CharonY

I disagree with that. The blackboxing is based on empirical data and very rough statistical inference, i.e. we know that they grow at roughly that particular rate and then expect them to be ready in roughly the same time frame. The key here is that normal biological noise is being suppressed (i.e. using chemostats or standardized batch-techniques, for instance) so that fairly rough models that use little if any biological information and mechanism can give out (simple) parameters with a certain degree of accuracy. The equivalent in economics would look at the same resource distributions and roughly predict flow under the very same conditions and predict the outcome, which is somewhat feasible. But as with biological behavior under realistic conditions the data is usually much, much noisier. Now I challenge you to predict the growth rate of a cell population with a new sugar source with any degree of accuracy. Now with several parameters changed. Now add a stress and try to predict metabolic changes. Now with several varying parameters and a given mutation. Now let us add gradients and microenvironments and complex populations. And how about predicting behavior of single cells? We are not able to predict e.g. the proteome or metabolome changes in an organism upon environmental changes, nor are we able to use that data to accurately predict the current state of a given cell. Predictive biological models are really very very unreliable.

Cell differentiation is a complex topic, but the key as already mentioned, are regulatory responses, as well as gradients of signal molecules. Cells communicate with each other and differentiation is guided by gradients of certain signals that allow the cells to coordinate and form distinct tissues, for instance. You may want to read up on morphogens.

However, not all economics is about predicting outcomes. If that was the case a lot of natural sciences would be considered useless, too. Try to predict complex cellular behavior with some level of accuracy, for instance. Economics deals with relative fuzzy mechanisms and these often allow the existence of competing theoretical framework within which they are explained. One could draw a parallel, to say biochemistry. The micromechanisms (i.e. biochemical reactions/individual transactions) can be explained/described relatively accurately, e.g. in terms of reaction kinetics or economical constraints. However, the combination of all these mechanisms results in new and complex traits that are not easily explained and much less predicted. It does not mean that trying to understand them is worthless, though. However, one could accuse economists, especially those own economic interests and ties with decision-makers that they may be pandering to certain theories despite inconsistencies with data. This is something that (should) happen with less frequency in natural sciences. Not necessarily because we are better people, but likely because that there are fewer ties with companies, partisan think-tanks, etc.

Nope, nothing in there suggest that they live. In fact I mentioned earlier that they do not posess a metabolism and I classified them as mobile genetic elements. It should be noted that classification of life can be a tricky business, if you go down to the biochemistry of it all.

If only partial polymerization occurs it seems that your solution is not well mixed. First add TEMED, use a stirring bar or something else to mix really well, then add APS, allow for stirring, then pour.

You would have to know how much the cells produce and derive the amount (in whatever unit) of enzyme that pertain to a given activity. The cell number will generally be insufficient. Enzyme kinetics (not velocity, with exception of motor proteins enzymes are not running around) is therefore normally only measured in in vitro assays. You can approximate those values, but it usually requires a lot of assumptions that are likely not true (i.e. quasi-steady state of enzyme production, relative constant synthesis and degradation rates, constant activity within cellular systems etc).

I am not aware of viruses that have sufficient enzymatic properties to do so in the absence of dedicated transcription/translation systems. Considering that no metabolism is involved the mentioning of oxidizing conditions does not really to the argument. Exposing their genetic material to the outside is doing them no good. Again, the whole system is geared towards infecting cells. In a prebiotic system a virus is hopelessly useless. The only commonality is presumably the existence of nucleic acids of sorts, probably with at least partially enzymatic functions and possibly of peptides, again with enzymatic functions. But they would be certainly not recognizable as viruses. Just to summarize, the chemical capabilities of viruses is not going to change miraculously to something entirely different just by altering the media or environmental conditions.

I am familiar with MPIs, too (worked in, collaborated with some), but again, not the one you are interested in. Since I have no idea about the program in Zurich I can at best compare MPIs with Unis. Most of timo's observation match with mine. This is partially also because their mentors (i.e. group leaders) have fewer teaching responsibilities compared to their Uni counterparts. This depends largely on the supervisor, of course, but I would agree that the pressure could be larger. They are better funded and often need to show a higher output (whether it is feasible or not) than unis. The programs in either MPI or Uni do not differ in quality much. The only real difference is the group that you are going to join. For that matter, I can recommend you to talk to people there, but also to people (i.e. postdocs) that have left a particular lab. If there are horror stories of some sorts or if you get canned phrases "oooh we have no problems here, we all just live for science" be wary. You won't believe how important a good lab atmosphere is to be productive.

It is kind of possible, if you cook yourself. However, in the US it appears that less and less people actually have time (or bother) to learn to cook. Especially in worker families (with both parents working full-time) it is more common to grab food from somewhere. And considering the dominance of food chains (Panda express, Burger King etc,) that all cater to a taste (i.e. greasy and sweet), I am not even sure where one could get healthy food, much less to a competitive price. I think an important part would not only be to subsidize healthy food, but also to get people reacquainted to unprocessed food.

Oi, 15% is rather bad for de novo sequencing (something I am more interested at). Guess I am stuck with 454 or solexa for the moment. Having a wide range of tools is nice. Although I learned that for getting a job it is sometimes better to reduce the range as not to confuse the search committee.

Virtually all viruses utilize self-assembly, but the point is that they utterly lack the ability to propagate. I.e. self-assembly is not a sufficient property of early life.

The common factor is self assembly. However, they would be nothing like viruses today. Viruses are highly evolved mobile genetic elements that specialize in hijacking the hosts cells. Early pre-cell life forms would have totally different requirements.

The easiest is probably doing a BLAST search on blast.ncbi.nlm.nih.gov. It will make similarity searches and allow for differences within the sequence.

In the metaphase you see the usual condensation, however, the chromosomes are not separated. You will have to google and see if you got access to the paper. I think it has free access, but I may be wrong.

This part is correct, however, one would probably not say that the chromsome consists of nucleosomes, as there are also non-packaged parts of the chromosome (especially active areas). The nucleosome is really a term to refer to basic DNA packaging within the chromosome.

Not only that, of course during transcription, there will be RNA present. However, functionally the nucleosome is not assumed to be actively replicating or transcribing. In fact, nucleosomes appear to be displaced during transcription, for instance. Note that the nomenclature are context-driven and just convenient terms to give certain elements specific names. Usually, they do not capture the complete dynamics of what really is going on.

From what I remember meiosis still occurs, however, no chromsome separation happens. Essentially there will be a restriction and a non-nucleated cytoplasm bud will be formed (and the rest maintains the whole genome). For nice pictures see Transactions of the American Microscopic Society Vol. 58, No. 3, Jul., 1939). Note that sometimes also diploid males are found, and not all of them are sterile (just remember that it was krieger et al. sometime in the 90s but forgot the whole reference).

I would not think of it that way. A nucleosome is only a very limited area of the chromosome, whereas the nucleoid contains the whole. Also functionally nucleosomes shift around to facilitate transcription, other mechanisms are in place in various areas of the nucleoid. Also a nucleoid is not a compact form per se, there is a lot of relaxing and coiling going on, etc etc. To put it simple, a nucleosome is a means to locally organize the chromosome, whereas a nucleoid is functionally closer the whole nucleus. Bacteria have no need for that level organization that many eukaryotes have. Nonetheless, they also have certain proteins there that fulfill scaffolding functions. It is just not researched as well yet, as the level of organization is lower and the effects less dramatic and less accessible.

Without education, people tend to have a limited perspective. In fact, I believe that one of the most important aspects of colleges is not necessarily to convey technical skills, but to show students that there is a whole world out there that we do not really know much about. To show that our preconceptions and anything we learned are but a limited facet of what is really going on. That what we think and believe is quite possibly wrong or at the very least very narrow-minded. That we should be open to new concepts. All these are of course anathema to rigid, self-contained belief structures. Moreover, it makes people much more easy to control. If you grew up in such a self-contained environments it is much more easy to accept "facts" without evidence.

It won't be able to replicate if it cannot at some point expose its genetic material to its host. Some infection pathways actually require the intact virus to be internalized, but at some point the nucleic acid (be it RNA or DNA) will be delivered to the host and eventually translated. If the host does not produce the material required for virus assembly, there will be no propagation.

While it should be clear, I would like to emphasize that nucleoids is not the functional equivalent to nucleosomes (just because the two are contrasted here).

I prefer the muppet lyrics to the original one by Schiller, though.

6 kb is really nice. Read length is actually one of the biggest issue with most next-gens are relatively short read lengths. Many are aimed at massive parallelization. But with the arrival of high-sensitivity monitoring together with submicrolitre volume handling the traditional approaches can be happily married with traditional enzymatic assays and fluorophore detection, such as the PacBio system. Some are exploring alternative approaches that, in theory, allow the sequencing of a complete DNA molecule in one go in enzyme-free systems, but I still more skeptical regarding those. I am not doing any real sequencing any more (moved on to way more downstream stuff), but I can say that from a technical and especially price viewpoint the technologies available are quite exciting. Though as a biologist, I am more stumped with what to do with all the data .

All good points. Especially PIs of large collaborative projects can be swamped by hundreds of mails per day (I have seen that personally). Adding to that admininistrative mails and student's mails from existing courses, there is simply not enough time to answer even most of them. Also there are people who basically mass-mail people with requests to join labs, become graders etc (I got a sizeable amount of those myself). Thus, if the mail even looks remotely like a mass-mail/spam (e.g. by being generic and impersonal) it will end up in trash mostly unread. If you really want to join someone, research him/her, ask for a time for a call, or, if possible, show up during office hours. In other words, make it personal. Also, try to leave a positive impression, but do not try too hard (no one likes the guy who pretends to be a know-it-all).

Your are confusing DNA replication with transcription. The latter results in RNA that have either structural functions or are later translated to proteins. The DNA replication does not involve transcription. So maybe you should read a little bit up or look for videos that depict actual DNA replication and I would be happy to clear up things that may still be unclear then?