Study in Nature shoots down three basic claims of evolutionary theory

[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.

[benkirk (Benjamin Kirk)]

You’re really not getting the point. This is about effective communication of science to laypeople.

Would you say that biologists have effectively communicated evolutionary science to the public?

[NonlinOrg]

@cwhenderson

Ok, humor me a little bit and check out this website: http://www.austincc.edu/microbugz/citrate_test.php

Done. Fine, let’s assume all Lenski’s starting E.coli were citrate negative and genetically identical. You still didn’t answer if your immunity reaction is built in or “evolved”. Because if ‘built in’ (the correct answer) then Lenski’s E.coli may also have the built in capacity to adapt as organisms generally do to a certain extent.

@cwhenderson

I would be willing to bet that a few mutants would adapt and indeed evolve to the environment of your kitchen

Now you’re talking science. Let’s do the experiment. Who said “evolution” cannot be tested: http://nonlin.org/evotest/ ? I hereby volunteer my kitchen, although you do understand my/your kitchen are also controlled environments just like Lenski’s lab. The ultimate test is release in nature which has been inadvertently done with many organisms including ab-resistant bacteria. Guess what? None of them took over the universe.

I didn’t say " antibiotic resistance is a bad thing for a bacterium". Read again.

@jpm

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.

Thanks for your thoughts, but… No! You simply don’t know and have no way to know “new information”. See AIDS that was observed in 1981 but now is thought to have “originated in the early 20th century”. But who knows? They simply do not have the baseline information from before.

The article you quote is a generic “appeal to fear”. If it were true, mankind would have been long gone given the innumerable mistakes humans have made. But we live in a nonlinear universe (hence Nonlin): “…current trends are assumed to continue unabated, causing great misdirection of human energies. Positive feedbacks reinforce trends while negative feedbacks reduce and stop these trends. Observations of the Universe show that negative feedback always intervenes eventually to stop all trends, thus making our Universe nonlinear”. I suspect MRSA is misinterpreted, just like AIDS.

[jpm (Phil McCurdy)]

The resistant bugs may not take over, but there is some evidence that they thrive in sewage tr,eat meant plants etc. Evolution of course holds that if an organism has no advantage , then it may well die out in a new environment. If in a sewage plant, it may thrive

[NonlinOrg]

@gbrooks9

Is that Evolution or Devolution?

Good point. I don’t subscribe to either “evolution” or “devolution” …until demonstrated with a proper experiment, not children stories.

@benkirk

Do you not realize that the antibodies and T-cell receptors created during the adaptive immune response are clearly new?

Cells might be new, but the mechanism is built in, not “evolved”.

@Argon

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.

Interesting, but how is this different than your garden variety - built in - immune response? And where did the mix with “wild type” happened? In the same lab environment? As far as I know, antibiotic resistance goes away eventually.

[cwhenderson (Curtis Henderson)]

Sorry, @NonlinOrg, I skipped over the immunity question. @T_aquaticus gave a great, quick summary of the process that generates our tremendous array of antibodies. A similar process also occurs to generate a tremendous array of T-cell receptors. My answer (although you won’t like it) would be that my personal immune system is built-in as a result of evolution. I’m also a little fuzzy on how this relates to Lenski’s bacteria. Speaking of which:

@NonlinOrg

I hereby volunteer my kitchen, although you do understand my/your kitchen are also controlled environments just like Lenski’s lab.

I am absolutely NOT volunteering my kitchen for the E. coli experiment. Actually, you called my bluff! I wouldn’t set E. coli loose in your kitchen, either. I have a healthy respect for microbial evolution. Switching from a nice, warm 37 degree incubator to the 23 or so degrees of your kitchen would be a shock, not to mention the loss of the steady supply of nutrients. But I wouldn’t want to take my chances on some of those bacteria surviving, adapting, and then growing on a surface somewhere.

I’m really not sure what you are stating about antibiotic resistant bacteria. These are a serious and growing problem in health care facilities, AND infections caused by antibiotic-resistant bacteria are not confined to those facilities. MRSA outbreaks have occurred in NFL locker rooms on more than one occasion, and here is an example: (http://www.nfl.com/news/story/0ap3000000553694/article/mrsa-infection-leaves-giants-daniel-fells-in-dire-situation)

@NonlinOrg

I didn’t say " antibiotic resistance is a bad thing for a bacterium". Read again.

I read your comment on devolution, I guess I just need it explained to me. I assumed that devolution would mean genetic changes that result in a loss in fitness. Somehow, I never learned about devolution in my 28 years in biological higher ed…

[gbrooks9 (George Brooks)]

@cwhenderson

I read your comment on devolution, I guess I just need it explained to me. I assumed that devolution would mean genetic changes that result in a loss in fitness. Somehow, I never learned about devolution in my 28 years in biological higher ed…

@cwhenderson

I am of the hunch that Devolution is supposed to mean a “net loss” of genetic information. If so, then I would ask the following:

1. If we don’t know what all the genetic sequences are doing, if there is no visible loss to anatomy or to capability, how would anyone know whether there is a net loss or net gain?

2. If humans lose the genetic information for a primate tail, and gain the ability to walk upright, is that a net loss? Or isn’t it a net gain?

3. What’s wrong with the occasional Net Loss in genetic information? I’m pretty sure that human chromosomes have lost all sorts of traits - - that are useless to us in our new way of life.

Ultimately, my biggest complain is there is no way to “measure” information loss in an objective way, unless you are really counting the letters of the DNA. There are organisms that many might consider “primitive” compared to humans … with a lot more genetic information than human chromosomes, yes? Do we agree on this as a “factoid”?

So, loss of genetic information may be a pretty wonderful thing if its the right information to lose!