CharonY

Basically it is correct. Bacterial reduction of methylen blue is usually done by oxygen consumption and secretion of reducing metabolites. Bacteria do not have organelles as lysosomes. Also, the reduction of oxygen does not reduce methylene blue per se, it only prevents the re-oxydation of reduced methylen blue. Finally, there are different kind of bacterial strategies with regards to oxygen consumption. The obligate aerobes require oxygen as terminal electron acceptors, that is, they essentially respire oxygen as we do. The facultative anaerobes can do the same, but they are able to switch over to anaerobic metabolism, which does not require oxygen to generate energy. This can be facilitated by respiration of different substances with a sufficiently low redox-potential like e.g. Fe(III) to Fe(II), or they can do fermentation. Then there are obligate anaerobes that not only cannot use oxygen as terminal electron acceptors but are often sensistive against oxygen. These are the ones that can actually killed by oxygen exposure. The so-called microaerophiles can use oxygen, but only in low amounts and then there are some forms in-between. The composition of milk bacteria is somewhat complex. Two often found genuses, lactobacilli and propionibacteria for instance, are facultative anaerobes. Exposure to oxygen won't kill them. However if methylen blue is reacts with oxyge, reactive oxygen species are formed which in turn can harm bacteria.

Well "weak" is relative, of course. There are receptors and antibodies with different binding constants. For direct measurement of forces there are some AFM papers around, otherwise normally dissociation constants are sometimes given. I cannot easily point you to a certain group of paper in this regard. You'd have to be slightly more specific.

Wrong. He is asking how species arose (that is, were they always there or did they develop into the form the are now), not how life in general began.

Yes, however the authors also did not show that the observed changes were inheritable. Of course, these extreme changes are unlikely merely the result of diet changes, but as far as I can see it has not been unequivocally established. Also I think that the author's use of macroevolution might be not that one defined as evolution at or above the species level. In the reference they cited the following statement is found: "Historically, macroevolution has been equated with substantive adaptive change, and rapid and fluctuating evolution has been regarded as evolutionary noise. Thus, debate continues over what constitutes trivial versus important evolution. We argue that the real distinction between macro- and microevolution may lie only in the degree to which the factors causing evolution are fluctuating or are gradually and persistently directional, and not in the ecological significance of that evolution." The observed adaptation (if genetically based) would likely fit into this particular definition. Of course, the authors only implied that their work is an example of macroevolution (and that only briefly in the introduction), but i guess that is what the New Scientist took up and beefed up a bit.

That is actually strange. I would not think that pure water should actually stop the reaction. Adding a lot of water might reduce the buffer strength but if the added water is pure, the pH should not shift too much. I would have thought that the reaction might actually be stopped with some alkaline solution. Edit: one thing that may be happening is that the invertase concentration was very low. If diluted sufficiently enough the reaction will be effectively slowed down.

Not that I know of. There are just too many hints from various directions that point at the bacterial origin of mitchondria.

As John already mentioned, most bacteria dissolve gelatin (via proteases). It is not really suited for bacterial cultivation.

Technically adding, removing or changing a gene is a genetic modification. But legally only non-naturally occurring techniques are considered to be genetic modifications. Basically it is because it would be silly to try to regulate naturally occurring processes by law. "Drop that conjugative plasmid you bastard. That cell is underage!"

Also you can derive more or less unique feature from about every species. In a way you can state that every species is unique, but I assume that does not really say much.

Also, the personality of Darwin should not have an impact on the validity of modern evolutionary theories.

Actually... no. There has to be metabolic activity

Ehem, sequence don't govern the one or the other. What they do encode are RNAs of which a subpopulation, the mRNA is used as a template to form proteins. The latter are the movers and shakers. This is of course quite a simplification. And in the end, there is no clear distinction between physical and behavioural traits, given the fact that behaviour is a function of the brain, which is basically a physical entity.

Not really, it is just another layer of complexity. For example, humans are nothing more than a bunch of cells, too. Yet a cell line is something different than a complete human.

Well, an organism usually cannot be a catalyst, what they do is metabolize stuff. I suppose we do have a problem with definitions here but it should not really affect your question. Actually, I can actually only point back to my former post. Basically it does not matter if you remove add or do whatever with the genetic material. The main criterion is that you use a means that is different from that what might occur naturally. If you remove the gene that allows the synthesis of a product it does not count as genetic modification (under the law) if you use, for instance radiation or cross-breeding to achieve it. However using recombinant DNA techniques to get to the same result would count as genetic modification.

First, bacteria where the first oxygen producers. Regardless of aquatic or terrestrial life, it appears that most more complex eukaryotes require oxygen to produce sufficent energy to sustain themselves. This is one example of a limiting factor. If, for some reasons, photosynthesis has not evolved, life would consist almost exclusively by bacteria or archaea, capable of anaerobic respiration. Complexity of an organism does not translate to size of a genome. Bacteria for example have a higher gene content to mass ratio than any other organism. Also M. genitalium is an extraordinary bad example to make your point as this bacterium has a reduced genome because it adopted a parasitic life-style. Consequently copious genes have been deleted out of its genome.

Sequencing an eukaryote, is still awfully expensive and time consuming (and identification of genes is even worse). After skimming over it I could not see any reference whether the morphological changes are at some point genetic. This is btw. quite interesting. According to the Darwinian theory of evolution (remember, Darwin knew nothing about genes) this would be an example of adaptive evolution. However according to modern synthesis it would not. It would be interesting to breed them with a different diet, though. It would only be lamarckism if the traits are becoming inheritable regardless of diet.

Hrmmms it is not really related to the the question, however the (human) lung only retains a small fraction of the O2. On average your breath contains ~15% O2 (with an average concentration of ~21% O2 in the atmosphere). But what really has an effect on pH is CO2 (which is an acidic oxide).

I am not sure what you mean by "catalyst" in this context. Actually the definition of genetic modification is simply the alteration of genetic material of an organism by means that could not occur naturally through mating and/or recombination. This is a definition as issued by the EU, but afaik it is rather similar in the US. The rules that follow are different, though. To clarify, in your example it is not critical what the end product is, but how it is achieved. I will now simply assume that you are talking about an organism expressing genes (or alleles) a, b and c. Adding d is a genetic modification if you for instance create recombinant DNA and introduce the DNA e.g. via micro-injection. If, however d is introduced by conjugation or other naturally occuring DNA transfer mechanism then it is not a genetic modification. Likewise if you delete d by using mutagenic agents, for instance it s not genetic modification, but if you use a recombinant deletion construct, it is.

Hmm, Pubmed central has been around for some time already (~8 years, with only few journals, though) and I assumed that the rule regarding NIH funded publications was also longer in place. I may be wrong with the latter, though.

Also, although it already has been mentioned, I just want to stress again that evolution and theory of evolution are two distinct things. In addition the current theory of evolution is quite different from the original Darwinian notion. For example Darwin could not be sure how inheritance. The original Darwinian theory evolution included for example Lamarckian inheritance as a possibility. This was only refuted by the Neo-darwinistic theory. This again was surpassed by the modern synthesis which started to develop around the 1930s and 40s. However many basic tenets of the modern synthesis have been found not to be as universal as believed half a century ago and a new modern synthesis, sometimes referred to as postmodern synthesis is starting to form. Note that in all case not evolution as a process is challenged, evidence for this are rock-hard (literally in some cases), however the actual mechanisms are the element of the theories. What has survived from the Darwinian notion is that a populations are inherently variable and that natural selection is acting on it. What has been challenged is the relative importance of natural selection compared to other effects and mechanisms, especially when it comes to speication.

Right, it is short for Biosafety 2 Lab. The details how the setup has to be is likely differ from country to country, though. This includes e.g. restricted access, biosafety benches, available autoclave etc. Anyhow, getting the exact amount for consumables is tricky, if not impossible. The best you can do are rough estimates and then add a chunk more, as usually during the grant review process a big chunk will be slashed off again. Also you cannot know beforehand what will work and what has to be repeated how often. E.g. you may design four primer that looks perfect on paper only to find out that one (or both) pairs do not amplify. What you can do is to identify every component you need, take down the price, and then add 25% or so for replicates. It is going to be an estimate, anyway.

Well you need a medium with agar with it. But two caveats: a number of mouth bacteria are potentially pathogenic. So I would not advise to use media in which they can propagate. I probably would not want to do the experiment with younger kids, actually. Second: unless you brushed teeth just before sampling, the amount will not be significantly different between humans and dogs. Expect in the area of 10^9 bacteria per ml of saliva (so dilutions are necessary to count the colonies). And yes, definitely wrong forum section.

I assume this is just a "training" proposal? Usually you first to have to make sure that basic equipment for handling is present P. falciparum, as well as labspace (e.g. you need at least a BS2 lab). Most project grants do not cover basic equipments. Before I comment on the consumables I would advise you to look at existing protocols for the manipulation and maintenance of Plasmodium cells, though. You need to know this before you can write the grant. Check the malaria journal (it is open access) as well as some of the parasitology journals for this. I recall a paper about the assessment of different deletion protocols for P. falciparum around last year or so in the malaria journal. For standard cloning techniques check out "Molecular cloning" (Sambrook and Russell). There are tons of information in it and I recommend it to everyone. If you got a basic idea of the experiments you want to do, you can start checking out prices. Mutagensis kits are, btw. not essential. What they do is creating a mutated insert. Most of the time you can do it just with the right primers for less money. In order to get an idea how much the kits cost, I'd advise you to browse at least to Promega, Qiagen, Invitrogen, as well as general lab equipment vendors (e.g. VWR and Fisher).

Well, these are two issues. Basically if the data (analysis) is not of sufficient quality one cannot declare an effect as busted. This problem does not go away if you just do something else with the same lack of rigor. Also they usually do not really produce an awful lot of data. Usually there are only two to three data points per experiment. Much of the fun is not in the results but the whacky way they try to approach it. Also the replicates are quite often not really replicates in the strictest sense and so on. Of course there are limitations due to time and cost and it is an entertainment show after all. However, sometimes they do use the word "science" or "scientifically" quite a bit too often for my taste.

Also what they do as replicates are usually not statistically significant. It is often fun, though. Maybe a bit like CSI for the forensic community, only better. Well, Zombie Feynman is quite convincing, though.