Evolution in a Bottle

Yellow_Number_Five
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Evolution in a Bottle

For those that don't know, quietly, behind the scenes, Richard Lenski and his team have been conducting one of the most important experiments in evolutionary biology in a few beakers in their lab for the last 20 years.

Lenski is a prominent name in the field and very well respected, he's done some amazing work and had a hand in Michigan State Universities DevoLab - (AVIDA) the evolution simulator I've linked t in several threads: http://devolab.cse.msu.edu/software/avida/

Anyway, about 20 years ago they put some E.coli in a few flasks, and have been watching what happens to them in this new environment - they've been evolving now for 44,000 generations. They figured it should spur selection and adaptation. It has. In one of these beakers, the bateria have quit eating the sugar they've been feeding them, and started chowing down on the media used to dissolve that sugar - what's more, these new bacteria reproduce 75% faster than the original stains.

You can find more here:

http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php

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been there/ seen that

 

     This was covered in a post by Shakko,  June 3,   under the heading  "End of debate; evolution observed"

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But it was not posted here,

But it was not posted here, where it belongs.


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I'm all for making this

I'm all for making this study common knowledge everywhere possible.  I posted it on myspace, too.  I can't wait to see WoM get a hold of this. 

 

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Hambydammit wrote:I'm all

Hambydammit wrote:

I'm all for making this study common knowledge everywhere possible.  I posted it on myspace, too.  I can't wait to see WoM get a hold of this. 

 

 

This is exactly what they will say: "That's micro-evolution! Not Macro-evolution! Did those bacteria evolve into frogs, or cats, or anything? If they didn't then it ain't evolution!"


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Evolution takes place in the lab!

I thought that this was a very cool report -

Researchers witnessed a strain of bacteria evolve right in front of their eyes -

Read about it here:

 

www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html


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How is this evolution

How does choosing to eat something different qualify as evolution?  Did their DNA change to allow this strain to eat the solution when the other strains could not?

 

If they simply started eating because there was more of it than sugar, then that is adaptation, not evolution.


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Quote:How does choosing to

Quote:
How does choosing to eat something different qualify as evolution?

Umm....  Joe, I'm guessing you don't know very much about bacteria.  You see, bacteria are what we call "very small."  They don't have these things we call "brains," and so they don't make "choices."  People make choices about what they eat because they have big brains and grocery stores that sell lots of different kinds of food.  Bacteria don't make choices because they don't have grocery stores or brains.  What bacteria can eat is determined by these things that are even smaller than them.  They are called "genes."  Genes are very small bits of chemicals that work with other chemicals to make something called a genotype.  A genotype is a fancy word that very smart people, called "scientists," use.  It means, "What makes a life form what it is."

You see, Joe, E coli is a kind of bacteria that can't eat a chemical called "citrate."  That's one of the things that makes it E coli.  It doesn't have the right chemicals in its genome to eat citrate.  It's like a Panda.  If you feed a panda steak and eggs, it will die because Pandas can't eat steak and eggs.  Some bacteria do eat citrate.  They aren't E coli because E coli can't eat citrate.

When the smart men called scientists wanted to watch evolution (which is something that all smart scientists know about) they put E coli in a bottle and let it grow for a long, long time.  One day, it had new chemicals in its genome, and it could eat citrate.  The scientists, who were very smart because they knew about evolution, knew that the very small chemicals in the very small bacteria weren't the same ones that are in E coli, because E coli can't eat citrate.

I hope this helps, Joe.  Maybe one day, you'll get to go to school like the other smart people, and you can become a scientist yourself.

 

 

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Quote:If they simply started

Quote:
If they simply started eating because there was more of it than sugar, then that is adaptation, not evolution.

Joe, bacteria don't have brains.  They have genes.  The only way they can adapt is if their genes change.  If their genes change, that's what very smart people called scientists call "evolution."

 

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Quote:When the smart men

Quote:

When the smart men called scientists wanted to watch evolution (which is something that all smart scientists know about) they put E coli in a bottle and let it grow for a long, long time.  One day, it had new chemicals in its genome, and it could eat citrate.  The scientists, who were very smart because they knew about evolution, knew that the very small chemicals in the very small bacteria weren't the same ones that are in E coli, because E coli can't eat citrate.

To put the same thing in less child like language (no offense to Hamby, I understand perfectly what he was implying and know he is fully capable of speaking the proper terms), I don't like the phrase "one day it had new chemicals in its genome". Not so. The chemical makeup of the central replicative heriditary molecule for organisms has not changed in chemical makeup in 3.5 billion years, when the Uracil in RNA was replaced with thymine and the ribose was replaced with deoxyribose.

Evolution is all about how organisms inherit characteristics and how the frequencies of characteristic variation change over time due to natural selection. The study of the descent of characterstics is called phylogeny. Phylogeny is tricky because we are trying to reassemble the sequence of events that we never saw, based on the evidence that it leaves in its trail. That evidence comes from the molecular basis of the organism, its genotype, and its phenotypes. We speak, therefore, of the similiarity of organisms in terms of shared characteristics. An ancestral characterstic, usually called a0, is one that is held by a common ancestor of a group of taxa under discussion, which will then change or remain the same depending on the course of natural selection for the different lineages from that ancestor. This is especially complicated because under some circumstances, an ancestral characterstic can become more conserved than before, such as when one of its homologs becomes a psuedogene, or it can become less conserved than before, such as when it undergoes a homologous duplication. So, we can think of an organism as a set of characteristics, and we can group organisms based on their characteristic sets. When two distinct organisms have an identical or very similiar characterstic, there are two possibilites. The first possibility is that this similar characterstic is because the two organisms have a common ancestor. This is then called a homologous character between the two organisms. Or, the organism could belong to a different lineage, but have evolved the characteristic independantly. This is called a homoplasious characterstic. It is also called convergent evolution.

A characteristic could be anything, a radical change or not. In this case, it is the development of a new enzyme. If a bacteria acquired the ability to digest citrate which it could not before, the most likely scenario by far is that one bacteria acquired a homologous duplication of another enzyme. This form of homologous duplication occurs when a failed mitosis event leaves a bacteria with extra genetic material, and because one copy of the homolog is no longer conserved, it underwent a modification at the codons of the active site to produce a new binding site, something which would have occured over many generations under natural selection, which was then shared promiscuously with other bacteria via horizontal transfer. This would have seperate the "have citrate" bacteria from the "no citrate" bacteria. This is an example of a cladogenestic split, and, as such, if the two populations were then more distinctly seperated and left for longer, more differences would accumulate over time, because natural selection would favor different traits in the environments.

 

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Quote:I don't like the

Quote:
I don't like the phrase "one day it had new chemicals in its genome". Not so. The chemical makeup of the central replicative heriditary molecule for organisms has not changed in chemical makeup in 3.5 billion years, when the Uracil in RNA was replaced with thymine and the ribose was replaced with deoxyribose.

True and fair.  Obviously, I was more interested in a childlike explanation than precision, and should have been a little more careful.  I guess I should have said that the arrangement of the chemicals changed, or something like that.  I've discovered that as simple as the concept of evolution is, explaining the details with any precision at all, and in simple words, is rather daunting.

 

 

 

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Oh, just humor the

Oh, just humor the creationist.

Yes, the bacteria "decided" to eat citrate rather than sugar, and one day, they will decide to eat petri dishes instead. At that point, they will break loose into the world and decide to eat us. Thus, the bacteri-apocalypse shall be loosed. This is because science is evil.

But you'll have your Rapture, so quit bitching.

Now piss off, the adults would like to discuss things based in reality.

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Hambydammit wrote:Quote:How

Hambydammit wrote:

Quote:
How does choosing to eat something different qualify as evolution?

Umm....  Joe, I'm guessing you don't know very much about bacteria.  You see, bacteria are what we call "very small."  They don't have these things we call "brains," and so they don't make "choices."  People make choices about what they eat because they have big brains and grocery stores that sell lots of different kinds of food.  Bacteria don't make choices because they don't have grocery stores or brains.  What bacteria can eat is determined by these things that are even smaller than them.  They are called "genes."  Genes are very small bits of chemicals that work with other chemicals to make something called a genotype.  A genotype is a fancy word that very smart people, called "scientists," use.  It means, "What makes a life form what it is."

You see, Joe, E coli is a kind of bacteria that can't eat a chemical called "citrate."  That's one of the things that makes it E coli.  It doesn't have the right chemicals in its genome to eat citrate.  It's like a Panda.  If you feed a panda steak and eggs, it will die because Pandas can't eat steak and eggs.  Some bacteria do eat citrate.  They aren't E coli because E coli can't eat citrate.

When the smart men called scientists wanted to watch evolution (which is something that all smart scientists know about) they put E coli in a bottle and let it grow for a long, long time.  One day, it had new chemicals in its genome, and it could eat citrate.  The scientists, who were very smart because they knew about evolution, knew that the very small chemicals in the very small bacteria weren't the same ones that are in E coli, because E coli can't eat citrate.

I hope this helps, Joe.  Maybe one day, you'll get to go to school like the other smart people, and you can become a scientist yourself.

AHAHAHAHAHAHAHAHA  *gaaasp*  HAHAHAHAHAHA

*rolls off chair*

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If evolution was fact and

If evolution was fact and not theory, then how can we use bacteria or e.coli in the experiment if there was nothing in the beginning?


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Because they didn't conduct

Because they didn't conduct this experiement before the beginning of energy/matter, if such a 'time' ever existed.


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Yellow_Number_Five

Yellow_Number_Five wrote:
Yes, the bacteria "decided" to eat citrate rather than sugar, and one day, they will decide to eat petri dishes instead. At that point, they will break loose into the world and decide to eat us. Thus, the bacteri-apocalypse shall be loosed. This is because science is evil.

Didn't that already happen?  I'm sure I saw it in some old black and white movie.

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Cadalyst wrote:If evolution

Cadalyst wrote:

If evolution was fact and not theory, then how can we use bacteria or e.coli in the experiment if there was nothing in the beginning?

The "theory" of evolution (actually various theories of evolution) is based on a ton of evolutionary "facts".  Evolution is a fact.  How evolution works is explained by a few closely related evolutionary theories.

FYI: goddidit is not one of the evolutionary theories for how evolution works.

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Cadalyst wrote:If evolution

Cadalyst wrote:

If evolution was fact and not theory, then how can we use bacteria or e.coli in the experiment if there was nothing in the beginning?

 

1. Don't confuse the scientific term "theory"  with the common term "theory". A scientific theory is an explanation which makes predictions that can be tested or falsified. A good scientific theory, one which stands the test of time, is backed up by new evidence and new experimentation. We generally call this evidence factual, and a "fact" is a piece of evidence which is generally agreed to not be in error. The theory of evolution by natural selection is backed up by many facts, one of which is that organisms are observed to evolve and change over time, as demonstrated in this experiment.

 

2. Don't confuse evolution with abiogenisis. Abiogenisis theories refer to how life first came about on this  planet, and theories of evolution seek to explain how and why they changed over time. So the fact that there was no life "in the beginning" is irrelevant to the study of evolution, because theories of evolution generally assume that life already exists before evolution takes effect. If the researchers were trying to prove a theory of abiogenisis, they would have started with an experiment  free of life. However, since they were studying evolution, they began with life and saw how it evolved.