Study in Nature shoots down three basic claims of evolutionary theory

[benkirk (Benjamin Kirk)]

[quote=“T_aquaticus, post:183, topic:35830”]
Comparing genomes indicates that you will look at both similarities and differences.[/quote]
Colloquially, not in formal English. And using it colloquially definitely helps creationists misinform others, who ignore nested hierarchies and pretend that all that sequence analysis only yields vague similarities.

You’re helping them by not explaining the contrasts.

[quote] Like love and marriage, you can’t one without the other.
[/quote]Huh? You can have either without the other. It’s analogous to denialists’ misinformation, too.

[NonlinOrg]

@cwhenderson

Ok, so now back to @NonlinOrg’s “good question” - How do you know this is a new ability? Lenski knows this is a new ability because the E.coli was unable to utilize citrate at the beginning of the experiment. This is rather straightforward, don’t overthink it.

Correction: Lenski’s particular strain was not metabolizing citrate in that particular lab at that particular time. Did he even start with a single bacteria (i.e. a true baseline)? Doubtful. Do you understand what a ‘true baseline’ is and why it is so critical?

Would you say you have a built in mechanism or “evolve” when developing immunity to a certain pathogen? Not everything that appears “new” is indeed new.

@cwhenderson

Your speculation that a gain must also come with a loss is completely unsupported by scientific observation.

@Dredge

every “evolution” is matched by a corresponding “devolution”.

Actually, we do know that. Antibiotic resistance is not “evolution” but a “devolution” also. How so, you ask? Because despite all fears, it never spreads outside of the specific environment. It goes away by itself once favorable human intervention is removed.

Now ask Lenski to release all his “evolved” e-coli in nature and see what happens. Will they take over the universe of e-coli? No! Wanna bet?

[cwhenderson (Curtis Henderson)]

Ok, humor me a little bit and check out this website: Welcome to Microbugz - Citrate Test
You will find that what I said (and you ignored) in the previous post is that diagnostic tests for enteric bacteria count E. coli as citrate negative (meaning it doesn’t metabolize citrate).

It really doesn’t matter how many bacterial cells Lenski used to start the experiment - they were ALL citrate negative. I can see that you think you have a legitimate argument, but microbiologists do not start cultures from single cells. This would be ideal, but is logistically near-impossible. Instead, microbiologists start cultures from isolated colonies - cells that are all derived from a single live cell. I expect Lenski would have done the same. Using “he didn’t start with a single cell!” is a pointless and fruitless argument.

Lenski’s bacteria would indeed suffer some “culture shock” (microbiology joke!) if dumped into the environment. I’ll bet you still would balk a little if I wanted to let it loose in your kitchen. Most would probably die out of their nice, comfortable flasks, but I would be willing to bet that a few mutants would adapt and indeed evolve to the environment of your kitchen. Would you “wanna bet” on that? I sure wouldn’t…

I know you are probably tired of hearing this, but you really don’t understand evolution (or microbiology) if you think development of antibiotic resistance is a bad thing for a bacterium and[quote=“NonlinOrg, post:185, topic:35830”]
Because despite all fears, it never spreads outside of the specific environment.
[/quote]

[jpm (Phil McCurdy)]

Not sure how you can say antibiotic resistance is “devolution”. There are multiple ways resistance develops, some of which involve mutations to existing enzymes making them more active, mutations resulting in changes to proteins in binding sites, phage transfer of DNA from bacteria to bacteria, both within and between species, and others, all of which results in new information. And unfortunately these new capabilities persist in the environment, as the spread of such things as MRSA attest to. Here is a pretty good overview article a quick google turned up:
http://mmbr.asm.org/content/74/3/417.full

[gbrooks9 (George Brooks)]

@NonlinOrg

Actually, we do know that. Antibiotic resistance is not “evolution” but a “devolution” also. How so, you ask? Because despite all fears, it never spreads outside of the specific environment. It goes away by itself once favorable human intervention is removed.

Anybody who talks about devolution like it’s an obvious conclusion has been listening to too much YEC radio.

If someone genetically engineers a new kind of mouse … that can tolerate double the levels of rat poison, but also has one less digit on his four appendages …

Is that Evolution or Devolution?

And if a different strain of mouse can tolerate double the levels of rat poison, and has perfectly normal appendages, is that Evolution or Devolution?

And if fish breeders take the largest specimens of each generation, until they have a stable genotype where the fish is twice as large, and twice as fast … is that Evolution or Devolution?

[Argon]

@NonlinOrg

Correction: Lenski’s particular strain was not metabolizing citrate in that particular lab at that particular time. Did he even start with a single bacteria (i.e. a true baseline)? Doubtful. Do you understand what a ‘true baseline’ is and why it is so critical?

Lenski’s strain used in the experiments started with a single cell. Here’s the technique microbiologists use to start colonies from a single cell.

Antibiotic resistance is not “evolution” but a “devolution” also. How so, you ask? Because despite all fears, it never spreads outside of the specific environment. It goes away by itself once favorable human intervention is removed.

That turns out to not be the case in many instances. It had been proposed by some that antibiotic resistant bacteria would tend to disappear from the local population if the antibiotic was removed from use for a period of time. However, when bacteria were surveyed after 5, 10 or more years, researchers found that resistance persisted in the populations. The key factor seemed to be the development of secondary, mutations that suppressed the negative effects of the initial resistance mutations. These further mutations allowed the bacteria to retain the resistance phenotype and compete the the ‘wild type’ non-resistant strains even when the antibiotic was not present. Here are three journal articles that people should be able to publically access (1,2,3). There are several conditions that can lead to this outcome. The emergence of secondary suppressor mutations could also be reproduced in the lab. Interestingly, in Lenski’s experiments, this sort of mutation/suppression change was found to continuously progress through the generation of cultures.

[benkirk (Benjamin Kirk)]

[quote=“NonlinOrg, post:185, topic:35830”]
Did he even start with a single bacteria (i.e. a true baseline)? Doubtful.[/quote]
They (not he) did, of course. That’s SOP to start from a single colony (a clone)! Why would you doubt something that incredibly basic? More importantly, why not read the paper before offering a criticism based entirely in your imagination?

[quote]Do you understand what a ‘true baseline’ is and why it is so critical?
[/quote]We both do. Now that you know that you’re wrong, what’s the next Gish Gallop?

@NonlinOrg

Would you say you have a built in mechanism or “evolve” when developing immunity to a certain pathogen? Not everything that appears “new” is indeed new.

We say that developing immunity is clonal selection. It’s inherited variation filtered by selection.

Do you not realize that the antibodies and T-cell receptors created during the adaptive immune response are clearly new? That when challenged with the same antigen, we’ll make different antibodies and T-cell receptors that recognize it?

[benkirk (Benjamin Kirk)]

@NonlinOrg

Now ask Lenski to release all his “evolved” e-coli in nature and see what happens. Will they take over the universe of e-coli? No! Wanna bet?

They wouldn’t survive, of course, and that’s by design. Are you not aware that lab strains of E. coli have been deliberately crippled?

[gbrooks9 (George Brooks)]

@Dredge

And I suspect that there is only a certain amount of genetic information to go around, so a mutation that produces a functional “gain” in one area will produce a corresponding functional “loss” somewhere else - ie, every “evolution” is matched by a corresponding “devolution”.

@Dredge and @NonlinOrg

So … if for every Evolution, there is a countervailing Devolution … Doesn’t that mean there is no Evolution at all? If you gain something and lose something … that’s just as much Evolution as Devolution, right? So why do the YEC’s always say: “… so it must be devolution?”

Using your own words, there’s no Evolution at all … even though the genetics has certainly changed, right? Do you folks ever play a tape of what your saying and listen to it to catch yourself saying really crazy things?

[benkirk (Benjamin Kirk)]

@T_aquaticus

I have yet to see a single creationist show how creationism makes this same prediction, or see a single creationist explain why we consistently see this pattern when we compare genomes.

Nor will you see one. You’ll have a hard time finding a creationist who will even acknowledge the existence of this pattern, which is not accurately described as vague similarity.

[Dredge]

@cwhenderson

there have been some very interesting observations, such as mutations allowing one of his lines of E. coli to now use citrate as a carbon source – highly unusual since diagnostic tests classify E. coli as “citrate negative”.

Ok, so now back to @NonlinOrg’s “good question” - How do you know this is a new ability? Lenski knows this is a new ability because the E.coli was unable to utilize citrate at the beginning of the experiment.

It’s my understanding that the E coli Lenski started the experiment with were known to already have the ability to metabolize citrate under anaerobic conditions, but a mutation occurred that allowed them to utilize citrate under aerobic conditions.

[Dredge]

@benkirk

[quote=“Dredge, post:174, topic:35830”]And I suspect that there is only a certain amount of genetic information to go around…

I don’t. Why do you?
[/quote]
Because I believe there’s a kinds boundary.

[gbrooks9 (George Brooks)]

@Dredge

Because I believe there’s a kinds boundary.

@Dredge

So, the fact that you have answered a question with a circular reference tells your audience that your belief in the limits of information each “kind” is allowed to have is based on your readings of the Bible, not based on any real world test evidence of any kind.

You simply think that God has set the limit to information for each life form.

I don’t believe I’ve ever heard this proposed before.

[Chris_Falter]

Your statement is correct. Were you also aware that Lenski’s team identified several specific mutations that collectibely provided the ability to metabolize citrate under aerobic conditions?

[cwhenderson (Curtis Henderson)]

@Dredge

It’s my understanding that the E coli Lenski started the experiment with were known to already have the ability to metabolize citrate under anaerobic conditions, but a mutation occurred that allowed them to utilize citrate under aerobic conditions.

This is correct, I should have been more precise. As @Chris_Falter has mentioned, the utilization of citrate under aerobic conditions actually required multiple mutations. Here is an excerpt from a blog entry (On the Evolution of Citrate Use | Telliamed Revisited).

Zachary Blount, formerly a graduate student and now a postdoc in my lab, has spent the last decade studying the evolution of this population and its new ability. His two first-authored papers in PNAS (2008) and Nature (2012) demonstrated, respectively, that (i) the origin of the ability to grow on citrate in the LTEE was contingent on one or more “potentiating” mutations that happened before the “actualizing” mutation that conferred the new function first appeared, and (ii) the actualizing mutation was a physical rearrangement of the DNA that brought together a structural gene, citT, that encodes a transporter and a previously unconnected regulatory region to generate a new module that caused the phenotypic transition to Cit+.

It has been argued that this is not an example of evolution because “no new information was added” since the major event in allowing the aerobic growth commandeered a promoter from another location to now work with the citT gene. But this argument is too narrow. If you were a single-celled organism that was given the opportunity to explore new ecological niches, you would be “grateful”, in your own unicellular way, for the opportunity without concerning yourself too much about what did or did not happen in your genetic code that gave you the new opportunity.

Interestingly, the blog post also discusses a bit about whether or not this metabolic change can be considered a speciation event. Not sure if I want to open that can of worms…

[T_aquaticus]

@benkirk

Colloquially, not in formal English. And using it colloquially definitely helps creationists misinform others, who ignore nested hierarchies and pretend that all that sequence analysis only yields vague similarities.

You’re helping them by not explaining the contrasts.

It doesn’t take a math whiz to understand that 98% similarity indicates a 2% difference.

[T_aquaticus]

@NonlinOrg

Lenski’s particular strain was not metabolizing citrate in that particular lab at that particular time.

Do you think the laws of physics were somehow different in Lenski’s lab?

Also, the experiment used a single colony to found the original population which means that the experiment started with a single bacterium.

@NonlinOrg

Would you say you have a built in mechanism or “evolve” when developing immunity to a certain pathogen?

First, we need to keep in mind that immunity is somatic and not germ line, so any immunity that develops can not be inherited.

Second, the answer is both. We have both an adaptive and innate immune system. The adaptive system uses antibodies which are the result of gene shuffling. While you are still developing in your mother’s womb a section of your genome shuffles a handful of gene segments producing a library of B-cells, all with different antibodies. Those B-cells display their specific antibodies on their surface, and if they bind an antigen they will start dividing like crazy and pumping out that antibody. This process is very much like random mutation and natural selection.

Once a B-cell line binds and antigen and starts dividing like crazy it also starts to randomly mutate the genes involved in producing that antibody. Mutations that more strongly bind the antigen will divide at a higher rate than those B-cells with mutations that produce less binding, and this is due to interactions with T-cells.

However, these mutations are not passed on to the next generation because B-cells are not used to produce offspring. Therefore, this is not evolution in the sense of the evolution of species.[quote=“NonlinOrg, post:185, topic:35830”]
Antibiotic resistance is not “evolution” but a “devolution” also. How so, you ask? Because despite all fears, it never spreads outside of the specific environment. It goes away by itself once favorable human intervention is removed.
[/quote]

How does that disqualify it from being evolution? Also, these antibiotics exist outside of human intervention. Bacteria and fungi have been producing antibiotics for millions of years, and they use them to fend off other bacteria in their environment. Bacteria have been evolving antibiotic resistance long before there were any humans on Earth, and probably before there were any vertebrates moving about on land.[quote=“NonlinOrg, post:185, topic:35830”]
Now ask Lenski to release all his “evolved” e-coli in nature and see what happens. Will they take over the universe of e-coli? No! Wanna bet?
[/quote]

Take a polar bear and plop him down in the middle of a hot desert. Will he survive long? Nope. Does this mean that the polar bear is not evolved? Nope. You can’t take a species out of the environment they evolved in, place them in a different environment, watch them struggle, and then claim that they did not evolve to best survive in the other environment. Those bacteria evolved in the lab setting, and they outcompete naturally occurring E. coli in that lab environment.

[T_aquaticus]

@Dredge

It’s my understanding that the E coli Lenski started the experiment with were known to already have the ability to metabolize citrate under anaerobic conditions, but a mutation occurred that allowed them to utilize citrate under aerobic conditions.

That is correct. A random mutation put a new promoter in front of the citrate metabolizing gene that allowed it to be expressed in the presence of oxygen.

[T_aquaticus]

@benkirk

Nor will you see one. You’ll have a hard time finding a creationist who will even acknowledge the existence of this pattern, which is not accurately described as vague similarity.

The hard part is finding a creationist who even understands what a phylogeny is to begin with.

[Christy (Christy Hemphill)]

@T_aquaticus @benkirk

Enough of the “let’s bash creationists as a group” type comments. Thank you.