..."an existing transporter has been coopted for citrate transport under oxic conditions." Lenski then says that "This transporter may previously have transported citrate under anoxic conditions," or "it may have transported another substrate in the presence of oxygen."...
Either way, no new functional information has been added.
Have the bacteria evolved? Sure. But this is not the kind of evolution that could eventually change said prokaryotes into fungi or plants or animals over time.
Why not?
These types of mutations haven't added the functional specificity that would be required.
This seems a lot like hand-waving to me. At the end of the day these bacteria have a new biochemical function - aerobic metabolism of citrate. You can whine about the mechanism all you want, but at the end of the day that is a new biochemical trait. And in the realm of energy generation this is a huge change. After all, the way e coli generates ATP is identical to the way we do it. No huge jumps needed to go from one to the other.
Edit: Yes, they were more fit for their environment, but they did lose functional specificity (or at least early evidence seems to suggest that based upon Lenski's own words) and even lost other functions as well.
Mechanisms Causing Rapid and Parallel Losses of Ribose Catabolism in Evolving Populations of Escherichia coli B -- Cooper et al. 183 (9): 2834 -- The Journal of Bacteriology
It seems all the lines of e. coli lost the ability to catabolize ribose.
You're mixing and matching papers to support a claim not made by the researchers. To be short, the citrate metabolizing e coli were derived from SEPARATE STRAINS from the ribse-deficient and DNA-repair defective strains. THE CITRATE-METABOLISING STRAINS CATABOLIZE RIBOSE JUST FINE.
Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli — PNAS
For example, in regards to the mutation rate:
"
In fact, the mutation rate of the
ancestral strain from Cit to Cit is immeasurably low; even the
upper bound is 3.6 1013 per cell generation, which is three
orders of magnitude below the typical base pair mutation rate."
Clearly, the DNA repair enzymes are working just fine.
Keep in mind that this experiment has lead to the derivation of tens of thousands of separate bacterial strains. A few of which (6?) lost ribose catabolism; the rest catabolize ribose just fine, and one of those also catobolizes citrate.
And others lost the ability to repair their DNA even.
But not the strains which developed the ability to utilize citrate.
Actually, I don't assume that. However, the "progression," if you will, from single celled prokaryote to all the diversity of life we see today has been explained to have happened via the mechanisms of evolution. I'm not debating the obvious directly observable kinds of changes that are happening (for example the Lenski experiment we have been talking about), I'm talking about the prokaryote to all life diversity kind of evolution.
It's all the same process - you cannot just divide it up into "acceptable" evolution and "not acceptable" evolution.
And, at the end of the day, the conclusion is supported by evidence. If you think its wrong you need to provide evidence that is the case. Whining that "we don't see it happening today" doesn't cut it - it took 2.5-3 billion years to go from simple bacteria to the simplest of eukariotes. To expect to see that kind of change again, within the 30 or so years science has been able to monitor those things, is pure idiocy. The simple fact that it took 2.5-3 billion years to do it the first time pretty clearly shows its a rare and seldom set of changes that are unlikely to occur again.
EDIT: This is worth adding. Modern eukariotes arose as a product of cooperative parasitism; basically our energy-generating organelles are bacteria that we paracitized (or vice-versa). So the "jump" to eukariot-ism wasn't much of a jump, genetically speaking. In fact, this form of paracitism is observed among bacteria today - Bdellovibrio and e coli for example. Likewise, and as pointed out earlier, most of the other major steps needed to make a man from bacteria has also been observed - the rise of multicellularism has been observed more than once. Speciation has been observed several thousand times, changes in morphology, new biochemical pathways, etc, etc, etc. So at the end of the day many of the steps known to be involved in making "bacteria into men" have been observed occurring separately. All that is missing is seeing them all happen in sequence - and if you happen to have 4 billion years of free time, you may just witness that as well.
EDIT of an EDIT: Just to add to the above, many bacterial species today actually have evolved mechanisms to avoid the eukaryote-type parasitism I described above. Some species of bacteria will actually commit suicide to prevent falling subject to the "tyranny of the eukaryote".
It seems that kind of evolution going on in the Lenski experiment (and others) does not show the kind of evolution that could possibly produce the entirety of living organisms we see today from prokaryotes...even given lots of time.
There is only one kind of evolution, so yes, the Lenski experiment shows exactly that. At the end of the day his experiment demonstrated the evolution of a novel function where that function did not exist previously. Put tens of thousands of those together and you're in for some big changes.
Just Lenski's own words from the PNAS paper giving his 2 possible explanations for the mechanism...both of which do not take into account gene duplication.
And? Gene duplication is not required to gain a new function. Its only required if you want to have a good chance at gaining a new function without loosing a prior function.
And you also failed to mention he didn't eliminate the possibility of gene duplication either - he was pretty clear that he did not know what the mutation was, and until he does no one can make conclusions as to whether or not a duplication occurred.
Maybe after he gets the details worked out we will know more. But thus far, it seems that mutation followed by a decrease in functional specificity has resulted.
Remember, e. coli can already utilize citrate. They only needed a way to get the citrate into the cells in oxic conditions. And based on early evidence, it seems loss of specificity is the explanation.
No, based on the evidence no conclusion can be made. You desperately want this all to not be true, so you pick the one conclusion which is consistent with your religions beliefs. We scientists don't have that option - we have to consider the facts. That is why Lenski did not make any conclusions vis-a-vis mechanism, and why I pointed out several mechanisms by which it could have occurred. The facts are not in, so therefore there is no explanation, and any claims such as yours are nothing more than a shot in the dark.
Bryan
