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Everything posted by CharonY

  1. Bascule, you are of course correct. What I meant with repetition is a tautaology as a stylistic device rather than in the context of logical statements. I should have been more preciese. Dak, the statement is true, but tautologies are invalid as a logical argument. Basically in the same way that circular arguments are.
  2. Essentially there is no real conflict between gradualists and punctualists (as in fact the dissent was rather smaller than it appeared to the public to begin with) any more. It is clear that evolutionary rates can and do vary. The real question is whether apparently faster evolution in terms of geological time scales can be interpreted as an absence of microevolutionary modifications (based on estimates of reproductive time scales). That is if there are macroevolutionary events that are not linked to microevolutionary ones. The evidence is quite lacking though, therefore the general consesus (as far as I am aware of) is that it is still explainable by microevolutionary models.
  3. Tautologies are in general some kind of truisms or repetitions that possess some kind of redundancy and hence do not add information. A tautological logical statemen is for instance: "all swans are white or not." This statement will always be true making this an empty statement. In everyday language tautologies can be empty repetitions like e.g."Salsa sauce" or "HTML-language." In most cases it is considered a bad style because you essentially do not add any information but only repeat yourself by stating the same (this is another one btw).
  4. There is no significant difference in xxx contamination between rural and city environments. While it is not my field of expertise I am a little bit doubtful regarding nitrate and possibly iron contamination between rural and city areas, btw. I am not sure if for instance fertilizers in rural areas might not raise the contamination to city levels. And regarding iron, especially in anoxic subsurfaces and aquifers the concentration can be extremely high. Just some random thoughts, though.
  5. CharonY

    Bad Test

    Actually only few organisms maintain a certain temperature and furthermore, the question was (at least as I understand it) if they could actually convert it to energy. And here the answer is quite obvious, as electron transport is clearly involved in energy (ATP) production, whereas heat is not. Sorry, while I am not a big fan of making multiple choice tests (but they are sooo much more time efficient). I actually fail to see that they are badly constructed (with the caveats Atheist gave).
  6. CharonY

    Perfect, I love it

    *Alaps snail on the head-hard* Ahh. I needed that.
  7. With my full name I only get my papers. Suppose no one is really that silly to give a kid that kinda name Except, obviously, my parents.
  8. In the simplest case there are two pools on which selection can work on. First are mutations that only exist but have not yet been subjected to selective sweeps (that is, they are already spread in the population but are dormant as stated above) or they are new traits or alleles that are not fixed yet. In the latter case (and that is probably what gmacrider is thinking of) the frequency of the new trait being fixed in the population (that is not being directly eliminated after selective sweeps) is a function of the frequency of its occurence and its effect on the fitness of its carrier. If the increase of fitness is vast, only few occurences (or as proposed above, possibly one single mutation) might be needed in the population before it gets fixed and may start to spread. But this is a rather rare case. In most cases the effects beneficial effects are very low. As such most models would require at least a moderate frequency of occurence of a particular mutation to allow it become a fixed element of the gene pool.
  9. The definition of transient species is a bit fuzzy. For instance, all now existing organisms can actually be seen as transient form between neighboring taxa. But just to add some to transient fossils, there are quite a lot of examples around. Not only hominids, but also foraminifera or the famous transition from fish to tetrapods. As such the given claim that no transitional fossils have been found is ridiculous at best.
  10. I am aware that the question was not directed at me, but actually you could answer the question by yourself by careful reading. The varying replicators are essentially the genes (read a lil' bit about the selfish gene theory to understand why Dawkins is talking about genes as the replicating units and not the ). Genes vary randomly (as mutations usually do not follow a predictable pattern, resulting in different alleles), but there is a non-random selection against detrimental alleles. That is, those that survive improve the fitness of their carriers, or are at least not detrimental. This is a selective process and hence, non-random.
  11. Basically the mechanisms of evolution (mutation, genetic drifts etc.) are random, but selection shapes it. Those that survive are those that under the given selective force have a higher fitness. Therefore this process is not random. Of course, if you take a global historical view one could argue that the changes of selective forces do not follow a distinct pattern and thus the whole process is random.
  12. Well I suppose it can be argued that a Liger is not a species as tigers and lions are allopatric species. As far as I know that do not have a species name assigned because they of course do not exist in natural habitats. So in theory they do have an isolation of gene pools. But in general I do agree. Species concepts are not clear cut functions and especially with regards to protists and especially bacteria more a matter of agreement. With regards to hybridization, if its effects were significant I would argue that with time the gene pools should eventually merge. This is outside of my expertise but to my knowledge there were no reported instance of large-scale mergers of sympatric populations. With regards to bacteria, this would probably make sense if we got a more thorough view on ecotypes. But our knowledge to bacterial diversity is atm rather sketchy at best.
  13. Actually it is more reasonable to assume that there was no new development of the described immunities, but that they already existed (e.g. due to mutations) and only now they are selected for. It is likely that the given immunity trait was already in the gene pool but only in presence of the disease do we see a phenotype. In other words, introducing a disease will not lead to a new development of resistance, but will only select agaisnt those, who did not already have it.
  14. If genetic engineering/biotechnology is your thing I'd recommend the Molecular Biology part. It looks like quite a lot of it will be a technology show, but learning microarray technologies is never wrong. The first part in Genetics is merely RNA-isolation and RT-PCR, which is kinda boring but is useful, too. This technique is often needed to identify genetic targets to maniplulate. However, this is now also often done with microarrays. Isolating DNA from various (food) samples is the least interesting one if you want to into the direction of gentics.
  15. ecoli, well hybrids are not considered as species as they usually do not reproduce and are therefore usually ignored. They pose a problem in plant taxonomy, though. daneeka, actually there was a proposition to remove species tags from bacteria and possibly only refer to ecotypes. But for microbiologists this is of course out of question. Assinging species even though the definition is fuzzy is simply too useful to give up.
  16. Per definitionem every pathogenic organism posesses virulence factors. As such a long list does not make much sense (except in the context of each specific organism). Actually virulence is usually measured within a given host-pathogen interaction. Therefore strains that kill most efficiently are regarded as the most virulent ones. The resulting fitness reduction of the pathogen is usually not taken into account. For a given system there is of course some kind of optimal virulence which has the optimal fitness for the pathogen, but this is something different.
  17. Demosthenes, it is not that confusing if you read carefully. In the first quote they are refering to genes. That is, defined stretches of DNA that has been annotated to carry coding information. 99% are annotated to have the same function, but may vary slightly in the sequence. In the second quote they compared whole DNA stretches (I admit, I got the issue lying around here somewhere but did not actually read it...). So in the second quote they basically say that we do not only have the same genes, but even the sequence of them is very similar (with exceptions).
  18. The most accepted definition is probably "an interbreeding population that are reproductively isolated from other populations" as coined by Ernst Mayr I think. In general this means that the transfer of genetic material is the barrier that distinguishes one species from another. This works reasonably well with complex organisms, but does not apply to asexually proliferating organisms. In addition, horizontal gene transfer can further muddy this concept. Therefore for bacteria no simple species definition exists. At the moment most have a pragmatic approach based on 16s rRNA comparison. Bacteria are often grouped depending on the similarity in this sequence.
  19. Well, virulence factors are, as you pointed out correctly, factors that contribute to or modulate the pathogenicity of organisms. However, purely from this definition you can easily deduce that there is no simple way to distinguish between virulence factors and factors essential for apathogenic growth. For example, the presence of iron transporter produced by bacrtera is essential for the acquisition of iron during host body invasion. If they are absent the bacteria won't proliferate and chances are that they are apathogenic. However, even if they live outside their hosts they need to acquire iron for survival and it might be the very same system (e.g. siderophore mediated iron transport to name an example). Therefore in a pathogenic organism a given system can be defined as a virulence factor, but the same system can also exist in apathogenic organism (and hence cannot be attributed as virulence factor anymore). The characterization as virulence factor is therefore context dependent. In general virulence factors are (as already pointed out) proteins produced by the bacteria which contribute for instance to: attachment (e.g. fimbria), invasion (e.g. invasins), colonization and proliferation (e.g. subtrate uptake), host defence avoidance (e.g. hydrolases, cell envelope modifications) and finally toxins. However, toxins are often characterized as pathogenicity factors rather than virulence as they can be often directly responsible for the disease rather than contributing to its strength.
  20. I see. Well, if this primer cannot be changed, have you tried another complementary primer and calculate dimers etc.? If GC is not an issue from personal experience I'd rather toy around with primers (or in some cases with polymerases, e.g. hotstart, or for high GC templates etc.) rather than trying a gazillion conditions.
  21. It is indeed assumed that chloramines are mainly responsible for the irritation and smell in swimming pools. However, it is wrong to assume that chlorine is odourless. You just need a bright student performing electrophoresis with HCl-containing buffer... Chlorine gas has a very strong odour, however the amount used in pools is rather low.
  22. If such a high overhang is really needed first check if it makes stemloops. What is the calculated annealing temperature for the primers? What you could also try in theses cases are typically betaine and DMSO.
  23. Basically that is correct. In about any case I can think of the virus attaches to certain receptors. The mode in which the virus inserts genetic material varies though, as described above.
  24. It also depends on the organism/tissue you want to isolate the DNA. For PCRs the above cooking lysis is often sufficient, for blots or other things higher purity is needed. Most protocols not using columns incorporate a phenol step to remove proteins and similar stuff.
  25. Dak, journals typically only publish the results. Although in some cases I have heard that they also pay other labs for verfication of certain results (only heard it from a physics journal, though. not really my field of expertise). In almost all cases (at least of journals I know of) the editors are scientists themselves, though. Of course they are responsible for the review process, however the reviewers are not paid. More recently some online journals indeed started to appear. Most of them allow free access to the articles, but still charge money from the authors (often less, then many print journals though). I do have the feeling that it is not always about covering costs from the journals as the charges can vary extremely.
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