CharonY

I think the reasoning is based on ignorance. In school, often natural selection is presented as the main force affecting observed allele frequencies. The ignorance part is that it is but one of many possibilities as chadn737 explained. Therefore many may assume that in the absence of knowing the precise events the main explanation must be selection. However, the claim of selection is a highly specific hypothesis that can be tested under certain models. If that fails it is simply inaccurate to assume selection. In most cases it will be very tricky or impossible to correctly calculate precise contributions of all events on observed allele frequencies. Yet claiming one specific model to be true without any data to support it is at best intellectual dishonesty.

One assumption is that it protects the cell from sudden influx of stimuli. I.e. as a kind of noise filter that suppresses sudden peaks but still reacts to persistent stimuli. Some more intricate studies found that this type of regulation may modulate e.g. responses during pathogenic interactions. However, these are specialized mechanisms that often are not fully explored yet and which are probably outside of the scope you want to convey.

Let me ask you this question. Why is "traditional" modern breeding (which utilizes random mutations) safer than new any of the new methods? Agriculture has always had a tremendous, usually negative effect on ecology. So how much more in terms of risk does it add above the background of existing practices? Does it rise above the noise at all? This is the part where research should and in many cases is focused on. Taking the lack of findings as proof that they are clearly present and to call that denialism is disingenuous. Ignoring context is akin to concentrating on the effects of solar flares on temperature change whilst ignoring CO2.

It is probably one of the 77% of statistics made up on the spot.

The precise molecular mechanism of plasmid replication is a bit complicated and would require a serious write-up that I won't be able to do quickly. But what I can answer quickly is the use of sugars, I am not sure of P. aeruginosa specifically, but most bacteria have various amino acid degradation pathways that enter the TCA cycle at various points. I believe P. aeruginosa primarily uses alanine and glutamine that directly enters as pyruvate or alpha-ketogluterate, respectively. But P. aeruginosa is also well known to utilize quite a variety of C sources including e.g. acetate or citrate.

Well, there are two things that happen. First is mechanical disruption and the second is heating. Both will kill some off. That being said, it depends a lot on the type of blender and the time it is being blended. Generally, the mechanical part will only kill a small fraction (at best) as they are so small that they are getting pushed around by the blade rather than being crushed. Quantitative lysis of bacteria using mechanical shear forces generally requires the addition of very small beads that crush the bacteria during agitation (referred to as bead beating). This is not the case with kefir in a blender. Likewise you are probably not blend it until the kefir gets really hot. Obviously, handling cells will always harm some, but chances are that the effects are at best small.

Does this make sense to anyone? With regards to OP, naively I would have thought that it is not essential under aerobic conditions. However, the produced acetaldehyde could also be funneled into other pathways which could negatively affect growth. Actually, I faintly recall a paper in which multiple pyruvate decarboxylase mutants were described. It was a Dutch group, but I cannot recall the names right now (must be around the 90s and for some reasons I remember that they were big on chemostats). But if I recall correctly they would grow on complex medium but not minimal with only glucose. Or something to that effect, at least. If OP is still interested I can try to dig it out (have not worked with yeast for a loooong time),

Well, a satellite system would work and it would basically only need to send out the last GPS coordinates. If it only kicks in after an accident (when the plane is not moving anymore) the movement should not be an issue. Unless it is used as position device but I am wondering whether there are not equivalent technologies already in place to track plane movements during routine travel. What I am also wondering is whether existing satellite comms would work under water. Edit: scratch that. I just remembered that transponders have been used to track sharks, so that should work, unless I am missing something.

A typical GPS device is a receiver, not a sender. AFAIK flight recorders come equipped with transmitters, probably with a few km in range. A cheap, tiny solar powered emitter would probably have a range of a few meters.

Absolutely. However, if you bring your expertise to a complex problem it is worthwhile to actually try to establish the foundations first. The reason why biology exists at all is that we are not able to rebuild the system based on first principles. As such, biology has developed methodologies that are less precise, but can at least tackle the questions to some extent. The point where progress happens is not where biology does fundamental physics and vice versa but where the problem is dissected into components that can be optimally addressed by the different methodologie (and ideally assembled into a coherent body of knowledge). What the authors in the OP did where recasting a biological problem completely in different terms that actually do add little to its solution. In a way they are revising a straw man. What they (correctly) challenge is a deterministic flow from gene to phenotype. At the same time, it ignores another point typical to biology is that it does high-level simplifications with implied complexity (if that makes sense). However, depending on which level you investigate genetics (from molecular to population, for example) there are different methodologies that investigate this issue either by e.g. normalizing against environmental aspects (as in many molecular biological/biochemical approaches) or using models to take them into account. The simplistic view being challenged is rarely maintained above bio 101. With regards to your example, it sounds faintly familiar but I only recall a paper from the MPI in cybernetics in which the lead author was actually a physicist, IIRC. While the paper phrased it in terms of noise of sensorimotoric system, the explanation is the same. The question why they looked at it was also from the direction of how we are able to recalibrate our positioning. So that is actually a great example how physics can be used and phrased into a biological context (by using noise analysis in a sensory feedback loop). I actually do not think that they expected a straight line at all (at best as null) but may have expected a more systematic bias. In the end they found that the patterns match up better with noise accumulation. What is true is that biological research sometimes is a bit too empirical and lacking certain theoretical frameworks in many areas. But again, these are the areas were collaborations may shine. The Dutch and German system is (or used to be) a bit different to both the Australian and the US systems as most of the selection happens before graduation. Only a fraction of the students enter actually graduate with a degree (before Bologna it was a Diplom). Only with that degree a few can actually obtain a PhD. Also, there are generally no grad schools as those in the US. Instead, you have full-time research and the ability to obtain a PhD is solely in the hand of your PhD advisor. There are so-called grad schools but they were not comparable in terms of workload. Especially younger Profs are letting their students get a PhD eventually, as it may reflect badly on them, if they do not have sufficient graduates from their labs. Often the Diploma time (which is about 6-9 months of research) is used to gauge their ability to eventually obtain a PhD.

That is quite correct. Though I would think that the rules are a bit clearer in the pharma area as neglecting to present the assessment data in full does automatically result in punishment of the company (though I am unclear about the scope) whereas in the financial sector the situation appears to be more ambiguous.

That is what I meant, the advice the MDs are giving advice based on risk assessment on incomplete data because a) they have no other option and b) they generally are only peripherally if at all involved in the ongoing research of mechanisms. This risk assessments tend to be based on epidemiological data that are occasionally cross-fed by molecular information. As such, it is obviously not that the scientific view of system immune function that has been changed but rather the medical advice that is being derived from what we know. Both are quite different beasts.

Oh, but in academia everything is a success, too. Problem is only that there are not enough journals such as Applied "why the heck dioesn't it work? It did last time?"; Journal of the Royal Society of "the new student did what? Why is he/she still alive?" and Proceedings of "which hypothesis can we make up to fit the data?"

Interesting. I am pretty sure that I have read about that before (or another GlaxoSmithKline product). But you are right, these incidents do come to light only after an audit , if someone decides to obfuscate things in reports. I believe something similar also happened with weight-reduction medication. That being said, unless their profits offset all these issues it should have been in their interest to put the label on. But there is another issue, that comes to my mind. While the company may not benefit from this type of misreporting, the involved managers could. I wonder what the backlash for them is. If they get a golden parachute (or no repercussions at all) there is an incentive to push products out to appear more productive within the company...

Just as an update, China decided to abstain on a vote one the UN resolution on Crimea. Yupp they are really pushing very hard to start a conflict...

Supplements are an excellent example. But I am not so sure about reporting negative results. There are relatively strict audit trails (including e.g. the use of software that does not allow deletion of runs) and the company has an interest in detecting toxicity before mass use is initiated (could be different for specialty drugs, though). There may be attempts at lowering the bars to prove efficacy, however (but I do not know sufficient details to go beyond mere speculation).

That xkcd popped into my mind immediately. It is not that uncommon, unfortunately. But I also had very positive collaborations in which all sides at least made a token effort in trying to understand each other. Obviously having access to copious amounts of beer and coffee helped.

Lobbying will mostly revolve around factors that could affect their overall bottom line. This could be for instance legislature especially in federal programs such as medicare or medicaid that would keep prices high. Other areas could involve intellectual property issues and inhibiting entry of foreign drugs into the market, for example. Meddling with trials and testing would be a bad idea as negative effects would then only manifest after it hit the market. And that is going to be a very costly matter, if something happens.

I think the basic underlying mechanisms have been well-researched for decades and while there are incremental changes I am not aware of something radical. If you are thinking about prevalence of food allergies, risk assessment and risk mitigation the question is still quite open (some some progress is being made in understanding the role of immunoexclusion and immunosupression mechanisms to module inflammatory responses. Again, advances rather than radical changes.

Also one should note that development in pharma is a high-risk-high-reward endeavor. Only something like 10% of all drugs that they try to put into the market actually survive the pipeline (including clinical trials). As such I am sure they are heavy lobbying to maximize profits on those that do. But as swansont mentioned, it is hardly unique to the pharma industry.

They are interesting, no doubt. I just wished that science journalist would try to stick to facts instead of resorting to hyperbole, if they are not familiar with the subject.

Sorry to say, but the article is badly misrepresenting the results. Far from inferring taxonomic distinctions, the paper is showing that they do possess regulatory mechanisms (specifically their post-transcriptional regulation of mRNA) that are similar to those of plants. However this does not change in any way that they are cnidaria and firmly belong to the kingdom of animalia. They are nowhere near half plant. In fact the article does point these things out but for some weird reasons draw completely false conclusions and put that into the title.

I probably should have added the M (though his prose in his non sci-fi novels is still very good). Use of weapons I presume. One of the few authors that IMO are able to evoke some degree of alienness even if much is still (intended or not) fundamentally human. Which, in turn is a limitation of our own imagination.

Three-letter abbreviations without context are just pita and hti.

For higher throughput arrays would indeed be the better option. I have not done it myself but I believe LaBaer's group has done precisely that. I do not have the paper titles off the top of my head (I am more an omics person) but if you search for his name in conjunction with protein microarray you should find quite a number of hits.