CharonY

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.

Well, in transposons quite often glucuronidase or galactosidase activity are often used. Positive selection is usually done with e.g. X-gal or X-gluc plates.

Some unis with core facilities also allow you to generate preliminary data using their facilities (typically things like sequencers, mass spectrometers, NMRs etc) on a tab under the assumption that you would reimburse them once the grant hits.

In addition to what chadn737 said: check the tree again. You will see that archaea and bacteria have a common root (look at the red part and do not get confused by the branching of archaea and eukarya, As a side note, bacteria are not species.

Actually, all cockroaches have wings...

Well there are news reports on that alligator. And apparently it was not trying to get through the fence, but on top of it, presumably to hunt a racoon. Link

Considering how established GR is, it would have to demonstrate in the proposal a certain likelihood of success. If that is worked out well, the reviewers would have a hard time refuting it. In addition the reviewer are generally not in contact with each other before they submit their reviews. Finally the panel often does not only consist of said referees and for controversial projects it is not uncommon to have panelists arguing either side. If everyone is established in the panel, there is actually a bigger chance that some want the unknown one to succeed just to spite their rival, with whom they may have built up decade-long animosity (several layers of cynicism have been added which may not represent reality).

Yes most studies point towards a common ancestor between archaea and bacteria and would be the common ancestor to all. There is at least one proposed deviation from it, but to my knowledge it is not very well substantiated (though Arete may want to comment on this).

Well, the ancestor is not around anymore and for unicellular organisms it is highly unlikely that fossils will be found. I am not sure whether there is a misunderstanding, however. Consider humans and chimpanzees (different level of trees, similar principle), for example. Neither spring from each other, but both share a common node, or ancestor.

I think in the US it is getting more vocal as the issue is being politicized here. In other countries there are generally no parties that have voting stake into supporting that (fundamentalist) stance. The reason why the arguments appear to get crazier is obviously that this is all that is left. To be honest, I was a bit apprehensive when starting to teach in the US, but neither me nor colleagues (including those specialized in evolutionary biology) have little trouble with students, indicating that at least among those interested in science the number of (vocal) creationists is low, even in the US.

Nope they are not placed after bacteria. That would imply that archaea are a group of bacteria. Current molecular (well, since Woese in the late 70s) evidence point to a common ancestor of archaea and bacteria, i.e they are different groups and are the result of an early split. Also note that many archaea are not extremophiles and there are also bacteria that are.

This is an excellent point and a cautionary tale with regards to extrapolating certain biochemical processes to organismal or phenotypic changes.

I think the initial confusion was whether the fire ant venom would be called a venom? The application to themselves obviously would not classify it as a venom. However, they are able to spray it. There are actually a few more definitions being in used for venom, which does include presence of toxic proteins, for example, all of which would be the case for fire but not for crazy ants. However, spraying as mode of delivery is a bit of an issue. For example, spitting cobras are undoubtedly venomous. However, they can spray their venom which does harm without a delivery system into the body other than ingestion or absorption. And again, we see that these kind of definitions are often trickier than they appear (and more importantly, nature does not care for these distinction). Passive vs active are generally useful rule of thumbs, though experts in these areas would use some finer terms to distinguish between the mode of toxin production, delivery and mode of action. Edit: also crossposted. With regards to the nettles, most likely not, but it would be interesting to see how topical application to fire ant stings would work (or any mild acid for that matter),

No, it is used accurately. The distinction is normally based on delivery (simple thing to recall, if you bite it and you die => poison, if it bites you and you die => venom). Fire ants deliver their venom actively and are not simply covered in it. With regards to the mechanism It is possible that the formic acid denatures the proteins in the venom, though it is pretty much speculation at this point. Edit: I should add that fire ants also have stingers, albeit relatively delicate ones, compared to some of bigger ones out there.

I agree, the methodology of the provided article appears to be more sound to me (judging from abstract alone). It is also interesting to note that fewer articles are likely to have a definite stance on AGW as all the evidence towards it and it appears a bit moot to ruminate on it.

Found a neat paper about how tawny crazy ants (Nylanderia fulva) are able to take on and displace the aggressive fire ants (Solenopsis invicta). Apparently crazy ants somehow use formic acid that they produce themselves to somehow detoxify the strong venom produced by fire ants. While the crazy ants are now starting to displace the fire ants in the US, the arms race between those two species probably originated in South America where there habitats are overlapping. Article