CharonY

[nitpick] You mean mammalian erythrocytes, right? [/nitpick]

nope, I copied it from another site, but then I probably just overlooked your quote. You will note however that the definition of the NAS is not precisely the same as Futuya's, which you brought forth in the first place. And these two are not the only definitions that are currently used by biologists. Well, I thought I implied it. Here essentially Futuyma states that biological evolution begins with changes in allele frequencies and ends with the diversity of species as we have now. This reflects my point of view also. Apparently this is the main point of our disagreement, though. Yet if one explores the statement "descent with modification" closer I'd say it is not too far from change of allele frequencies over time. It does not (at least as I would interpret it) require speciation for instance. And everything below that would be a shuffling of alleles. Yet, it does not define how much shuffling is needed to accept it as a evolutionary process. And this in turn also has an impact on evolution of proakaryotes. Here you do not have easily definable endpoint frequencies (e.g. fixation) due to extensive horizontal gene transfer. BTW the genetic species concept as applied to prokaryotes is an extremely arbitrary distinction (70% hybridization). re fixation: Well I am apparently misinterpreting you but this: I'd rather say that it is one accepted definition of evolution. As you will note from lucaspa's posts it is not undisputed (and rightly so). I'd say that changes in allele frequencies is the minimal definition because this is the proximal result of evolutionary effects. On the "maximum" side one could argue that once we obsever specietion we know that evolution happened.

Actually I do not think that any poster argues differently (even the non-American ones). Yet, it should also be allowed to criticize what they say (especially if one is as incoherent and illogical as Coulter). On another note, I assume people do not like to work at Walmart due to the bad working conditions.

In this very interesting paper it is indicated that at least in Pseudomonas aeruginosa anitbiotic sensitivity accumlates faster than resistance. This indicates that there might not be a trend for accumlation of resistances. Quite the contrary as usually expected! Antimicrobial Agents and Chemotherapy, July 2006, p. 2506-2515, Vol. 50, No. 7

Well Futuyma's concise quote regarding evolution is: I copied that from somewhere else because frankly, I cannot find my copy atm. This quote (especially the last sentence) implies that biological evolution happens within a continuum including also simple alterations of allele frequency (with fixation being the endpoint of such a process). One has to keep in mind that "changes in allele frequency" is not the definition of evolution per se, but it can serve as a minimal definition. Regarding species while what you said has some truth in it, you have consider that there are inherent problems with the definition proposed by Mayr. Take prokaryotes for instance. I assure you, you will have problems defining a species concept that suits them. Moreover, evolution and species concepts are to some point intertwined. You need somewhat closed populations in order to observe evolution and in turn evolution is the reason why different populations exist in the first place. So a fuzziness regarding species will also have an impact on the definition of evolution. I'd be glad if you can prove me wrong but so far I did not ran about anything like sharp, universal definitions for both concepts... Actually how did we come to this. Oh yeah, wheter evolution is only happening when fixation occurs. right.

In theory you are correct, dak (correct me if I am wrong, Bluenoise). In case of known sequences (for screening purposes) one could indeed try complete digests with a number of enzymes combinations, but with a sequence of a couple megabases it can get a bit tricky. Using singular enzyme the fragments will probably too short for compelte digests (~256 bp for a tetrameric recognition site). If however, the library is intended for sequencing purposes there is hardly another way than incomplete (hopefully) random digests.

Suppose for that small fragments it is the way to go. First a couple of test runs to estimate digestion rates, then resolve amd and elute appropriate band(s) from gel.

Maybe putting it a bit simpler, organisms that do meiosis have (at least) a diploid genome, meaning they posses two sets of a given chromosome (one from each parent). During meiosis the pair is split and the offspring will only get one pair (and the other one from the other parent). Prokaryotes only posses on chromosome which is replicated and given to the daughter cell asexually. Therefore there is no need (or possibility) to split chromosome pairs.

Well with DNase I (as with every other partial digestion for that matter) you have to carefully time your digests. More importantly, you have to redo it for every new batch of enzymes (within a manufacturer often but not always it is reproducible, though). Regardung DNase I specifity: as I mentioned a bit obscurely the interaction of DNase I is dependent on the local structure of your DNA strand and less on the sequence. More precisely it is sensitive to the structure to the minor grove. There is (at least afaik no interaction with the bases per se, which is the reason why DNase I does not recognizes sequences. So it does not simply find a pyrimidine and cleaves there, which would, as you pointed out, yield theoretical cleavages at every site. Instead the rigidity and depth of the minor grove are the parameters that are recognized by DNaseI. But as you are aware of, these parameters are of course sequence dependent. More importantly though, the groves are unsymmetrical structers as such the position of, in this case, a pyrimidine on one strand is not equal to the presence on the other one. Thus if you have got certain number of pyrimidines (or maybe it was pyrimidine-purine transitions, I forgot) on the "correct" strand you will yield a higher chance of cleavage. This can be a bit of a problem if you have repetitive regions, for instance.

This does not agree with our experience as well as literature, I am afraid. DNAse I preferentially digests in dependence on the sequence specific local structure, especially at sites adjacent to pyrmidines. See for instance: Nucleic Acids Res. 2002 December 15; 30(24): e139. Journal of Molecular Recognition Volume 7, Issue 2 , Pages 65 - 70 However you are right in so far that for small fragments enzymatic digests is probably the way to go. Alternative enzymes migh be CviJ1 (check Sambrook: "Molecular cloning" for more)

Is there a special reason why it has to be 500bp? Most shotgun libraries have inserts of around 1-4 kb. These can be easily achieved with several shearing methods. How large is your genome? The problem with DNase (or other enzymatic treatments) is that the resulting libraries are often non-randomly distributed...

Just a thought, is it possible that you mean meiosis? This would be true, of course.

Well, one probably has to remember that evolution is a gradual event and, what is even worse, the definition of evolution is not as sharp throughout biology than one might want to (slightly similar to the species concept). A situation in which allele(s) became fixed clearly defines a state that is different from the starting population, so one can say that it has evolved. On the other hand evolution is the process that leads to the changes in a population. As such changes in allele frequencies even if fixation has not happened yet is still evolution. Fixation itself is a rather rare event and mainly occurs in highly inbred populations and is mostly used as a quasi-steady state model (at least in my understanding).

Out of memory: P = probability (cough); in this case of fixation N = population number/size s = selection coefficient (that is whether the allele confers selective advantages/disadvantager or not/being neutral). And just shortly, fixation with regards to an allele indeed means a frequency increase to one. Maybe there is a confusion with internal equilibria frequencies? In addition, for instance for bacterial population the models are quite different(as offsprings are clones). Ok and there are about a gazillion models trying to estimate fixation probabilities and times in dependence on about the same amount of paramteres, but that's another discussion...

I am not familiar with that particular region, however chances are that carbonate minerals play an important role. Carbonate buffers are often found in aquatic sediments.

Re: China, as long as you keep your head down and do not mettle with politics it ain't that bad. Especially if you got a specialist function as a foreigner (e.g. being scientist) you will be granted certain privileges. So probably having more than one child would not be a problem, if you are a Prof. for instance.

What YT2095 said You'd have to be extremely unlucky to get something serious out of that, especially if you got a tetanus shot. I grew up with about a dozen dogs, many of them ex-strays with slightly aggressive tendencies in presence of food. I only feel like chasing mailmen every now and then.

For metabolome analyses we disrupt ~10-30 mg cells in 80 % methanol using bead beating. -incubation 15 min at 70° C -centrifugation -supernatant was evaporated for GC/MS: -Methoximation of carbonyl moieties: 50 μl of a 20 mg/ml solution of methoxylamine hydrochloride in pyridine, incubation 37°C for 90 min (stirring) -Protection of acidic protons: 50 μl N-methyl-N-[trimethylsilyl]trifluoroacetamide, incubation at 37°C for 30 min

I stand corrected. I only had memorized that it contained two chains and I assumed that it was the results of two gene products. However, if I recall correctly the first hetereologous expressions of insulin was done by expressing both chains seperately and then combining them chemically (hence my errror).

In principle yes. However the complete insulin consists of two gene products. The A and B chain have to make disulfide bonds in order to get to the correct quartiary structure. On a different point, I think nowadays yeast cells are used as hosts as they can easily be made to secrete active insulin...

Granted. You have to shift the sand in 6 minutes. I wish I had first authorship on a Nature paper.

Without enrichments? And to what purpose (that is, how much yield/purity do you need)? if you just want to make some PCRs on it, it might be sufficient to concentrate the water (e.g. using filters) then take the concentrate and make a general lysis (e.g. cooking, bead beating....). Otherwise you might need a cleanup with phenol. Alternatively there are some kits, but you need quite a lot of bacteria to get enough DNA (otherwise they just get lost in the columns).

Or how about prokaryotes? On the one hand they got asexual reproduction, on the other hand heavy horizontal gene transfer. Here we got, well, gene pools that flow into each other so to say...

Wait a tick. How was that determined (from a paper, possibly?)? And more importantly, how many of these were neutral and how many beneficial? I would assume that the vast majority should be neutral and only a fraction beneficial. As such lumping both data sets together would not allow a direct comparison with detrimental mutations.

We studied together at the same university, however I never had much interested in her (and vice versa). I was (am) somewhat nerdy with workoholic tendencies and As such I never really assumed that a woman would ever play a signifcant role in my life (except being born and raised by one that is). However during nightly workshifts in the lab I found out that she was a workoholic, too. And also a nerdette (she knew all episodes from STNG from her memory, I could only counter with Monty Python), although she really did not look like one. We got interested in each other after some night sessions and have been together for over six years now. We do not have kids and are unlikely to ever have some. We do share a number of papers, though. And rabbits. Edit: forgot that it is 2006 already. Seven years together now...