The End of the Debate: Evolution Observed

shikko
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The End of the Debate: Evolution Observed

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

 

In short, a researcher let flasks of E. coli bacteria breed over several thousand generations.  They saw some really interesting changes occur:

- different colonies of bacteria independently evolved the ability to breed faster.

- different colonies of bacteria independently evolved more efficient digestion of food.

- one colony evolved the ability to digest citrate, which is something E. coli are known to NOT be able to do; their inability to digest citrate has actually been used as one of the bacteria's identifying features.

 

So, in short, evolution denialists are no longer allowed to:

- claim we have never seen evolution.

- claim we have no evidence of evolution.

- claim we have no record of evolution.

- claim that mutations are almost always bad, and therefore would be a hindrance to organisms instead of a help.

- claim that random mutation cannot give rise to a new trait because the odds are so low.

- claim evolution is not repeatable, and is therefore not scientific.

 

In short, if you don't want to be called a liar, don't lie: evolution happens, we've seen it, it can help an organism adapt to its environment, and it's repeatable.

 

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You'll still get theists of

You'll still get theists of the Hovind and Comfort ilk saying crap like:

"But they're still bacteria! They didn't evolve into a non bacterial form!"

Or

"It just shows that the designer planned for the bacteria to have the ability to adapt"

They're already so good at ignoring evidence - why would this make them change?

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What an awesome

What an awesome experiment!  The citrate adaptation is just pure gold, although there will still be theists who say things like, "well... he said that bacteria don't have species, so that's not really a new species..."  but anyone with fifth grade brain power ought to be able to recognize this for what it is.

I've always thought that it's ironic -- if theists demanded the level of proof for God that they do for evolution, there wouldn't be any theists on the planet.  As nice as it is to be able to point to this study as a "proof of evolution," scientists have been watching evolution in action for decades.  This is just a "Proof of Evolution for Dumb-Dumbs" that is so clear that it can't be reasonably argued against.

 

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jcgadfly wrote:You'll still

jcgadfly wrote:

You'll still get theists of the Hovind and Comfort ilk saying crap like:

"But they're still bacteria! They didn't evolve into a non bacterial form!"

Or

"It just shows that the designer planned for the bacteria to have the ability to adapt"

Yes, which says more about them, their ignorance, deceitfulness and fear than it does about science -- but we already knew that.  There are some people that are beyond help because they don't want to be helped; they prefer their warped version of the world, so no amount of conversation, reasoned argument or gnashing of teeth will do anything to dissuade them.  What's worse is that they do this not out of some lack of capacity to understand (I have a lay understanding of this material, and I'm far from the sharpest knife in the drawer), but because they're scared.  I've stopped being angry with these kinds of people and instead just pity them and their need of self-deception to stay comfortable.

Quote:

They're already so good at ignoring evidence - why would this make them change?

Oh, it wouldn't, and I have no illusions that it it would.  However, as has been pointed out may a time, these conversations/debates are not about trying to persuade the other arguer that you are correct; it's about persuading the audience.  We now have one more way to persuade the listeners that the science deniers are either lying or ignorant, and that's a good thing.

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I agree wholeheartedly -

I agree wholeheartedly - thanks for posting

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I was under the impression

I was under the impression that they had done experiments like this in the past and had similar results. 

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Hambydammit wrote:What an

Hambydammit wrote:

What an awesome experiment!  The citrate adaptation is just pure gold,

I know!  I thought that was great.  Taking advantage of the waste byproduct of some other reaction: what a cool adaptation.  This is sort of how I envision the rise of the animal kingdom; there were these organisms (plants) that were dumping tons of digestive waste byproduct (oxygen) into the ecosystem, and so it was almost inevitable that a mutation would occur to allow some of these organisms to take advantage of these free molecules to aid their metabolisms with some rather energetic reactions (oxidation).

Quote:

although there will still be theists who say things like, "well... he said that bacteria don't have species, so that's not really a new species..."  but anyone with fifth grade brain power ought to be able to recognize this for what it is.

I think you've spotted the trait that lessens the potential impact of this research on your classic god-botherer.

Quote:

I've always thought that it's ironic -- if theists demanded the level of proof for God that they do for evolution, there wouldn't be any theists on the planet. 

Yes.  I've been looking for a way to articulate that thought for quite some time; thank you.  I was trying to voice the ridiculousness of their double standard, but couldn't get it right in my head.

Quote:

As nice as it is to be able to point to this study as a "proof of evolution," scientists have been watching evolution in action for decades.  This is just a "Proof of Evolution for Dumb-Dumbs" that is so clear that it can't be reasonably argued against.

Exactly; it's sort of like proving the possibility of the internal combustion engine by having a running car: argue if you want, but I'll just gesture at the car, then point and laugh at you.

Of course, the Achilles Heel here is "reasonably".  I'm sure someone will try to swift-boat his credentials, character, integrity, reliability, honesty and motives.  After all, when you can't argue against the evidence, argue against the person.  Assholes.

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LtPaint wrote:I was under

LtPaint wrote:

I was under the impression that they had done experiments like this in the past and had similar results. 

If it had been (not saying it hadn't been done earlier), why are there still evolution v. creationism arguments?

Is it just an "ignorance is bliss" thing?

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Good stuff, thanks for

Good stuff, thanks for posting that!

 

But alas, it won't matter. Given the amount of scientific evidence already ignored by Evolution Deniers and YECs, what's a bit more?

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LtPaint wrote:I was under

LtPaint wrote:

I was under the impression that they had done experiments like this in the past and had similar results. 

It's entirely possible, but I'll admit ignorance as to the particulars of any of them.

What caught my eye about this one is that the experiment was designed to be repeatable, and for interim results to be confirmed.  They thought that it was perhaps a fluke that the citrate digestion adaptation occurred, so they tried to repeat it: they went back several thousand generations to previous stock that lacked the adaptation and started again.  The same adaptation cropped up again after thousands of generations and trillions of bacteria.

Just awesome; not only did they show the adaptation occurred, they showed the same adaptation occurred twice under the same conditions.

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Quote:I was under the

Quote:
I was under the impression that they had done experiments like this in the past and had similar results.

Scientists have been observing evolution in bacteria for decades.  I'd say there have been tens of thousands of experiments that had similar results.  What sets this study apart is the duration.  I am not aware of any other study with so many generations.

One of the significant results of this is that it empirically demonstrated an entirely new trait arising from random mutation.  This is something that theists have always clung to as a last ditch attempt to separate evolution into micro and macro. 

Incidentally, the argument that bacteria aren't really divided into species, so this doesn't apply to humans, is specious for one main reason.  The concept of a species doesn't really apply perfectly to ANYTHING.  It's simply a convention, and doesn't represent a real wall between organisms.  In a very real sense, every single organism that has ever lived has been evolutionarily distinct from every other organism.

 

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shikko wrote:Just awesome;

shikko wrote:

Just awesome; not only did they show the adaptation occurred, they showed the same adaptation occurred twice under the same conditions.

I thought it was interesting, along with the adaptation occuring twice, was the fact that it was brought into question if the strain that developed in fact had became a new species.  Any opinions on this?

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LtPaint wrote:shikko

LtPaint wrote:

shikko wrote:

Just awesome; not only did they show the adaptation occurred, they showed the same adaptation occurred twice under the same conditions.

I thought it was interesting, along with the adaptation occuring twice, was the fact that it was brought into question if the strain that developed in fact had became a new species.  Any opinions on this?

My opinion is that it calls into question the definition of "species", as Hamby mentioned.  There is no good way to meaningfully delineate organisms on this planet in a uniform way: shigella is still talked about as a separate species of bacteria that causes a specific disease (shigellosis) , but it's isn't: it's a strain of E. coli, as was pointed out in the article I linked to in the original post.

When I was in grade school, the rule I was taught was that if two organisms can breed and create offspring that can also breed (i.e., the offspring is not sterile), then these two organisms are the same species.  If they cannot breed, or if the offspring are sterile, then they aren't.  But what about asexual reproduction?  What about bacteria that simply subdivide, with mutations creeping in at a low but steady rate?  I don't know.

It's a tricky issue; if an adaptation occurs in an organism that allows them to digest something others of their kind cannot, is that enough to classify it as a separate species?  Clearly not, as this would make lactose tolerant humans (I've heard the ability to digest lactose described as the most recent adaptation in humans) a separate species than their lactose-intolerant cousins.  So then how many of these kinds of adaptations does a subgroup need to collect to become a different species?

It's a really cool question to consider.  Where do we draw the line?  Given that a single gene change does not generally lead to a new species (weasel words intended, because there may certainly be a case where it could), it would suggest that speciation is a spectrum of changes, not a set number.  Can you draw a meaningful straight line through a spectrum?  If not, should we devise a more meaningful metric, such as percent shared genes, rather than a binary yes/no state?

The thing I love about science is that the more questions that get answered, the more questions crop up that you didn't even know needed answering.  The more you learn, the more you realize you don't know.  Love it, love it, love it.

 

 

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One of the questions in the

One of the questions in the article that popped up was do certian characteristics seperate a species, while others don't ("If E. coli is defined as a species that can't eat citrate, does that mean that Lenski's team has witnessed the origin of a new species&quotEye-wink.  In this case, the question is if E. Coli is defined as a species that can't eat citrate.

Of course, like you said, some humans are lactose intolerant, does this make them a seperate species from humans who arn't lactose intolerant?  In my opinion, no.  So is it the same for the E. coli? 

I suppose a question could be,"Is the ability to eat citrates by this strain of E.Coli cause such a significant change in the way this organism function and lives that it should be defined as a seperate organism?"  I don't understand E. coli enough to make a call on this though.

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LtPaint wrote:I suppose a

LtPaint wrote:

I suppose a question could be,"Is the ability to eat citrates by this strain of E.Coli cause such a significant change in the way this organism function and lives that it should be defined as a seperate organism?"  I don't understand E. coli enough to make a call on this though.

A good question.  How would you answer it?

Personally, I have no idea. Smiling

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LtPaint wrote:I thought it

LtPaint wrote:

I thought it was interesting, along with the adaptation occuring twice, was the fact that it was brought into question if the strain that developed in fact had became a new species.  Any opinions on this?

It's important to note that "species" is a completely artificial construct. We use it for the sake of convenience, because we apes seem to enjoy grouping like things together. It is helpful, to a point, but I think it can also be a hindrance.

Discussing whether this is a "new species" is more about our artificial construct, and not so much about biology.

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Let me be more clear about

Let me be more clear about the species thing.  The concept of the species was invented before DNA was discovered, and before we knew that all life descended from the same ancestor.  When zoologists started classifying animals in the current system, they thought that each animal was a separate entity, and that each type of animal was pretty much what it had always been, and would always be.

In reality, this is not even remotely true.  We share something like 90% of our DNA with mollusks.  When you start getting down to brass tacks, there's hardly any genetic difference between closely related animals, and from the gene's point of view, they're pretty much the same thing.  Even the delineation of breeding isn't really concrete, for there are closely related species that can breed and make fertile offspring, but for reasons of geographic separation, or interspecies competition, they just don't.

Life is a continuum, not a bunch of individual groups.  To be blunt about it, species are a reasonably good way for scientists to get around the problem of having to deal with trillions of individual organisms as discrete genetic entities.  It's just a system of boxes for labeling, not a representation of actual divisions.

With bacteria, the concept of species doesn't apply well precisely because of issues like the citrate eating E coli.  If we gave a separate species name to every strain of bacteria that developed a new ability, we'd spend so much time labeling boxes that we'd never get any research done.  With larger animals, it becomes much easier because of complexity.   If an animal has, say 10,000 relevant traits, and two of them change, we don't have a problem thinking of it as the same species.  In a bacteria that has only ten or twelve relevant traits, it's murkier.

 

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Quote:  I don't understand

Quote:

  I don't understand E. coli enough to make a call on this though

I do hovever. In bacteriology, species which reproduces asexually (hence all)has no formal classification for being a species seperate from some other group of organisms except for their divergence of highly conserved genes such as the 16S RNA, which was the cheifly analyzed code string upon which it was realized that life would be better grouped into three domains (Eukaryota, Eubacteria and Archaea) as opposed to just two (Eukaryota and Prokaryota). Genes like 16S are those whose sequence difference must be examined in phylogeny before inferring familial relationships, because the clock is fixed. Whereas other sequences of DNA can be rendered redundant and hence unconserved, and others can be made conserved when one of their homologs becomes a psuedogene, it is very hard to estimate phylogeny on the basis of non-conserved sequences. With something like 16S this problem doesn't exist because ribosomal subunits haven't changed in about 3.5 billion years.

In bacteriology, estimates for phylogeny become further muddied because of horizontal transfer, but this problem can again usually be sidestepped with the use of conserved genes. E Coli has the distinguishing of being the most studied organism on the planet. Because the genome of prokaryota like E Coli is so small, a change in enzymatic capabilities, like the ability to break down citrate, would give justification for the researchers to call it another species. Remember that for asexual organisms, the definition of species is more arbitrary and as such, we examine characteristic differences. 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 and underwent a modification at the codons of the active site to produce a new binding site, 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.

This means that, yes, the two bacteria can be considered a new species. Granted, the difference between them isn't very pronounced, but since we know for a fact that we have just created a distinct new lineage on a phylogenic tree, then by definition we have created a new species. Charactetistic differences is how we tell species apart. If a researcher took two E. coli at random, and compared them to this new organism, it would respond differently. For example, it would respond differently to pH changes in the environment.

In evolutionary biology, although the definition of species is quite vague, the definition of a taxa is quite precise. For asexaully reproducing organisms, one way to define species is to define it as a seperate lineage, which will therefore appear as a different branch coming from the common ancestor. Of course, this ignores the possibility of anagenesis or "outmoding" which is why I said it is only one way. In this case, species aren't defined by how many characteristics they differ in, they are defined by how they are found on the phylogenic tree (of course, the phylogenetic tree is drawn on the basis of the characterstic differences of species, among other things, but in this case, it does not matter, as we shall see).

It is usually hard to construct a tree, but in this case we can because we made it ourselves. This means we engineered a cladogenesis break. This means that although the new species is very similar to its common ancestor, ie "just diverged" it is still a new species, because it formed a seperate lineage. It is important to realize that under normal circumstances, we would look at two organisms and say "they diverge at many characteristics and hence are part of or diverge from different lineages". Here, we can say "we made a new lineage, hence a new species, which will become more apparent if we leave it for a while".

EDIT: It is important to understand the manner in which I am defining species and by that, recognize the fact that the concept is not defined well among biologists. Two populations that undergo a geographic seperation will diverge over time in terms of genotype and phenotype, even accounting for the possibility of independant convergent evolution, which is not uncommon. This is called cladogenesis. If two organism populations have such a split and . Take humans for example. The out-of-Africa hypothesis states that the various races of humanity are the result of phenotypic divergence that occured by the migration of different populations of humans from Africa before the last ice-bridge broke away. Of course, there hasn't been a great deal of divergence given that there hasn't been a great deal of time, and more importantly, the modern human gene pool is tremendously heterozygous, for obvious reasons. 

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Quote:It is usually hard to

Quote:
It is usually hard to construct a tree, but in this case we can because we made it ourselves. This means we engineered a cladogenesis break. This means that although the new species is very similar to its common ancestor, ie "just diverged" it is still a new species, because it formed a seperate lineage. It is important to realize that under normal circumstances, we would look at two organisms and say "they diverge at many characteristics and hence are part of or diverge from different lineages". Here, we can say "we made a new lineage, hence a new species, which will become more apparent if we leave it for a while".

AHH.... Thank you for this clarification.  It makes a lot more sense now.

 

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Quote:In bacteriology,

Quote:
In bacteriology, estimates for phylogeny become further muddied because of horizontal transfer, but this problem can again usually be sidestepped with the use of conserved genes.

Just to be sure, you're saying that by comparing slowly evolving genes between distantly related bacteria, we can eliminate much of the horizontally transferred genes from consideration in closely related bacteria?

In general, slowly evolving genes duplicate more efficiently, right?  So that would mean that when a bacteria shows up with a new gene, we can compare it to its own genes, compare it to distantly related bacteria, and between the two measures, be reasonably certain whether we are looking at horizontal transfer or duplication, right?

 

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Bravo

Hambydammit wrote:

Incidentally, the argument that bacteria aren't really divided into species, so this doesn't apply to humans, is specious for one main reason.

"Specious," eh?

Was that intentional?

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Quote:In general, slowly

Quote:

In general, slowly evolving genes duplicate more efficiently, right?  So that would mean that when a bacteria shows up with a new gene, we can compare it to its own genes, compare it to distantly related bacteria, and between the two measures, be reasonably certain whether we are looking at horizontal transfer or duplication, right?

Well, think of it like this.

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. Horizontal transfer falls into its own category of derived genes, and is hence unique in evolution, for the manner in which it is spread is neither homologous or homoplasious. Distinguishing between them is the basis of drawing accurate phylogeny trees and is hence the central study of phylogenetics. There are a variety of methods to do this, some of these methods having been around since before DNA was discovered. But it is very difficult to say "x is horizontal" or "x is vertical" when we have a population of bacteria which share some non-ancestral characterestic, because there remain the possibilites that one of the bacteria spread a mutation to the others via transfer, or that all the bacteria are the result of a common ancestor with that derived characteristic. The problem is not trivial. There are a variety of non-phylogenetic methods for telling whether something is the result of a copy-and-paste. In humans, we can detect retrotransposons and endogenous retroviral insertions because they have conserved sequences at either end that hold the sequence for ligase. But most of them are so old that they have long since stopped transposing and many of them have simply faded into the junk sequence. In bacteria, there will be clear signs when a gene is the result of a transfer that have nothing to do with phlogeny. Because such copy-and-paste is done by virtue of plasmids which are held by bacteriophages which transport the copied genes, some of the copied genes will have transposes inserted into them. Non-phylogenetic methods for determining horizontal transfer are usually more reliable for bacteria.

 

Back to conservation.

The principle of conservation is that which is behind the molecular clock. The clock is a controversial idea, and it doesn't run for every gene and hence for every characteristic. But we do know that the clock runs for highly conserved genes, and I shall tell you why. This is why we use highly conserved genes as the basis of genetical studies of phylogenetic trees. For some genes, the clock does not run at a constant rate because the conservation of their sequences can change depending on what is being naturally selected for. This is a big problem. But a highly conserved gene such as H2 or 16S will never have this problem because they are so central to biological life, and so finely tuned, that most mutations will destroy them and hence the organism that holds them, and as such, the clock runs very slowly and it runs very constantly. This is why they are used as a "master clock" to ascertain the change in base pairs between organisms, which, together with our inferred understanding of the relationship between taxa from the fossil record, will tell us how distantly related two organisms are on the basis of the number of base pair substitutions which have resulted.

The other sort of gene for which we will want to use in phylogeny is that which has no conservation whatsoever, which mutates solely on the basis of random frequency. The problem with this is that such genes will mutate out of existence very quickly. There were several proponents of the intelligent design movement who claimed that traits like the Kreb cycle set were put in place as "dormant" before they were needed, shaped by the creator of the mechanism in question. They were forced to retract that claim after they were cornerned by mainstream science and it was pointed out that a gene which serves no function will mutate out of existence very quick. Notice I say "gene", not "DNA sequence". The two are not the same so don't confuse them. A special sequence of unconserved but also undiscarded sequences called fibrinopeptides, which are discarded during fibrinolysis, form the basis of a "master clock" which, together with highly conserved genes, will tell us the relationship between organisms based on the rate of change of sequence. These sequences have no conservation, but they also serve a function. They are unique in that this function does not depend on their amino acid sequence, and as such, they are tremendously important for phylogenetics.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

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Thanks for the detailed

Thanks for the detailed explanation.

Quote:
Because such copy-and-paste is done by virtue of plasmids which are held by bacteriophages which transport the copied genes, some of the copied genes will have transposes inserted into them. Non-phylogenetic methods for determining horizontal transfer are usually more reliable for bacteria.

So, am I understanding that horizontal transfer is always via plasmids?  How frequent are inserted transposes in the copied genes?

Quote:
There were several proponents of the intelligent design movement who claimed that traits like the Kreb cycle set were put in place as "dormant" before they were needed, shaped by the creator of the mechanism in question. They were forced to retract that claim after they were cornerned by mainstream science and it was pointed out that a gene which serves no function will mutate out of existence very quick.

That puzzles me.  How did they decide that the Kreb cycle predated its own evolution?

 

 

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deludedgod
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Quote: So, am I

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So, am I understanding that horizontal transfer is always via plasmids?  How frequent are inserted transposes in the copied genes?

No, but viral vector transfer by bacteriophages during the lysogenic life cycle is more common. Another manner in which it is accomplished is via conjugation, where bacterial cells contact each other directly, an especially common process during chemotaxis when bacteria collide. But the first method is far more efficient, for bacteriophages can infect and insert their genome into the host much quicker than bacteria can fuse. Hence, the first method of gene transfer can proceed at a geometric rate, because each host produces more viral particles, whereas the second can only proceed at an arithmatic rate.

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That puzzles me.  How did they decide that the Kreb cycle predated its own evolution?

Hey, I didn't make it up. The idea was that the mechanism was shaped many millions of years before the evolution of respiring organisms.

 

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

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Hambydammit
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Quote:No, but viral vector

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No, but viral vector transfer by bacteriophages during the lysogenic life cycle is more common. Another manner in which it is accomplished is via conjugation, where bacterial cells contact each other directly, an especially common process during chemotaxis when bacteria collide. But the first method is far more efficient, for bacteriophages can infect and insert their genome into the host much quicker than bacteria can fuse. Hence, the first method of gene transfer can proceed at a geometric rate, because each host produces more viral particles, whereas the second can only proceed at an arithmatic rate.

AHH... I remember now.  (It's been, let's see... 15 years since I took this course.)  I understand perfectly.  Thanks.

 

Atheism isn't a lot like religion at all. Unless by "religion" you mean "not religion". --Ciarin

http://hambydammit.wordpress.com/
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