Summations Only

I half heard on the radio today a geneticist arguing for genetic modification of crops.The big concern for those that care about such things is that the man-made changes will seep into 'normal' crops and before we know it we'll have frankenstein toast.The geneticist said that that was an unnecessary fear because what has actually been found is that the new genetic breeds just fade out of the genome when interbred. Now that seems counter-intuitive because a plant that is immune to a predator should have a competitive advantage. Anyone aware of this work?

I'm not aware of the work, but it does make sense. The traits that we introduce are often beneficial to us, not the plant. For example, the "Golden Rice" that produces beta-carotenes, important for preventing vitamin A defeciencies (which can lead to blindness) in third world Asian countries. What does beta carotene offer the rice? Probably nothing.A very popular gene here in the states is the gene for Roundup resistance. Unless a plant population is under constant selective pressure from Roundup the gene will probably not stick around.

A second factor to consider is that those folk doing genetic modification of plants make their money by selling seeds and stock each year. One way they do that is by making sure that the plants will not reproduce.

As the conversation on the mice genes has fizzled out pending further work, would this be a good time to reappraise the nylon eating bacteria?I read a thread back in 2004 where there was still some debate about whether that was a fully convincing, new genetic mutation. Do we know more yet?

There is more than one form of nylon eating bacteria, the first and most commonly cited case is the purported frame shift mutation identified by Susumu Ohno in the 80's (Ohno, 1985) in a strain of Flavobacterium. Ohno makes a convincing argument that the nylon degrading enzyme originated from a frame shift mutation in an already existing open reading frame that coded for a sequence with no apparent enzymatic function. Since the nylon degrading strain was isolated in the wild there was no direct ancestral population to compare it to so there is no concrete evidence that the hypothesised point mutation is what actually occurred. Additionally the fact that the nylon degrading sequences occurred on a plasmid, and is associated with a transposase like sequence IS6100, has been used to argue that the enzymes were imported from some external population or that plasmids are some sort of intelligently designed system for metabolic diversity in bacteria.Similarly functioning enzymes, again associated with a plasmid and sequences similar to IS6100, were identified in Pseudomonas. The sequences for one pair of the enzymes between the species was also very similar with 99% homology (Tsuchiya et al, 1989) which has been taken to suggest that in this case there was horizontal transfer of the enzyme between species.More convincing evidence for a novel origin of nylon digestion comes from in vitro culture experiments were nylon digesting strains have been dervied in the lab. This has been done for Pseudomonas (Prijambada et al., 1995) although no specific molecular basis has beenidentified for the trait. A similar experiment in Flavobacterium only managed to identify a further, previously unrecognised, nylon degrading enzyme on the pOAD2 plasmid.So there is no clear ambiguous novel molecular mutation giving rise to nylon digestion that has actually been well documented. We have a well documented origination in Pseudomonas, from the in vitro experiments, but no molecular basis, and a good candidate for a molecular basis in the case of the nylb gene in Flavobacterium but no clear ancestral population/strain for comparison.TTFN,WK

If memory serves, there are wild populations that do not have the frameshift mutation in the nylC gene. I think it is more than fair to state that we can not be 100% certain that one descended from the other. However, a simple one base frameshift mutation is easilyt produced by the known mechanisms of mutation, so the point is moot. Whether that mutation occurred in Flavobacterium or Pseudomonas has little to do with the fact that mutations can produce novel enzymes.ABE: The Ohno paper can be found here:
http://www.ncbi.nlm.nih.gov/...345072/pdf/pnas00609-0153.pdfA quick snippet from the abstract:

quote:

---

Analysis of the published base sequence residing in the
pOAD2 plasmid of Flavobacterium Sp. K172 indicated that the
392-amino acid-residue-long bacterial enzyme 6-aminohexanoic
acid linear oligomer hydrolase involved in degradation of
nylon oligomers is specified by an alternative open reading
frame of the preexisted coding sequence that originally specified
a 472-residue-long arginine-rich protein.

---

Edited by Taq, : No reason given.

If that snippet is supposed to support the idea that there was a wild type sequence that Ohno compared then reading the rest of the paper would quickly disabuse you of the notion. Ohno puts in many qualifiers and caveats that make it clear that the 'pre-existed' sequence he mentions is a hypothetical one inferred from the current ORF, for some examples see Message 4.There may have been a wild type gene that was sequenced, but it isn't in this paper and I'm not aware of a paper that it is in.TTFN,WK

That is very true. The abstract led me astray on that one. The original sequence is completely hypothetical, but well argued by Ohno.Overall, I would say that the nylon bug is a much weaker argument than the pocket mice. I think it would be more productive to search for something other than the nylon bug as an example of a novel enzyme produced by mutation.

I'm beginning to feel a little more sympathy for creationists - not much but enough to make me feel a tadge humbler.I did my zoology degree in the 70s, genetics was really only just beginning - my university only started its first dedicated degree in genetice in my second year. Evolution was of course, assumed, it was never ever questioned - it would be like questioning 2+2. But in fact we are still assuming or deducing evolution aren't we?Science has rightly been convinced beyond doubt of the fact of evolution to the extent that I'm prepared to bet (a small beer) that virtually nobody is researching an empirical proof for evolution. Getting funding for it would be as difficult as getting archaelogical funding for looking for the ark.But given the political impact of creationism in the USA, it would make a lot of sense to spend a few million finding the smoking gun.Anyway, where do we look next?

But what would be considered an "empirical proof" of evolution? I think molecular phylogenetics have very well established the validity of universal common descent.

Or gravity. But we would notice if it didn't work.The research happens by default. When people went looking in Canadian rocks for early tetrapods, they'd have noticed if they'd found a giraffe. We found the smoking gun. Creationist won't admit that it's a gun, or that it's smoking, but that doesn't change the fact that it's a smoking gun. Anywhere you please. Look anywhere in the fossil record, and you'll find evidence consistent with evolution. Creationists themselves know this, that's why they're not actually doing any work right next to paleontologists with their own picks and shovels.

Genomicus, Dr A.Sure, but you're preaching to the converted with me. No giraffes in the Cambrian and molecular philogenetics provide strong evidence, as does the fossil record and so on.But this forum only exists because some people - and if the polls are true - a very sizeable number of people around the globe don't believe it and demand proof.Now we all know that they don't actually want proof and that the majority even if shown a fish turn into a dog would still deny it, but the fact remains that we still haven't shown a direct and uncontroversial mutation of a gene that provides an obvious benefit to the organism which is then selected for naturally and consequently developed a new trait in a population.Very close with the mice, lizards and nylon bugs, but still no slam dunk.

How can any example be "uncontroversial"? All you need is one creationist to be wrong about it and you've got a controversy.

By uncontroversial I don't mean some uninformed idiot doesn't believe it, I mean that we have got to the stage where science can remove words like "strong evidence for," from its papers and replace them with "and therefore we have demonstrated that" to the extent that other scientists can't second guess it.What we've seen in this thread is that we haven't quite been able to prove to our own satifaction that a mutation of a gene has produced a beneficial change that has consequently been selected for and caused a population change. We need to kick the last brick away don't we?Once upon a time creationists argued that species couldn't change at all, now we have them (well the saner ones, at least) arguing about the mechanisms of molecular genetics. They're being pushed further and further back.

Oh, there are lots of those. As a first instance, let me direct you to the Ames Test. The initial state is known, the final state is known, and the mutation keeps the bacterium from dying of malnutrition.