKt

I would be surprised if China actively tries to get involved in it. Unless they have some significant investments into the Ukraine (which I really do not know), there does not seem to be any benefit to side with either of them.

Science disagrees with you. There is a large body of evidence describing empathy in numerous social animals, including humans. This also includes lack thereof and association with certain personality disorders. A review on evolution of empathy: Decety Ann N Y Acad Sci. 2011 Aug;1231:35-45. Take a look at the abstract:

And that is why science does not care what you believe.

Serovar is the same as serotype. KW is a means to distinguish them in a clinical context, but their use in terms of taxonomy has changed quite a bit from the original proposal by Kauffmann. I.e. each serotype was originally considered a species. What you quote however, is at odds what you ask. The quote states that you cannot differentiate within serovars/serotypes. S. ser.Typhi (serovars are capitalized and non-italicized) and S. ser. Enteriditis are, as the name implies, different serovars. What it means is that strains within a given serovar cannot be distinguished.

So in that case we are talking about at least one step-analyzed data, which can be quite a different beast depending on the analytical technique (serial X-ray crystallography comes to mind). I am more open to that, but again, I do find nucleic acid data the easiest to handle. I do agree in many ways that re-analysis of data is valuable and i would put biomarker research pretty much in the front for this (at least when it comes to validation purposes). But again, for some of our projects we had to send out data using terabyte harddisks to collaborators, because it was simply not feasible to transfer that amount of data in a timely fashion otherwise. I actually do agree with microscopic image issues, but that opens up another can of worms. You could substitute best image with best set of images and the issue would not go away completely. The only way would collect all data in an unbiased way, including runs and examples that you may consider as failed. While they may contain information therein, the flipside is that there would be even more data to sort through and avoid spurious associations. As it is now, crap is already abundant in published studies, if we add everything to the mix I am not sure how look through all of them. I would maintain that this more appropriate for strong, high impact claims (in which case a more thorough review is more appropriate than yet another me too paper). I am not arguing that data should not be made available, but my main gripes are a) who is paying for the infrastructure and maintenance of the repositories? Grants certainly do not provide me with funds to do anything more than the experiments (and often barely so) and b) what would be a good system to make the sets useful for a range of applications so that we do not intellectually masturbate over data that is actually the result of bad experimental design? Biological studies are often so diverse in the way we try to tease out functions that trying to pulling differing types of data together is not working very well (and I could launch into the whole systems biology rant, but I will refrain myself here). Again, I am all for sharing data, but at least in my field the infrastructure is not there yet.

Actually I am not clear from the above post whether you are talking about the tiffs or the sequence. Although since you mentioned microarrays, I assume you mean the images or one step below, intensity traces. While I do agree that there is some value in it, even for simple things like using new normalization methods (or maybe improved image processing if we talk about the real raw here), it gets incredibly unwieldy if you run a lab that relies on high throughput instruments and methods. I do see both sides of the argument, although I still think that our ability to generate data has way outpaced our ability to keep them organized and accessible. The organization for DNA/RNA sequences is relatively straightforward, but it can be incredibly complex when moving to quantitative information on other biomolecules where massive deconvolution is done (e.g. metabolite/protein data,to some extent also RNAseq in this context). There have been all kinds of attempts to standardize elements (as e.g. MIAME), but often times biology is too exploratory to conform to them in a neat way. There have been proposals from various agencies to create the infrastructure that would at least allow hosting of that data (although I am not really sure how the discussions about funding have progressed) but especially for quantitative data I am always concerned that the biological part (including e.g. cultivation and manipulation) is often neglected and makes cross-study comparisons exceedingly difficult, which could limit the value of raw data repositories (again, depending on they type of information you wish to extract, and to some extent one could make that point for the majority of biological research). Quite frankly, I have no idea what a more or less unified platform would look like, without messing everything up.

That is probably just a minor point, but I think that only young earth creationists believe that the Earth is a few thousand years old. Crationism basically just stipulates that all organisms are created as they are and reject the notion of evolution (which has equally been shown wrong).

Well, to be fair, raw data is rarely useful even for researchers, much less than the public. For example sequencing reads are can be essentially fluorescent images (such as of the clusters in illumina systems). You could upload them but would it be worthwhile? Instead one would upload processed data (i.e. at the minimum after base calling). Same goes for large data sets such as mass spec data (I usually rack up a few gigs per hour) or, serial diffraction data (terabytes of data, much of it being empty images). Although sometimes it could be worthwhile to re-load data and run it through improved algorithms to e.g. deconvolute data, but even with today's storage capacities especially smaller labs would be struggling to maintain the raw data for a long time. Sometimes it is easier to replicate the experiment with newer equipment instead. For modeling papers it is usually customary to identify the data sources (as modelers do not often collect the data themselves) and present the parameters of their model. So it is generally possible to replicate them, although some complicated models would require serious computer time to do so.

I think beer is a strong motivator for this.

While I am very rusty in Latin, bonum is either an adjective (accusative singular neuter or masculine) but it would lack an appropriate noun. The alternative would be using bonum as noun, in which case "ipsum bonum" would mean the good itself (either nominative or accusative). In that case it would be something like 'I will be the good itself" (and one would also put the verb at the end). Doing good would be more appropriately translated to bene facere (sometimes contracted around the middle ages, I believe) which would then take the dative.

Partially. Most group Ds were found to be enterococci, but there are exceptions. Streptococcus bovis is a true Group D Streptococcus, for example. Quite an annoying classification scheme and somewhat outdated imo... edit: emphasized that S. bovis is but one example

IIRC the evidence for life within the Isua sediments are weak or at least debated. To argue that life was at least around at that time point is a bit premature. Based on current knowledge putting life around 3.4-3.5 Gyrs is a more conservative bet. But as it has been remarked multiple times already, without knowledge of mechanisms or other details it is impossible to estimate whether 500, 700 mio or more would be considered a long or a short time frame.

I think it is missing the general point that being adapted to a certain habitat does not determine how you perform in another. Given a set of traits you may perform better worse or equal when put into different habitats. The assumption that once adapted to a certain situations you are at the maximum possible fitness is simply incorrect.

First life could be a bit trickier, even, depending on when we put the start point. But for the common ancestor the properties most have agreed upon are somewhat close to bacteria/archaea in a very general sense. This includes for example possession of DNA or RNA genome and protein expression system (ribosomes) with the common genetic code, lipid membrane with embedded proteins (though types of lipids are heavily discussed) and I am pretty sure a couple of other things that I cannot remember right now.