CharonY

But that is an important point. There are large variation between species even within a genus. More distant animals, however, may have larger anatomic differences in their eyes, resulting in more fundamental differences in performance. I find it very strange to see cats in the list of bad eyes, however. I assumed that most would assume that cats have good eyes. In ambient light their acuity is close to human's, whereas their reflective layer increases the performance by a lot at low light.

There is really no scientific evidence of that. Obviously concentration plays a big role, i.e. a ginormous hunk of red meat is going to be tricky to digest in a given amount of time and adding more protein and fat to the mix (regardless of source) will not make things easier. But in a decent amount it does not really matter whether you eat/drink meat and or milk together or apart. As a side note, there are a couple of dishes where e.g. beef is stewed with milk.

I have two concerns. First is that the amount of CO2 actually produced under these conditions is quite low, so probably you are more likely to measure random fluctuations rather than true bacterial activity. In fact, I do not expect too much of bacterial activity under the described conditions as they need quite a bit more to grow actively enough to emit significant amount of CO2. With regards to oil, you should be aware that what you put on is most likely fat (as e.g. olive oil) and not crude oil or petroleum. Unless you enjoy toxic pizzas, of course. Alcanivorax is famous for being able to degrade petroleum (also slowly). Lipids, on the other hand, (i.e. fats) can be utilized by many bacteria with various efficiency. However, if the only thing the bacteria have is cellulose (cardboard) and lipids, it will not sustain bacterial growth. Additional macronutrients (such as a nitrogen, phosphorus etc) in a suitable form for the bacterium in question are needed. And even then, respiratory activity is likely not to be very high if other parameters (such as pH, temp. osmolarity, micronutrients etc.) are not matched. It will take way longer than a few days (IMO) to get stable CO2 readings that could be used. Sorry. Even counting the bacteria directly is probably not very efficient (again, the conditions are not terribly suitable for growth). Another issue is that if you actually observe growth, it could be tricky to link it exclusively to the utilization of the fats alone.

Duplication events are not a necessity, unless of course the gene in question is under selective pressure. There is not one gene that controls the formation of a single bone. Often, a simple duplication has little phenotypic change, especially at the beginning and even the production of an aberrant protein could be neutral in outcome. So one should step a little bit back from the imagery that a single gene controls a specific phenotype (if that was implied). Of course many genes act in concert and their expression in time and space together with certain environmental factors finally result in the development of certain phenotypes. From that point of view, you are correct in the notion that regulatory changes are going to have a much stronger impact. Indeed, developmental studies show that precisely to be the case.

We generally do not provide outright answers. Rather, our goal is to have students try it themselves first and then guide them towards answers.

It is a matter of dynamic (or linear) range which is actually highly dependent on the protein you look at (i.e. binding of the dye or UV absorption vary with the amino acid composition). For virtually all analytical procedures you get a more or less sigmoid curve. At the lower end the non-linear part is partially caused by the lower detection limit. Likewise, at the higher end signal saturation can become an issue. The part between those which is linear (or exponential) can really be used for quantitative analyses. This is true for Bradford as well as UV. You may not see it in UV as the dynamic range is often larger so if your measurements are far from the detection limit it will appear to go through zero. But if you sample close to the detection limit, you will see something similar to Bradford. Regarding precision, that is highly dependent on the type of sample. For crude samples Bradford is more robust and (if timed correctly) has therefore higher precision. For purified low-complexity samples UV is generally easier to handle and has mostly precision advantages due to reduced user-errors.

My take is that if there is a shadow biosphere, there will be metabolic traces that cannot be explained by abiotic processes. I am a bit sceptic on the biosphere on earth concept for two reasons. First, life as we know it is incredibly efficient. The shadow biosphere would only be competitive under very exotic conditions. And second, as above mentioned, we have not found anything (afaik) that could have not been done with life as we know it. The main argument of the proponents of a biosphere appear to be that DNA or rRNA based searches won't yield anything. That is kind of true, but they (often) neglect the fact that life also interacts with its surroundings which also leave traces. Interestingly the proponents of the shadow biospheres are often not biologists and do not realize that many (if not most) biological disciplines are not limited to molecular biology (i.e. looking at proteins, DNA, RNA, etc.) but also study the consequences and interactions of organisms with each other and the environment.

Technically a higher percentage has higher resolution. However, practically it does not help in every case. For very long runs buffer depletion and heating issues become more relevant. These effects are especially pronounced for larger DNA fragments. For these, electroosmosis could exacerbate the issues. So yes, in practical terms there are sweet spots for pore sizes.

That makes me wonder, does Spain have mandatory IQ tests (or at least in Catalonia)? I was just wondering about all the people who precisely know their IQs...

Has it ever occurred to you that being treated different may be the consequences of certain behavioral cues that may not actually be related with standardized test performance? Also, it should be noted that almost everyone performs better under special programs, where extra attention is paid to individual students. Sometimes it is less of a being gifted situation but more of a motivational. Regarding employment, Arete pretty much hit the nail right on the head. Performing well career wise means that one should also be able to focus one's intelligence on solving interpersonal problems. Feelings of entitlement have, as far as I can tell, never charmed someone into offering a job.

While this is a fair comment, there are several reason why I was discouraged to reading further(lack of clarity on the article side and lack of time on mine being the dominant ones). The only reason why I actually commented is my personal experience in collaboration with non-biologists who in most cases just try to invent the wheel and call it something else. It takes considerable effort to condense that little (but important) piece of novelty out of it. The recasting that I mentioned do not reflect well what is going on within a neuron and yet this discrepancies are glossed over. At this point I am inclined to side with Ringer, who clearly spent more time in trying to understand what the article is trying to say. For starters this appears to be a central premise: Would you care to describe to which biochemical processes you assign these functions? What precisely do you mean, for instance with route selection? Are you thinking in terms of a single input starting in the neuronal network and working its way towards a specific target? What about iterative signals? Or mechanisms such as LTP?

The immune system is a complex mechanism but it works on a completely different way than antibiotics. One of the main factor of our immune system is the recognition of foreign particles via antibodies. But the beauty behind it is that it does not require any knowledge of the particles that it will encounter. Instead we have a mechanisms that more or less randomly shuffles parts of the genes coding for the respective antibodies. That way we have a wide array of them that may (or may not) bind to stuff that enters our bodies (named antigens). The whole system then is geared towards producing those antibodies that actually found something to bind to (e.g. parts of bacteria) and thus induces the production of more of its kind. A bit like evolution on the micro level.

I only skimmed the posts and the provided links, but to me it appears to be a simple recasting of what we know about neurons using different terms from a different context (at best). I would have to do a proper read to ascertain whether there are errors made during the "translation", but to be honest, I do not (yet) see how this really adds to what we know about neuronal functions. There are some inherent problems with these approaches, although sometimes they can actually be useful. Both viewpoints (again, assuming that the premises of the articles are not wrong), would represent a different framing of our model on how axons work and which one is being more useful or accurate could very well be dependent on the context of the discussion.

It is very likely one function of sleep, but there is certainly more to it. First of all it is not only that we use less energy during sleep, but staying awake while being sleep deprived costs more energy than just being awake but not being sleep deprived. The energy cost associated with staying alive was calculated to be roughly two slices of bread (Jung et al. 2011 The Journal of Physiology, 589, 235-244). Considering other factors (e.g. influence of sleep on cognitive abilities) it is clear that sleep has far-reaching physiological effects beside conserving energy.

it is also a bit a matter of perspective. In these cases they are inducible or repressible by a given substrate. The mechanism in both cases is, as mentioned, is based on repression by a transcription factor. Most metabolic operons appear to be negatively regulated indeed. However, although it could also be that activators (proteins as well as sRNAs) are somewhat harder to detect.

This makes more sense than the earlier depiction. A thing you have to be sure of is whether only the DNA is labeled, or (as you claim) also the protein fragments. Based on this the first question you would have to answer is actually what is the lowest band that you see in each lane (is it always the same molecule?). Note that in the text you say that 2-4 contains only labeled protein fragments, whereas the annotations states that there is also DNA there. The difference is quite important. Based on that, why do you see only one band in these lanes? Finally one thing you should be clear about is lane 6-8. In the text you say that it contains one protein fragment plus DNA. However the annotations states that in each also the full-length protein is present. Does it make sense to do it that way? Note another thing, under non-denaturing conditions and in absence of external charges the protein migration does not correlate well with size, even within a gel (you have to things to consider, electrophoretic mobility and retardation by the gel). There is a reason to add SDS in standard protein PAGE. Whose migration are you really monitoring in EMSA? Without these points being clear you will be prone to doing to do guesswork.

I do not know what you mean to liquid composition, and no, they do not turn into dust. Dust is comprised of extremely large particles, much larger than any single protein. Instead, proteins get degraded over time. Tertiary structure (and hence function) can get lost very fast, further degradation depend a lot on the environment. The quickest degradation is generally due to protease functions.

Can we have giant mutated hamsters involved, too? Please?

Depends a lot on the the protein and the environment. Some are inherently more stable than others, but degradation due to external factors weigh in heavily. Relevant parameters include the liquid composition it is in, temperature, presence of other enzymes etc. It also depends a bit on what you mean by lose their structure. The tertiary structure is for the most part relatively unstable, at RT and without specific buffers most will readily lose their active confirmation (again, with some exceptions). But the proteins are still present and may be detectable (if inactive).

To be fair, the type of experiments you suggested have a very narrow scientific value. But the suggested book delivers protocols and is imo one of the best rounded books you could get to get an overview of current and basic methods in the area of molecular biology. For textbooks more towards the non-experimental side, the Alberts is quite good (Molecular biology of the cell). For Biochemistry the Stryer pops to my mind. There are many more but these are the titles that I still remember.

It should be noted that life is not an easily measurable property and as such precise definitions are going to be iffy. Especially as the definitions are exclusively based on what we found on earth so far. I would take it more as a guideline rather than a strict definition. But then this is true for much of biology in general. Squishiy things do strange things, as I like to say.

It is really blurry indeed. What I would recommend you is pick up a copy of Sambrook, Molecular cloning. it is a method-based book that also describes the processes involved quite well. There may also be more basic textbooks which would benefit you. At this point a good textbook is really your best friend.

From what I have heard analyst with a PhD are less common. Job prospects are tricky, especially now. With no job experience it is best to get your foot into the door somehow. One thing is obviously to search for open positions, but that alone tends to have a relatively low success rate. Ideally collect some names of people in the companies you want to work for. Job fairs are an easy way to get face time (and collect contacts). Alternatively ask around if someone you knows someone in the biz that you could talk to. In any case, try to get a (non-dead-end) entry level fast, with even a little bit of private sector experience you can increase you market value quite dramatically.

The problem I see is that high level assumptions are trying to be discussed but with no foundation on which to discuss it on. As others mentioned, learning that will take longer than a few lines in a forum and as such all discussions will be superficial and inaccurate at best. Also a true specialist in this area may be able to come up with some nice analogies that will satisfy the layman (without providing specific answers, though). But I freely admit that this is outside my range of expertise. That being said, perceptions or emotions are not the result of single or even few pathways, there is strong interconnection between certain neuronal activities but is also affected from feedback from the rest of the body. The area where these sensations finally arise are located in the brain, but even that is not quite as trivial. For instance, the amygdala is associated with the perception of emotions, including fear. In people with Urbach-Wiethe disease the amygdala is dysfunctional and as a result they show e.g. only minimal levels of fear upon stimulation. However, in these people an increase in CO2 levels still induces fear of suffocation, indicating that there are other pathways upon which the body senses and translates this sensations into a feeling. (see Feinstein et al. 2013 in Nature Neuroscience). One can speculate how things work without further reading up on the basics, but frankly, it is a bit like trying to do calculus using your fingers.

The high viscosity of the solution is not due to precipitation of SDS but due to the glycerol. Even if SDS precipitates, the solution would still be liquid (with SDS flakes floating around). Generally I would also avoid heating and at that concentration also unnecessary. Did you dissolve SDS only in buffer (i.e. without glycerol)? Alternatively you could reduce the SDS concentration a bit (common values are somewhere between 6-10%) as well as glycerol (down to 40%). Third possibility is to create less strongly concentrated loading dye, but if working with dilute protein samples that may not be ideal (though 5x concentrated is still very close and you are not as close to the solubility limit of SDS). Also, if you freeze your buffer, do not forget to let it get to RT before pipetting. For the most part I do not recall specific issues with creating 6x loading buffers, but for various reasons I started using 5x for most standard applications.