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Mattshark
Bacteria make major evolutionary shift in the lab
22:00 09 June 2008
NewScientist.com
Bob Holmes

Richard Lenski, Michigan State University
Jerry Coyne, University of Chicago

A major evolutionary innovation has unfurled right in front of researchers' eyes. It's the first time evolution has been caught in the act of making such a rare and complex new trait.

And because the species in question is a bacterium, scientists have been able to replay history to show how this evolutionary novelty grew from the accumulation of unpredictable, chance events.

Twenty years ago, evolutionary biologist Richard Lenski of Michigan State University in East Lansing, US, took a single Escherichia coli bacterium and used its descendants to found 12 laboratory populations.

The 12 have been growing ever since, gradually accumulating mutations and evolving for more than 44,000 generations, while Lenski watches what happens.

Profound change

Mostly, the patterns Lenski saw were similar in each separate population. All 12 evolved larger cells, for example, as well as faster growth rates on the glucose they were fed, and lower peak population densities.

But sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use.

Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species. The citrate-using mutants increased in population size and diversity.

"It's the most profound change we have seen during the experiment. This was clearly something quite different for them, and it's outside what was normally considered the bounds of E. coli as a species, which makes it especially interesting," says Lenski.

Rare mutation?

By this time, Lenski calculated, enough bacterial cells had lived and died that all simple mutations must already have occurred several times over.

That meant the "citrate-plus" trait must have been something special – either it was a single mutation of an unusually improbable sort, a rare chromosome inversion, say, or else gaining the ability to use citrate required the accumulation of several mutations in sequence.

To find out which, Lenski turned to his freezer, where he had saved samples of each population every 500 generations. These allowed him to replay history from any starting point he chose, by reviving the bacteria and letting evolution "replay" again.

Would the same population evolve Cit+ again, he wondered, or would any of the 12 be equally likely to hit the jackpot?

Evidence of evolution

The replays showed that even when he looked at trillions of cells, only the original population re-evolved Cit+ – and only when he started the replay from generation 20,000 or greater. Something, he concluded, must have happened around generation 20,000 that laid the groundwork for Cit+ to later evolve.

Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later.

In the meantime, the experiment stands as proof that evolution does not always lead to the best possible outcome. Instead, a chance event can sometimes open evolutionary doors for one population that remain forever closed to other populations with different histories.

Lenski's experiment is also yet another poke in the eye for anti-evolutionists, notes Jerry Coyne, an evolutionary biologist at the University of Chicago. "The thing I like most is it says you can get these complex traits evolving by a combination of unlikely events," he says. "That's just what creationists say can't happen."

If you want the journal article: http://www.pnas.org/cgi/content/abstract/105/23/7899
questionmark
QUOTE (Mattshark @ Jun 24 2008, 03:54 PM) *
Lenski's experiment is also yet another poke in the eye for anti-evolutionists, notes Jerry Coyne, an evolutionary biologist at the University of Chicago. "The thing I like most is it says you can get these complex traits evolving by a combination of unlikely events," he says. "That's just what creationists say can't happen."

If you want the journal article: http://www.pnas.org/cgi/content/abstract/105/23/7899


tongue.gif
DogsHead
That is fantastic Matt. How exciting that must have been - must still be! I will be watching to see if they can isolate the trigger event. Perhaps this deserves a topic in S vs S?
IamsSon
After 31,500 generations they are still just bacteria right? Basically, bacteria raised in lab conditions leanred to eat something new. This is big news?
Incorrigible1
QUOTE (IamsSon @ Jun 24 2008, 08:40 PM) *
After 31,500 generations they are still just bacteria right? Basically, bacteria raised in lab conditions leanred to eat something new. This is big news?

It's proof of evolution. That's big news. Did you expect them to become little humans?
DogsHead
QUOTE (Incorrigible1 @ Jun 25 2008, 12:00 PM) *
It's proof of evolution. That's big news. Did you expect them to become little humans?

Hee he he! pwned! You see Iams, this is why people diss you. That is the dumbest remark I have heard you utter. Please note I am not calling you stupid - I am suggesting you engage that brain/finger filter.
ETA:
Actually, I have more to say. This is not just another great big lump of evidence for evolution, it validates a particular theoretical mechanism - one that is now much stronger thanks to the efforts of the Michigan Uni lab. By validating the mechanism of mutation, and by being able to "rewind" the timeline, if you will, they can show conclusively how these random events effect evolution, how they can be incorperated into the theory, how they affect speciation, and a lot more. It is a huge discovery.
therion24
QUOTE (DogsHead @ Jun 24 2008, 07:48 PM) *
Hee he he! pwned! You see Iams, this is why people diss you. That is the dumbest remark I have heard you utter. Please note I am not calling you stupid - I am suggesting you engage that brain/finger filter.
ETA:
Actually, I have more to say. This is not just another great big lump of evidence for evolution, it validates a particular theoretical mechanism - one that is now much stronger thanks to the efforts of the Michigan Uni lab. By validating the mechanism of mutation, and by being able to "rewind" the timeline, if you will, they can show conclusively how these random events effect evolution, how they can be incorperated into the theory, how they affect speciation, and a lot more. It is a huge discovery.

Agreed. What an amazing thing to see! You think we will every witness something like this again?
Mattshark
QUOTE (IamsSon @ Jun 25 2008, 02:40 AM) *
After 31,500 generations they are still just bacteria right? Basically, bacteria raised in lab conditions leanred to eat something new. This is big news?

Oh for gods sake, saying they are still bacteria is like say they are still an animal or a plant. It is a bloody kingdom and there are more types of bacteria than anything else.
It proves that spontaneous, random, positive mutations can occur, just like creationist claimed they couldn't.
It is not eating either, it is digesting, huge difference.
And if it can happen in a lab it can happen in the wild.
DogsHead
QUOTE (therion24 @ Jun 25 2008, 01:34 PM) *
Agreed. What an amazing thing to see! You think we will every witness something like this again?

I don't know, but I think not. I think this is a one in a million thing. Having said that, so is spotting super-nova, but there's this guy in the Blue mountains here in Oz who has spotted dozens.
IamsSon
QUOTE (Incorrigible1 @ Jun 24 2008, 09:00 PM) *
It's proof of evolution. That's big news. Did you expect them to become little humans?

The fact that you immediately ridiculed my post shows your lack of certainty.

I was pointing out that all that happened was that after 31,000 + generations in laboratory conditions all we saw was that these bacteria changed the way they interact with a particular molecule. Is citrate a molecule that is as abundantly available to these bacteria in natural environments as it was under the carefully controlled and monitored laboratory conditions? Was the controlled laboratory environment set up in a way which encouraged this change which would not have occurred in a natural environment?

QUOTE (DogsHead @ Jun 24 2008, 09:48 PM) *
Hee he he! pwned! You see Iams, this is why people diss you. That is the dumbest remark I have heard you utter. Please note I am not calling you stupid - I am suggesting you engage that brain/finger filter.
ETA:
Actually, I have more to say. This is not just another great big lump of evidence for evolution, it validates a particular theoretical mechanism - one that is now much stronger thanks to the efforts of the Michigan Uni lab. By validating the mechanism of mutation, and by being able to "rewind" the timeline, if you will, they can show conclusively how these random events effect evolution, how they can be incorperated into the theory, how they affect speciation, and a lot more. It is a huge discovery.
No, people "diss" me because I don't worship the all-wise and powerful ones with the white lab coats and keep pointing out to those who do that they are shutting their brains down so they can continue to comfortably worship the all-powerful scientists. So, the only thing you're reacting to here DH is that I have once again pointed out how your belief system is so weak you try to make mountains out of highly dubious mole hills ...Please note I am not calling you gullible, I am suggesting you take off the blinders and actually think for yourself instead of letting the all-powerful and wise lab-coated ones tell you what to believe.

Now, correct me if I'm wrong, but based on scientific principles this isn't really much until it can be shown this is repeatable... so until a separate lab using different cultures sees the same results this is as momentous as the "Wow!" message... really interesting but not really a scientific discovery.

Additionally, all this has shown is that given proper controlled laboratory conditions bacteria can be bred to use a different type of molecule than that which they would do in their natural conditions.

... Oh, yeah, HUGE news there pffft.

QUOTE (Mattshark @ Jun 24 2008, 10:59 PM) *
Oh for gods sake, saying they are still bacteria is like say they are still an animal or a plant. It is a bloody kingdom and there are more types of bacteria than anything else.
It proves that spontaneous, random, positive mutations can occur, just like creationist claimed they couldn't.
It is not eating either, it is digesting, huge difference.
And if it can happen in a lab it can happen in the wild.

No, matt, all it shows is that scientists can breed bacteria to use different types of molecules... and actually, it hasn't really even shown that unless the experiment has been repeated with the same results.

And, no, just because it can happen in a lab it is not proof it can happen in the wild.. if you really believe that then I look forward to the results of your own personal attempt to observe this happening in the wild... but I'm not holding my breath.
questionmark
QUOTE (IamsSon @ Jun 25 2008, 08:28 PM) *
No, matt, all it shows is that scientists can breed bacteria to use different types of molecules...


You know that you just have validated Darwin with that sentence?
Mattshark
QUOTE (IamsSon @ Jun 25 2008, 06:28 PM) *
No, matt, all it shows is that scientists can breed bacteria to use different types of molecules... and actually, it hasn't really even shown that unless the experiment has been repeated with the same results.

And, no, just because it can happen in a lab it is not proof it can happen in the wild.. if you really believe that then I look forward to the results of your own personal attempt to observe this happening in the wild... but I'm not holding my breath.

Sorry you are simply wrong there. They did not force it to change, it changed spontaneously. That is the important thing. It is clear proof that such a thing can happen.
But you feel free to ignore the clear and obvious evidence.
Cimber
All you're trying to do is diminish their research through the use of diction and it isn't working.

Dubious mole hills? What white lab coats tell us to believe? These people have years of education under their belt. They are entitled to publish and spell out their findings to the world. Unlike you, the guys who know and publish their work in scholarly journals and articles (or through some other credited means) know a thing or two about science and more specifically, biology.

Spouting off nonsense like "I don't worship the all-wise and powerful ones with the white lab coats" and criticizing established science from research universities; scientists like myself, Dr. Lenski (who happens to be a distinguished professor and has received many fellowships and awards for his work), and Dr. Coyne who is a prolific publisher in areas such as genetics, is futile. Evolution is a fact of science whether you like it or not and no matter how many times people have tried to help you understand this, you would rather continue on your irrational pathway that is denial of fact and the theory that explains why it happens.

For some odd reason you choose to disregard the facts of nature and place your religious beliefs on a pedestal, high above these facts. Nay, you dismiss these facts all together as dribble and false accusations. And it is clear that this is exactly what you are doing by posting in science threads and trying to undermine the research being done. It is your irrationalism, not your religion that is an issue here, and this is further exacerbated by the fact that there is a vast majority of scientists at my research institution and others that are Christian and don't let their beliefs get in the way of accepting evolution or any other fact or theory in the field of biology. Frances Collins is a more notable example.

There has not been a single experiment of observation that has disproved evolution. The birth of Molecular Genetics could have, but it only served to reiterate it.
Tiggs
Ahem.

I'm aware that this is an emotive subject, but please avoid making Ad hominem attacks.

Please discuss the topic in hand, rather than the people discussing the topic.

Thanks in advance

Tiggs
[Forum Mod Team]
IamsSon
QUOTE (questionmark @ Jun 25 2008, 12:30 PM) *
You know that you just have validated Darwin with that sentence?

Intelligent, planned, purposeful, breeding is proof of random change? Wow! Now that is reaching.
IamsSon
QUOTE (Mattshark @ Jun 25 2008, 12:52 PM) *
Sorry you are simply wrong there. They did not force it to change, it changed spontaneously. That is the important thing. It is clear proof that such a thing can happen.
All it shows is that it can happen in specific laboratory conditions.


QUOTE
But you feel free to ignore the clear and obvious evidence.

I admit I skimmed through the journal article, so I may have missed it, but did the article mention the independent experiments which repeated the results?
questionmark
QUOTE (IamsSon @ Jun 25 2008, 11:08 PM) *
Intelligent, planned, purposeful, breeding is proof of random change? Wow! Now that is reaching.


No, to recognize the possibility of an organism inherently having the potential to change to adapt to the circumstances. But evidently you have not read Darwin.
IamsSon
QUOTE (questionmark @ Jun 25 2008, 03:11 PM) *
No, to recognize the possibility of an organism inherently having the potential to change to adapt to the circumstances. But evidently you have not read Darwin.

Changing and adapting to circumstances is not really an issue. Changing from one type of life form to another... that is quite a different thing. Additionally, all breeding shows is that guided change, intelligently guided change can happen... not at all the same as random change.
questionmark
QUOTE (IamsSon @ Jun 25 2008, 11:15 PM) *
Changing and adapting to circumstances is not really an issue. Changing from one type of life form to another... that is quite a different thing. Additionally, all breeding shows is that guided change, intelligently guided change can happen... not at all the same as random change.


If the circumstances keep changing long enough so does the life form. Or what we consider to be a life form. This same process happens every day everywhere on the world. The difference now is that it was actually demonstrated under laboratory circumstances.

Changing and adapting to circumstances is the whole issue... at least according to Darwin.

Cimber
QUOTE (IamsSon @ Jun 25 2008, 04:15 PM) *
Changing and adapting to circumstances is not really an issue. Changing from one type of life form to another... that is quite a different thing. Additionally, all breeding shows is that guided change, intelligently guided change can happen... not at all the same as random change.


It is not a different thing all together. The same basic principles and mechanisms are at work to cause change. Scientists in the mainstream research don't even differentiate between macro and microevolution, precisely because they are the same thing.

And evolution by means of natural selection is not random. Natural selection isn't a random process. There are pressures put in place by the environment which shape the outcome.

Evolution occurs and there has been a change in allele frequencies from one generation to the next. You can't argue this.
Copasetic
QUOTE (therion24 @ Jun 24 2008, 10:34 PM) *
Agreed. What an amazing thing to see! You think we will every witness something like this again?

QUOTE (DogsHead @ Jun 24 2008, 11:24 PM) *
I don't know, but I think not. I think this is a one in a million thing. Having said that, so is spotting super-nova, but there's this guy in the Blue mountains here in Oz who has spotted dozens.



Actually there are many examples of things like this from evolutionary biology, especially with microorganism populations. The difference with this one is the guy has kept the populations going for some 20 years. I posted an example similar to this to another member in the Evidence for creation topic. I'll copy and paste to recap.

QUOTE (Copasetic)
Hi Walkingwithfire,

I can't help but notice you seem to have some confusion concerning simple Mendelian genetics and how mutations and heritable changes occur. It certainly makes for a difficult discussion when one is so, ill-informed? What I am going to do, since I gather from other members you dislike having to click on links and certainly have no access to any of these scientific publications, is post an excerpt -followed by a layman's terms, or "plain English" as Koralis would say of what it means. I would greatly like your input as to how these distinguished fellows have drawn the wrong conclusions concerning mutations giving rise to "new genetic information" and what you, as a scientist, suggest they do/say/interpret etc. I don't think that is asking too much for one so well endowed in the sciences as you claim.


QUOTE

We have been able to identify in K. aerogenes strain W70 two enzymes, RDH and DRK, which are induced in response to D-ribulose, an
apparent intermediate of a specific ribitol catabolic pathway. A similar pathway is found in A. aerogenes strain PRL-R3 (22) composed of two enzymes similar in terms of induction and activity. Our decision to shift studies of A. aerogenes PRL-R3 to K. aerogenes W70 was influenced by the discovery of a transduction system mediated by phage PW52, which was reported by MacPhee et al. (13) and the discovery that K. aerogenes W70 was similar to A.
aerogenes strain PRL-R3 with respect to its degradation of naturally occurring C, compounds, and in its adaptation to growth on the
uncommon C, sugars and alcohols. The lone dissimilarity in this area was the inability of K. aerogenes to degrade those C5 compounds which
in A. aerogenes appear to be catabolized by a pathway involving L-xylulokinase. L-Xylulokinase activity is demonstrable in A. aerogenes, but we have been unable to demonstrate it in K. aerogenes. The procedures worked out for utilizing A. aerogenes for selection and isolation of mutants were, therefore, modified to work in K. aerogenes W70. The excellent background work in A. aerogenes on ribitol catabolism allowed us to develop similar information for K. aerogenes W70 on induction of the enzymes involved, the apparent inducer, and mode of adaptation to growth on the rare sugars D-arabinose and xylitol. The enzymes RDH and DRK are coordinately controlled, since mutants selected for constitutive synthesis of RDH by their ability to grow with xylitol as a carbon and energy source, or for the ability of starved cells to reduce tetrazolium dyes in the presence of ribitol, are constitutive for DRK, even though we can demonstrate the effectiveness of the selections in mutants lacking a functional DRK. In addition, L-fucose isomerase-constitutive cells, when grown on D-arabinose, produce high levels of RDH and DRK even though RDH is not involved in growth on that substrate. We have found that
L-fucose isomerase in K. aerogenes, as in A. aerogenes, converts D-arabinose to D-ribulose. This leads to induction of the enzymes of the
ribitol pathway. Mutants capable of producing D-ribulose from D-arabinose, but unable to synthesize RDH, still produce DRK in response to
the D-ribulose, indicating that reduction to the pentitol is not required for induction of DRK. Mutants lacking DRK activity, although unable
to grow on D-arabinose alone, produce, when grown on casein hydrolysate supplemented with D-arabinose, high levels of RDH, indicating that
the DRK is not required for production of the inducer from the D-ribulose formed. The role of n-ribulose as an inducer of these enzymes is
consistent with our inability to find mutants which produce DRK but not RDH when grown on casein hydrolysate supplemented with ribitol,
even though mutants which appear to induce DRK but not RDH are found if arabinose rather than ribitol is offered as substrate.
In addition to helping us identify the inducer of the ribitol pathway, growth on D-arabinose shows that K. aerogenes, like A. aerogenes,
mutates preferentially to constitutive synthesis of the L-fucose catabolic enzymes (in particular L-fucose isomerase) rather than to a modification
that allows induction of these enzymes in cells grown on D-arabinose, as found in Escherichia coli (10). The latter alternative, however,
can also be found in this organism.
In a similarmanner, growth on the unusual pentitol, xylitol, is the result of a mutation to constitutive synthesis of the ribitol catabolic enzymes. In
this case RDH converts xylitol to D-xylulose. The D-xylulose produced can be phosphorylated by specific D-xylulokinases. This will be considered
in greater detail in a subsequent paper. Our understanding of growth on D-arabinose and xylitol allowed us to map the sites for phenotypes which we had surmised to represent lesions in structural and regulatory sites of the ribitol pathway enzymes. Prior to setting up the crosses reported, we were obliged to construct a mutant which would allow us to score the various phenotypes on semisolid media. We, therefore, created a mutant with the following
lesions: (i) uracil requiring, to allow us to identify contaminants as such if they arose; (ii) L-ribulokinase negative, to eliminate conversion by this enzyme of D-ribulose to D-ribulose-5-phosphate as reported in A. aerogenes (10); (iii) L-fucose isomerase constitutive, to allow isomerization of D-arabinose to D-ribulose and subsequent growth potential on D-arabinose through the DRK as illustrated in Fig. 1; (iv) L-fucose negative, to prevent shunting of Dribulose through the L-fuculokinase and fucose aldolase, as reported in E. coli (9), in those mutants lacking a functional DRK. In this basic mutant we were able to set up two- and three-point crosses with mutants with the phenotypes listed in Tables 1 and 2, i.e., mutants which constitutively synthesized RDH and DRK or failed to produce one or both of these enzymes under conditions where these enzymes should have been induced. The lesions
were all closely linked genetically, as shown in the two-point crosses, and three-point crosses yielded the map order indicated in Fig. 3.

The map order is consistent with our concept of an operon, and the induction of the enzymes is consistent with the functioning of an operon. We have not examined the direction of transcription or the possibility of positive or negative control. Thus, although we have no data for this system which are inconsistent with the concept of an operon, we do not have sufficient evidence to report it as an operon. We have recently found that there appear to be at least two genetically distinguishable control sites, as defined by mutations to constitutive synthesis of RDH and DRK, but we cannot yet define
them in terms of operator and regulator functions. This aspect of the work will be considered in a subsequent paper.



So were under no impression that I am being sneak or deceitful, This entire paper is available HERE for free.


Now two important mutations were noted for this. First the mutant bacteria, had a mutation to the region that controlled expression for L-fucose isomerase, this left the enzyme always "on". Normally this would be selected against b/c of waste of resources but since it had a low activity for the 5 carbon sugar, it ended up accounting for its weight in energy. Meaning, that while it wasn't really helping the bacteria much in amount of available energy it really wasn't hurting it either, a neutral mutation (because the low activity for the 5 carbon sugar).

Secondly, a mutation occurred which altered the structure of L-fucose isomerase . Which increased its capacity to isomerize the 5 carbon sugar.

Now this is really interesting because it shows, not just beneficial mutations being selected for, but the evolution of whole new metabolic pathways. As in previously undeveloped. Furthermore, while mutations occur to existing genes or gene expression regions -changes constitute emergence of a new gene sequence, as it is no longer (functionally or informationally) the same gene.



LINK


QUOTE (Iamson)
After 31,500 generations they are still just bacteria right? Basically, bacteria raised in lab conditions leanred to eat something new. This is big news?


Undoubtedly you do not understand why this is big news, though I would expect that most layfolk wouldn't. I will explain below.

QUOTE (Iamson)
I was pointing out that all that happened was that after 31,000 + generations in laboratory conditions all we saw was that these bacteria changed the way they interact with a particular molecule.


They did not just simply "change the way they interact with a particular molecule". What has happened is the evolution of a new metabolic pathway (like in my example above). Here is the real important kicker though, the foundations for this new metabolic pathway were laid in the 20,000th generation. Some 10,000+ generations later, this particular population reaped the benefits of earlier, neutral mutations. A human generation time is around 22 years, this is the equivalent of ground work being laid for later evolution 220,000 years in the past. The advantage to using bacteria to demonstrate this is their short generation times -8 hours for some isolates of E. coli.

So what you have here is mutations that gave rise to:
New genes, New function, New pathways.

QUOTE (Iamson)
Is citrate a molecule that is as abundantly available to these bacteria in natural environments as it was under the carefully controlled and monitored laboratory conditions?

To be blunt? Yes. E. coli are normally intestinal organisms, if you have ever eaten an orange or other citrus fruit then you have introduced citrate into their natural environment. Furthermore, there are serotypes which live in soil, on skin and in rotting vegetation. All places that provide ample opportunity for the bacteria to come into contact with citrate.

QUOTE (Iamson)
Was the controlled laboratory environment set up in a way which encouraged this change which would not have occurred in a natural environment?


No it was not. Allow to again explain how this works.

Since I doubt many people reading this have access to PNAS or are willing to pay for the journal article allow me to copy and paste a bit from their materials and methods:
QUOTE
The twelve populations have been propagated for almost 20 years by daily serial dilution in DM25, a minimal salts medium that has 139 µM glucose and 1,700 µM citrate (2). Given 1:100 dilution and regrowth, the populations achieve {approx}6.64 generations per day, and they have evolved for over 40,000 generations in this experiment to date. Every 500 generations, population samples are frozen at –80°C with glycerol added as a cryoprotectant.


So the bacteria were grown in medium (aqueous media) where there was molecules present they could utilize. To simulate natural conditions though, they use a limited amount of glucose, thus making the experiment more "real". Because, in a natural environment source molecules would not be present in unlimited conditions, individuals bacteria must compete against one another for the food source. In this way they created an experiment in which resembles the competition that occurs in the natural world.

As we would expect, evolution plays a crucial role. Those bacteria that are best at taking up glucose are the ones that reproduce most successfully. This fills their *normal* niche, that of glucose consumption. But, in the experiment there was another niche open, one lineage just needed to have the necessary mutations to take advantage of it. In this case rather than compete for glucose, a lineage evolved another way to be successful --Utilizing a new niche.
Copasetic
QUOTE (IamsSon @ Jun 25 2008, 12:28 PM) *
No, people "diss" me because I don't worship the all-wise and powerful ones with the white lab coats and keep pointing out to those who do that they are shutting their brains down so they can continue to comfortably worship the all-powerful scientists. So, the only thing you're reacting to here DH is that I have once again pointed out how your belief system is so weak you try to make mountains out of highly dubious mole hills ...Please note I am not calling you gullible, I am suggesting you take off the blinders and actually think for yourself instead of letting the all-powerful and wise lab-coated ones tell you what to believe.


This is all irrelevant and does not change the outcome of the findings. I would not tell anyone to take off any blinders were I you, I would think it would be rather important to first understand the material which you are debating, and it is abundantly clear you do not.

QUOTE (IamsSon @ Jun 25 2008, 12:28 PM) *
Now, correct me if I'm wrong, but based on scientific principles this isn't really much until it can be shown this is repeatable...


No this is repeatable. Again since it seems you have not actually read the article but are attempting to debate it (huh?), I will post some of it for you:

QUOTE
Cit+ clones could be readily isolated from the frozen sample of population Ara-3 taken at generation 33,000. To estimate the time of origin of the Cit+ trait, we screened 1,280 clones randomly chosen from generations 30,000, 30,500, 31,000, 31,500, 32,000, 32,500, and 33,000 for the capacity to produce a positive reaction on Christensen's citrate agar, which provides a sensitive means to detect even weakly citrate-using cells. No Cit+ cells were found in the samples taken at 30,000, 30,500, or 31,000 generations. Cit+ cells constituted {approx}0.5% of the population at generation 31,500, then 15% and 19% in the next two samples, but only {approx}1.1% at generation 33,000. It appears that the first Cit+ variant emerged between 31,000 and 31,500 generations, although we cannot exclude an earlier origin. The precipitous decline in the frequency of Cit+ cells just before the massive population expansion suggests clonal interference (47), whereby the Cit– subpopulation produced a beneficial mutant that out-competed the emerging Cit+ subpopulation until the latter evolved some other beneficial mutation that finally ensured its persistence.


QUOTE
The third replay experiment was similar in design to the second, but on a larger scale. We isolated 20 clones from each of 13 time points in the history of population Ara-3, again through 32,500 generations. We generated and tested 10 replicate cultures of each evolved clone and 200 replicates of the ancestor. Each culture grew to {approx}1–2 x 1010 cells, which were pelleted by centrifugation, spread on an MC plate, and incubated for 45 days. In total, {approx}4.0 x 1013 cells were tested for their ability to use citrate in this experiment. Cit+ mutants emerged from eight cultures representing seven clones (Table 1), with one clone yielding mutants in two replicate cultures. Four clones that produced Cit+ mutants came from generations 31,000 and later, two were from generation 27,000, and one (the one that produced two mutants) was from generation 20,000. We found no Cit+ mutants among any of the 200 ancestral cultures, nor among any of the other 600 cultures that used clones isolated before generation 20,000.
My emphasis.


Because you cryogencially store samples of bacteria, one can go back through the experiment "slowing down evolution" and find out what exactly happened and when.

QUOTE (IamsSon @ Jun 25 2008, 12:28 PM) *
so until a separate lab using different cultures sees the same results this is as momentous as the "Wow!" message... really interesting but not really a scientific discovery.


Again, this is not the first nor will it be the last time this has been observed. See my post above with the example of L-fucose Isomerase. There are literally thousands more of these experiments and papers which detail the evolution of new genes and metabolic pathways in organisms.

QUOTE (IamsSon @ Jun 25 2008, 12:28 PM) *
Additionally, all this has shown is that given proper controlled laboratory conditions bacteria can be bred to use a different type of molecule than that which they would do in their natural conditions.


Wrong again! This is not selective breeding. As I said above the populations were grown in media in which a normal metabolic substrate was available. However, like under natural conditions, the supply of said substrate is limited --Which spurs competition within the populations. In other words, this experiment greatly mimicked natural conditions.

QUOTE (IamsSon @ Jun 25 2008, 12:28 PM) *
... Oh, yeah, HUGE news there pffft.


Again, irrelevant (your comment). Fortunately, you are not the judge of what is and is not news in science. Our peers (other scientists) judge this. And this experimental project is very big news.

QUOTE (IamsSon @ Jun 25 2008, 12:28 PM) *
No, matt, all it shows is that scientists can breed bacteria to use different types of molecules... and actually, it hasn't really even shown that unless the experiment has been repeated with the same results.


Read above where I already corrected this nonsense.

QUOTE (IamsSon @ Jun 25 2008, 12:28 PM) *
And, no, just because it can happen in a lab it is not proof it can happen in the wild.. if you really believe that then I look forward to the results of your own personal attempt to observe this happening in the wild... but I'm not holding my breath.


Huh? This happens all the time in the wild, its called *drum roll please* evolution by natural selection!!!!!!

As I said above, this experiment is based on competition for resources. If you could recall for a moment Darwin's 4 postulates of Natural Selection:

1. Mechanism of variation (mutations)
2. Some variation is passed on, in other words mechanism of heredity (genetics)
3. Individuals with best combinations of variation will be more likely to survive and mate. (extinction to less fit forms)
4. Differential survival --More organism are produced than their environment can support, spurring a competition for resources.

No need to do anything as silly as hold your breath though. One only needs to spend a few minutes on Google to look into documented cases of this in the natural world. For instance, you may want to check out Plant evolution and adaptability to heavy metal exposure near heavy metal mines.

Copasetic
QUOTE (IamsSon @ Jun 25 2008, 03:10 PM) *
All it shows is that it can happen in specific laboratory conditions.


See my above posts in which I demolish this simple argument of yours.


QUOTE (IamsSon @ Jun 25 2008, 03:10 PM) *
I admit I skimmed through the journal article, so I may have missed it, but did the article mention the independent experiments which repeated the results?


No need to be coy, we know you did not read the article. Its 30 dollars or one needs affiliations with an academic institution, The down side to scientific journals in my opinion. But then again, most people are not really interested in reading scientific journals.

As you will see in my posts above, the experiment has been repeated. Similar experiments have been done and repeated. The outcome of such experimentation???

When you have new niches available to living organisms, they fill them. They do this by evolution.
Copasetic
QUOTE (IamsSon @ Jun 24 2008, 08:40 PM) *
After 31,500 generations they are still just bacteria right?



This is a silly argument. Maybe though you are innocent and truly do not understand what you are saying???

This idea is another example of creationist "goal post moving".

For instance, had this been done with dogs, you would argue "Their still dogs right".

In the case of dogs we are talking about the same species. In the case of "still just bacteria" you are talking about a KINGDOM of organisms.
mnemeion
This is something like man finally eating leaves raw and being able to digest it. That means there was an evolutionary shift in our digestive system that enables the breakdown of cellulose.
Darkwind
You all didn't really think creationist would except this as evidence of evolution did you? There is evidence all around us and they except none of it. Not much point in arguing with them. I think is great now they can repeat the experiment.
questionmark
QUOTE (Darkwind @ Jun 26 2008, 02:45 AM) *
You all didn't really think creationist would except this as evidence of evolution did you? There is evidence all around us and they except none of it. Not much point in arguing with them. I think is great now they can repeat the experiment.


No, but I don't think that somebody who locked himself in his cellar, claiming the sun does not rise anymore, would change his opinion because you deflected the sunlight with mirrors into it either.

ED: Garble
Drayno
Well...despite the irrationality of some of our fellow members, this news is fantastic!
puridalan
I just wish we had dedicated humans like him to study our evolution inside our own body, I mean there are people...but they just don't seem to have that charisma or at least a lot of them, because I am still up for more lab tests! haha

As for the whole evolution, that is something else, but can't except them not to evolve as well, everything is evolving/adapting because if you don't you get booted off the earth! tongue.gif

But to see it in action, pretty impressive...but luckily I still have a higher immunity to 'flus' small pox and other viruses, maybe it's just in my blood type ha-ha who knows
puridalan
QUOTE (mnemeion @ Jun 26 2008, 12:20 AM) *
This is something like man finally eating leaves raw and being able to digest it. That means there was an evolutionary shift in our digestive system that enables the breakdown of cellulose.


And there are humans that can drink blood and other strong bases/acids that would hurt most, just like some eat raw meat/roots of certain plants. Humans can digest a lot more than most expect, in all honesty the whole don't eat the your food a day after it's left out or else you'll get food poisioning is only for the babies that can't handle it tongue.gif

I mean remember when no one cared if you went to go eat that piece of hamburger in your car the next day because you remember it was there! I just think some people make a big deal out of nothing and that oooo our bodies are so 'fragile' ha-ha...it really makes me angry.

I mean all the vaccines we give our children or drugs in general, it is not letting their body to naturally fight off the infection, I mean sure a few here and there...but now it is getting out of control, I think these traits are really showing up in our socities today because of this way of thinking.
IamsSon
QUOTE (Copasetic @ Jun 25 2008, 06:01 PM) *
This is a silly argument. Maybe though you are innocent and truly do not understand what you are saying???

This idea is another example of creationist "goal post moving".

For instance, had this been done with dogs, you would argue "Their still dogs right".

In the case of dogs we are talking about the same species. In the case of "still just bacteria" you are talking about a KINGDOM of organisms.

First, as I said in an earlier post, I did not get to do more than skim the journal article (life is currently quite busy), so I appreciate all the information you pulled from it and highlighted.

Second, the "goal post moving" seems to happen quite a bit among Darwinists. Even the meaning of the word evolution is changed back and forth from the very basic definition meaning a change to a term describing a process that takes a population of cow-like organisms and results in a population of whale-like organisms through incredible sequences of complex changes which occur randomly. I can already hear the shouts of, "It's not our fault that the uninitiated and uneducated misuse the term," but the problem is that the supposed experts play along with this "confusion" whenever it benefits them.

The reason I asked if they are still bacteria is because this is being lauded as a momentous event in pointing out the reality of the process that takes us from a cow-like organism to a whale-like organism, but it seems that the change that occurred over what in human terms (according to your numbers) would have 770,000 years worth of generations has not boosted this organism beyond a stage where it can be considered anything other than a bacteria. Yes, from my perspective, if this had happened in dogs, where populations of dogs had been placed in conditions controlled to appear as near "the wild" as possible and had been allowed to breed to the point where they could now digest arsenic... they would still be dogs. They would be a breed of dog which had managed to do something in controlled conditions which the wide variety of life forms we call "dogs" had never managed to accomplish in the wild, but still just dogs.
questionmark
QUOTE (IamsSon @ Jun 26 2008, 06:01 PM) *
Second, the "goal post moving" seems to happen quite a bit among Darwinists. Even the meaning of the word evolution is changed back and forth from the very basic definition meaning a change to a term describing a process that takes a population of cow-like organisms and results in a population of whale-like organisms through incredible sequences of complex changes which occur randomly. I can already hear the shouts of, "It's not our fault that the uninitiated and uneducated misuse the term," but the problem is that the supposed experts play along with this "confusion" whenever it benefits them.


That is not goal post moving, both concepts fall under evolution.

But before trying to discuss evolution you should read the basics, like The Origin of Species, available for free online at darwin-online.org.uk
Copasetic
QUOTE (IamsSon @ Jun 26 2008, 11:01 AM) *
First, as I said in an earlier post, I did not get to do more than skim the journal article (life is currently quite busy), so I appreciate all the information you pulled from it and highlighted.


No problem

QUOTE (IamsSon @ Jun 26 2008, 11:01 AM) *
Second, the "goal post moving" seems to happen quite a bit among Darwinists. Even the meaning of the word evolution is changed back and forth from the very basic definition meaning a change to a term describing a process that takes a population of cow-like organisms and results in a population of whale-like organisms through incredible sequences of complex changes which occur randomly. I can already hear the shouts of, "It's not our fault that the uninitiated and uneducated misuse the term," but the problem is that the supposed experts play along with this "confusion" whenever it benefits them.


This is irrelevant what other people do. Look at my signature, I have never claimed biological evolution is anything but what it says below. I have been a student of the biological and physical sciences for well over 15 years now (life is a learning process). In this time I have never seen anyone else describe biological evolution (the fact) as anything other than some variation of how allele frequencies change over time. Nor have I seen anyone change the definition of the theory of evolution, except with maybe new evidences in support thereof.

Furthermore, I consider myself well read in creationist literature. I have works by Phil Johnson, many ID think tank publications, Ken ham and those guys over at AIG, as well as numerous other sources (Like IRC and apologetic press). What I have noticed is in creationist literature, they (creationists) are constantly changing the definition of and making up their own definitions to refute. Now maybe this is a case of confusion on your part and who is doing the definition changing?

QUOTE (IamsSon @ Jun 26 2008, 11:01 AM) *
The reason I asked if they are still bacteria is because this is being lauded as a momentous event in pointing out the reality of the process that takes us from a cow-like organism to a whale-like organism, but it seems that the change that occurred over what in human terms (according to your numbers) would have 770,000 years worth of generations has not boosted this organism beyond a stage where it can be considered anything other than a bacteria. Yes, from my perspective, if this had happened in dogs, where populations of dogs had been placed in conditions controlled to appear as near "the wild" as possible and had been allowed to breed to the point where they could now digest arsenic... they would still be dogs. They would be a breed of dog which had managed to do something in controlled conditions which the wide variety of life forms we call "dogs" had never managed to accomplish in the wild, but still just dogs.



Firstly what I think you had missed in my point is bacteria entails a kingdom of animals. When creationist use the word "Kind" they constantly shift the goal posts of what entails a "kind". For instance; The bacteria Escherichia coli and Chlamydia trachomatis (yes the guy that causes the clap), these are both by your reckoning "just bacteria". But they both belong to different phyla within the kingdom of bacteria. Humans and dogs are much more closely related than the two. Looks are terribly deceiving in biology and simply basing the way that something looks as sole source of any assumption is a bad idea.
That is why we don't just simply class animals based on look alone.

So saying "its still just bacteria" does not make a lot of sense. Because "bacteria" encompasses such a wide domain of organisms. Get what I'm saying or have I confused you??


Also, its interesting to note you finished the math for me and came up with a number: 770,000 years. Today people are apes. We are one 4 extant great ape species. Interestingly, 770,000 years ago we were apes. In fact, we were still belonged to the genus Homo. Not surprisingly really though if one understands the time scales we are talking about in evolution. To leave the genus Homo one would need to travel back some 3.5 million years or in other words some 160,000+ generations or some 4+ times the number of generations these bacteria have been evolving in the lab (which to get to this point has taken over 20 years).

You seem like a clever fellow Iams, hopefully you can see what saying "their still just bacteria" is a rather nonsensical comment. And hopefully you understood why this just is not "scientist breeding bacteria in the lab" (which you don't actually breed bacteria for certain traits like you cattle anyway, which throws your notion of selective breeding out the window). If you're still not clear as to why "Still just bacteria" does not mean anything or you don't quite understand why this does not simply demonstrate selective breeding let me know. I would be glad to help.
Dragohunter
I thought this leap was obvious. I mean look at the almost unimaginable difference between single celled and multi-cellular organisms.
Mattshark
QUOTE (Dragohunter @ Jun 27 2008, 11:33 PM) *
I thought this leap was obvious. I mean look at the almost unimaginable difference between single celled and multi-cellular organisms.

It is only unimaginable if you don't understand the two. Otherwise you can see how they can form.
questionmark
QUOTE (Dragohunter @ Jun 28 2008, 01:33 AM) *
I thought this leap was obvious. I mean look at the almost unimaginable difference between single celled and multi-cellular organisms.


Not as unimaginable as certain type of fish and worms that are permanently attached to a member of its opposite sex. But there are several species because it is a necessity in its environment. At some point it was a necessity for a single cell to attach itself to another cell...and so on.

Fluffybunny
QUOTE (Mattshark @ Jun 27 2008, 03:44 PM) *
It is only unimaginable if you don't understand the two. Otherwise you can see how they can form.

My very first cellular metabolism course in college was taught by a professor that had an incredible grasp of the topic...made it so fun and animated...he was kind of like Michio Kaku of biology. I loved the guy...he could walk through the processes in such a way that even the person that was new to science to have a good idea of what was going on by the time he was done. It was an amazing gift. Anyway he would discuss the development of single cell and multicellular organisms and it really did make sense.

One of the things that I thought was interesting was how quickly the leap was dismissed out of hand, before it was even studied. It makes me wonder how many developments and viewable, repeatable, scientifically valid tests are going to be required before it is admitted that evolution could in fact, be onto something...

Test 1: "Bahh, its nothing...it's still a Bacteria!"

Test 2: "So What if it was repeated, it is in a lab! Do research out in the environment where it really matters..."

Test 34: "Well yeah it repeated 32 more times, but you arent even in a lab anymore...How can you trust the results?"

Test 71: "Yeah it continued to repeat dozens of more times in a clean lab under heavy scrutiny, but that took 41,000 generations...geez slowpokes! and plus its still bacteria!"

Test 5032: (Bacteria can collectively complete New York Times Crosswords Puzzle in 22.5 minutes, depend on human waste for sustenance and in return excrete gold flakes). "Yeah, so what...look at 14 across -River in Egypt, Starts with and N... I mean, DUH, anyone could have figured that one out...and they had to Google 7 Down for an answer...and they are STILL bacteria."

tongue.gif
Mattshark
QUOTE (Fluffybunny @ Jun 28 2008, 01:17 AM) *
My very first cellular metabolism course in college was taught by a professor that had an incredible grasp of the topic...made it so fun and animated...he was kind of like Michio Kaku of biology. I loved the guy...he could walk through the processes in such a way that even the person that was new to science to have a good idea of what was going on by the time he was done. It was an amazing gift. Anyway he would discuss the development of single cell and multicellular organisms and it really did make sense.

One of the things that I thought was interesting was how quickly the leap was dismissed out of hand, before it was even studied. It makes me wonder how many developments and viewable, repeatable, scientifically valid tests are going to be required before it is admitted that evolution could in fact, be onto something...

Test 1: "Bahh, its nothing...it's still a Bacteria!"

Test 2: "So What if it was repeated, it is in a lab! Do research out in the environment where it really matters..."

Test 34: "Well yeah it repeated 32 more times, but you arent even in a lab anymore...How can you trust the results?"

Test 71: "Yeah it continued to repeat dozens of more times in a clean lab under heavy scrutiny, but that took 41,000 generations...geez slowpokes! and plus its still bacteria!"

Test 5032: (Bacteria can collectively complete New York Times Crosswords Puzzle in 22.5 minutes, depend on human waste for sustenance and in return excrete gold flakes). "Yeah, so what...look at 14 across -River in Egypt, Starts with and N... I mean, DUH, anyone could have figured that one out...and they had to Google 7 Down for an answer...and they are STILL bacteria."

tongue.gif

lol, very true.

I think some over estimate the complexity of some multicellular organism and forget about the nice inbetween of colonial organisms.
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