"Endless diversity" in bacterial genomes?

"...the conclusions the authors have come to regarding bacterial genetic diversity---that it may be 'endless.'"

Oh my gawd! There really are a couple billion monkeys typing away for a few billion years... but the typerwriter only has four keys, A, C, G and T.

It's time to say, "Thanks, Tara!" for a series of great posts over the last several days.

How clever of the Designer not to paint himself into a corner...

Where's NS in all of this? If there is an infinite diversity, then obviously NS is not operative--or else it would pick one over the other. Now if NS cannot act on bacteria, then how did bacteria evolve?

I await enlightened responses.

Where's NS in all of this?

Where's NS in all of this? If there is an infinite diversity, then obviously NS is not operative---or else it would pick one over the other. Now if NS cannot act on bacteria, then how did bacteria evolve? I await enlightened responses.

— Blastfromthepast

Blast, Blast, Blast. When will you learn that you need to invest the time and energy to actually gain some rudimentary understanding of this stuff before you launch once more into your open mouth, insert foot routine.

Mutatation generates variation. The diversity of life-forms is the expected result. Within any given amount of time, natural selection begins to winnow that diversity within any given niche of any given prevailing environment, but those niches and environments don't simply stand still as time marches on. Because both the variation generated by the life-forms and the variation-winnowing environment are moving targets, the fitness match between life-form and environment never reaches perfection.

Otherwise we wouldn't have a diverse biome in the first place, just one not-very-interesting species of slime covering one not-very-interesting ball of rock (if that; one suspects that overly-boring "environments" most likely don't give rise competing replicators in the first place).

Reality is messier than you might like. You can get used to it, or you can keep wishing that it will turn out to conform to your rather simplistic and boring fantasies, but you can't do both.

I have no idea how you go from your first statement to your conclusion that NS can't act on bacteria. Either I'm not seeing several steps in your logic, or you've bypassed them.

— Tara Smith

One pictures colonies of bacteria each evolving like mad to adapt to a few somewhat different (and changing) square millimeters of environment, and being able to do so indefinitely. Given enough difference in territorities, the right rate of change, and an extensive enough buffet of mutations to choose from, and it would be astounding if something totally novel did NOT evolve from NS at work.

Thanks, Russell--it's so much clearer now. :)

I'll only remark that "infinite" and "endless" are not synonyms.

RBH

http://www.m-w.com/cgi-bin/thesaurus?book=Thesaurus&va=infinite

Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes. (Bolding added)

Very true. I think I cribbed "endless" from one of the write-ups about this paper. The authors consistently use "vast" throughout the manuscript.

Blast, I'm not sure how NS acts here, but I did notice that if you magnify the image really really big, you can see an extremely clear image of Bill Dembski in the pupil of the bacteria's eye.

And, of course, an unspoken assumption in Blast's devastatingly incisive query is that all of these infinite sequences are equally represented in the population of S. agalactiae; in other words its genome is entirely random! Don't you see? Blast has just disproved evolution... again!

— Russell

"Vast" is neither "endless" (in the sense that we'll continue finding new ones no matter how long we look) nor "infinite" (in the sense that the number of existing unique genes is greater than any arbitrarily large number).

— RBH

Nonetheless, there is plenty that science can't explain. And if that annoys you, then maybe that's a sign you've made science your god.

Blast, why on earth should anyone care in the slightest about your uneducated uninformed opinions?

Nonetheless, there is plenty that science can't explain.

It's annoying for someone to imply that what science might explain someday can't be explained at all.

— Flint

Comment #51993 Posted by BlastfromthePast on October 11, 2005 08:56 PM (e) (s) Yes, science is an "all knowing" god.

BlastfromthePast asked: "Where's NS in all of this? If there is an infinite diversity,..."

There's not "infinite" diversity. You have to get used to the fact that sometimes biologists speak with a bit of poetic license. There is merely more diversity than they can get their heads around at the moment.

What it means is that for these bacteria is that the fitness landscape is not a lifeless desert with only a few oasis to survive in, but a raging jungle where many diverse gene sequences can survive. They can tolerate a lot of diversity and not get selected out. It means life is easy for them.

Comment #51929 Posted by BlastfromthePast on October 11, 2005 02:24 PM (e) (s) Where's NS in all of this? If there is an infinite diversity, then obviously NS is not operative---or else it would pick one over the other. Now if NS cannot act on bacteria, then how did bacteria evolve?

I estimate that Blast is about 18.

What it means is that for these bacteria is that the fitness landscape is not a lifeless desert with only a few oasis to survive in, but a raging jungle where many diverse gene sequences can survive. They can tolerate a lot of diversity and not get selected out. It means life is easy for them.

— Norman Doerring

I estimate that Blast is about 18.

— Steve S

Unlike your non-existent religious icon that explains and does nothing.

— Moses

Given how you talk, and what you don't seem to know about, I don't see any reason to believe that you have degrees in zoology and engineering. I'll stick with my guess that you're 18 until I see evidence otherwise.

Given how you talk, and what you don't seem to know about, I don't see any reason to believe that you have degrees in zoology and engineering. I'll stick with my guess that you're 18 until I see evidence otherwise.

— Steve S

Yeah, well, given your loopy comments about Integrals and such, I don't think it's worth my time trying to educate you. I'll let someone else waste his time trying to enlighten you.

BlastfromthePast "Spoken like a true Darwinist-------all metaphor and no substance."

My words were metaphors, but things like "fitness landscapes" while being metaphoric are still genuine and precise mathematics used evolutionary programming and genetic algorithms, not just biology.

http://en.wikipedia.org/wiki/Fitness_landscape

The term was coined by Sewall Wright:
http://en.wikipedia.org/wiki/Sewall_Wright

BlastfromthePast "There's an article out about missense mutations which points out that one missense mutation is almost the same as another missense mutation---outside the funtional sites."

Link the article so people know what you're talking about. What you're saying just looks dead wrong. Missense mutations or nonsynonymous mutations is where a nucleotide is changed which results in a different amino acid. This in turn can cause diseases such as Epidermolysis bullosa and sickle-cell disease. How can that be "almost the same as another" if some cause disease and others don't or different diseases.

What you're saying makes no sense.

BlastfromthePast "Again, mutations, sequences, permutations, all, basically outside the putative influence of NS."

That's just dead wrong. The ID people are lying to you.

BlastfromthePast "I used to think that RM+NS actually had a role in biology."

They do! Anyone who says different is lying to you or you have misunderstood.

BlastfromthePast "It now is starting to look as though there's no such thing as a 'random mutation,'"...

A better word would be unguided mutation, mutations have causes and there are other mechanisms at work changing the genome, but the randomness is seen in the pointless death and disease in organisms.

BlastfromthePast "... and, hence, that there doesn't appear to be much to NS to act on, meaning that NS is just some trite historical invention which will one day (very soon) be hoisted upon the dustheap of ideas."

Natural selection works outside of biology. It's why buggy whips and model-T Fords are now pretty much extinct. Natural selection even works on things designed by intelligent agencies.

You have so little idea about what you're talking about and you're being lied to on top of that.

You very clearly represent the tragedy of education ID causes.

Nice post Tara Smith. This is an interesting finding. As a pathogen microbiologist, I've always felt that the "species" definition is only weakly applicable to bacteriology in general. This casts an interesting shadow on the evo-ID debate. The IDists are always saying there are no transitional forms, but in the microbial world where the "species" (or "kind" as creationists like to refer to it) are so blurred, the vast continuum of genetic diversity we observe, along with our continuing elucidation of the fitness advantages of certain genes in select environments leaves little need for conjecture and extrapolation to see evolution taking place.

I don't know much about GBS S. agalactiae, but if it is anything like GAS S. pyogenes, the observation of genetic instability is not too surprising. If I remember correctly (and I may be mixing up my recollections from my basic path micro class, so correct me if I'm wrong), the group A's, which cause the well known strep throat, are individually extremely susceptible to the adaptive immune response. I'm not sure how Blast claims this is problematic for evolutionary thoery, but just as higher eukaryotes have evolved hypervariant proteins to recognize antigens, like antibodies and T-cell receptors, some pathogens have evolved hypervariant regions using different mechanisms. GAS M proteins, the outer surface that is presented the immune system, is a classic example of how genetic instabilit/hypervariance provide a selective advantage by preventing the mammalian herds from acquiring adaptive immunity to the organism. HIV is another example. It is likely that we will find many organisms that are susceptible to adaptive immunity in fact use extreme variance to evade the immune response.

Since Blast seems to have missed the implication of these findings I'll spell it out: we are observing the processes of mutation and selection causing significant genetic changes in real time (over only the last few decades in both Strep and HIV), and we have a pretty plausible theory regarding the fitness advantage conferred by such changes.

I'm flattered. But since I have a degree in zoology, and a degree in engineering, you'll agree that I'm just a little older than that.

— Blast

*************I'm still waiting for an enlightened response.************

Nice post Tara Smith. This is an interesting finding. As a pathogen microbiologist, I've always felt that the "species" definition is only weakly applicable to bacteriology in general. This casts an interesting shadow on the evo-ID debate. The IDists are always saying there are no transitional forms, but in the microbial world where the "species" (or "kind" as creationists like to refer to it) are so blurred, the vast continuum of genetic diversity we observe, along with our continuing elucidation of the fitness advantages of certain genes in select environments leaves little need for conjecture and extrapolation to see evolution taking place.

— sanjait

I don't know much about GBS S. agalactiae, but if it is anything like GAS S. pyogenes, the observation of genetic instability is not too surprising. If I remember correctly (and I may be mixing up my recollections from my basic path micro class, so correct me if I'm wrong), the group A's, which cause the well known strep throat, are individually extremely susceptible to the adaptive immune response. I'm not sure how Blast claims this is problematic for evolutionary thoery, but just as higher eukaryotes have evolved hypervariant proteins to recognize antigens, like antibodies and T-cell receptors, some pathogens have evolved hypervariant regions using different mechanisms. GAS M proteins, the outer surface that is presented the immune system, is a classic example of how genetic instabilit/hypervariance provide a selective advantage by preventing the mammalian herds from acquiring adaptive immunity to the organism. HIV is another example. It is likely that we will find many organisms that are susceptible to adaptive immunity in fact use extreme variance to evade the immune response.

,One thing about these organisms, though---they're not easily transformed. I can't tell you how long it took me to electroporate a stupid plasmid into a strain of GAS when I was a grad student. GBS is similar. So I have to wonder, are phage mediating most of this diversity? Or are there signals in their natural environments that make them more transformable? We've spent so much time studying gene regulation in pure cultures, hopefully we can move toward a more realistic model with all the new genetic toys and answer some of these questions.

— Tara Smith

Yeah, it's probably a little bit of both. I did a lot of transduction experiments with GAS and A25 phage to get random transposon knockouts, and those were always relatively easy.

RE: transformation of various streptococci and bacilli. Here's a naive question from someone who's never tried to transform any bacteria except E. coli. Are all gram-positives similarly resistant to transformation?

Nope. Streptococcus pneumoniae, for instance, is naturally transformable--and it's been hypothesized that's probably one reason why GAS and GBS remain almost universally penicillin-sensitive, while S. pneumo has long been resistant.

It's always amazing for me to come to fora where real scientists hang out and talk about their work. It's amusing to contrast the comments of the biologists with the anti-evolution trolls.

I'm de-lurking to prove that not all engineers are insular idiots. The underlying mathematical order in biology--the simple mechanisms that lead to all the complexity we see--is fascinating to me, and I appreciate people who write interesting stuff at the level of a reasonably intelligent layman.

Articles like this are cool, and serve to underscore the everyday importance of evolutionary theory for working biologists. I can't imagine having to contend with people who dispute the existence of Maxwell's equations; you all have my support and sympathy!

Hi Robert, and welcome to PT! I did not imply btw, that all engineers are "insular idiots"...just the DaveScot clones. [rant]Some days I just get tired and picture them as one Ãœber-Troll with maybe multiple personality disorder (for instance, evopeach has been overly aggressive and vitriolic lately...see the ARN threads). Agreed, science is so much more interesting in the long run, than random psychopathology.[/rant] ;-)

Streptococcus pneumoniae, for instance, is naturally transformable...

Hi Tara,

Great post!

A few questions, if you have the time:

How do you define a population of bacteria? Is the bacteria in one puddle the same population as the bacteria in the puddle two blocks down?

How rapidly can bacterial populations (such Streptococcus agalactiae) spread geographically?

Why is this vast diversity such a surprise? Considering a) the large total population of this bacterium, and b) that it is spread out across the planet in a vast numbers of populations, and c) how easily it adopts new genes, wouldn't it be more surprising if this diversity did not exist?

Shenda

"One thing about these organisms, though---they're not easily transformed. I can't tell you how long it took me to electroporate a stupid plasmid into a strain of GAS when I was a grad student. GBS is similar. So I have to wonder, are phage mediating most of this diversity? Or are there signals in their natural environments that make them more transformable? We've spent so much time studying gene regulation in pure cultures, hopefully we can move toward a more realistic model with all the new genetic toys and answer some of these questions."

"Tell me about it. Electroporation of Bacillus thuringiensis or protoplast transformation of B. subtilis is not exactly easy either...makes you long for lab strains of E. coli optimised for transormation."

I just have to concur for a moment. Our lab works on Mycobacteria, and they are no day at the beach either. They can transform, but the worst part is sequencing a knockout mutant afterwards. I guess other people can use ligated loops or hybridization to locate a transposon, but we use a fun method called nested suppression PCR, which is basically a semi-specific PCR voodoo ceremony with about a 5% unpredictable success rate. It could be worse I guess, the lab across from ours studies Chlamydia, which have no known methods for genetic manipulation. They just use the guess and check method with natural mutant phenotype isolates.

Regarding the issue of transformability in vivo: I don't know how an IDist perspective would tackle the issue of diversity in natural isolates, but thinking about the evolutionary origin of their diversity, there are at least 3 possibilites: 1. The variant genes in the pan-genome are the result of LGT events, which seems likely since you are talking about phages and such. There should be a genetic trace for this, in the form of similarity to other organisms, att sites, IS elements, etc. If this is the case, the organisms with which the genes share similarity should give clues to both the source and environement in which the transformations take place. 2. The bacteria creates novel genes through genetic instability. This seems unlikely offhand, but if the pan-genome appears paralagous but not homologous to other strep spp., that would support this hypothesis. 3. The isolates are all descended from a more complex organsims. In Mycobacteria, there are purely environmental species (e.g. M. smegmatis, opportunistic pathogens (e.g.M. avium, and obligate pathogens (M. tuberculosis and M. leprae). Generally, it appears as though the more pathogenic strains evolved from the less pathogenic, and in the process they lost a lot of genes. They gained a few virulence factors, but overall the pathogenic ones are quite a bit smaller. This hypothesis may not apply, as I don't know offhand the location of S. agalactiae on the bacterial tree or their degree of core gene similarity to each other (as in, are they really one "species"?), but if there are environmental ancestors this may apply.

I too appreciate informed discussion, and also notice how it contrasts sharply with IDists baseless conjecture and wordplay coupled with an utter lack of working knowledge. Every time I read a post from Blastfromthepast I just want to show him the NCBI BLAST server. And on that note, I should get back to my bench...

How do you define a population of bacteria? Is the bacteria in one puddle the same population as the bacteria in the puddle two blocks down?

How rapidly can bacterial populations (such Streptococcus agalactiae) spread geographically?

Why is this vast diversity such a surprise? Considering a) the large total population of this bacterium, and b) that it is spread out across the planet in a vast numbers of populations, and c) how easily it adopts new genes, wouldn't it be more surprising if this diversity did not exist?

Hi Tara,

Thank you.

I just have to concur for a moment. Our lab works on Mycobacteria, and they are no day at the beach either. They can transform, but the worst part is sequencing a knockout mutant afterwards. I guess other people can use ligated loops or hybridization to locate a transposon, but we use a fun method called nested suppression PCR, which is basically a semi-specific PCR voodoo ceremony with about a 5% unpredictable success rate. It could be worse I guess, the lab across from ours studies Chlamydia, which have no known methods for genetic manipulation. They just use the guess and check method with natural mutant phenotype isolates.

— sanjait

Regarding the issue of transformability in vivo: I don't know how an IDist perspective would tackle the issue of diversity in natural isolates, but thinking about the evolutionary origin of their diversity, there are at least 3 possibilites: 1. The variant genes in the pan-genome are the result of LGT events, which seems likely since you are talking about phages and such. There should be a genetic trace for this, in the form of similarity to other organisms, att sites, IS elements, etc. If this is the case, the organisms with which the genes share similarity should give clues to both the source and environement in which the transformations take place.

2. The bacteria creates novel genes through genetic instability. This seems unlikely offhand, but if the pan-genome appears paralagous but not homologous to other strep spp., that would support this hypothesis.

3. The isolates are all descended from a more complex organsims. In Mycobacteria, there are purely environmental species (e.g. M. smegmatis, opportunistic pathogens (e.g.M. avium, and obligate pathogens (M. tuberculosis and M. leprae). Generally, it appears as though the more pathogenic strains evolved from the less pathogenic, and in the process they lost a lot of genes. They gained a few virulence factors, but overall the pathogenic ones are quite a bit smaller. This hypothesis may not apply, as I don't know offhand the location of S. agalactiae on the bacterial tree or their degree of core gene similarity to each other (as in, are they really one "species"?), but if there are environmental ancestors this may apply.

Our data clearly show that the strategy to sequence one or two genomes per species, which has been used during the first decade of the genomic era, is not sufficient and that multiple strains need to be sequenced to understand the basics of bacterial species.

Not grouchy at all, and I'd guess that even the authors would mostly agree with you. They mention that their confidence intervals are huge, and I'd assume most people would take their figures with a grain of salt. But it still represents a push to change the way researchers see GBS, and hopefully there will be much less of the "a serotype II is a serotype II is a serotype II," or "we have the genome sequence already--why bother with more?" kind of thinking.

Link the article so people know what you're talking about. What you're saying just looks dead wrong.

— Norman Doerring

You've received many enlightened responses, to which you've closed your eyes and stuck your fingers in your ears and gone "la la la la la la."

— Moses

Natural selection works outside of biology. It's why buggy whips and model-T Fords are now pretty much extinct. Natural selection even works on things designed by intelligent agencies.

— Norman Doerring

Nice post Tara Smith. This is an interesting finding. As a pathogen microbiologist, I've always felt that the "species" definition is only weakly applicable to bacteriology in general. This casts an interesting shadow on the evo-ID debate. The IDists are always saying there are no transitional forms, but in the microbial world where the "species" (or "kind" as creationists like to refer to it) are so blurred, the vast continuum of genetic diversity we observe, along with our continuing elucidation of the fitness advantages of certain genes in select environments leaves little need for conjecture and extrapolation to see evolution taking place.

— sanjait

BlastfromthePast wrote: "This statement is embarrassingly indefensible. It even has a name: "Berra's Blunder". You can look it up in Icons of Evolution."

No it's not indefensible. For one thing, I'm not saying the same thing as Berra, and for another, Wells missed the point or lied about the point of Berra's metaphor. So you missed on two counts.

There's a reason we don't buy model-Ts that's different than why we don't buy old style Corvettes. The old style Corvette would still be about as functional as the new style but the model-T isn't. The model-T can no longer compete in the "natural" environment of human marketing desires. Any modern car would beat a model-T on all points.

If you doubt that, then practice what you preach and throw away your car and drive a model-T and then tell me it's as functional as a modern car.

I said: Natural selection works outside of biology. It's why buggy whips and model-T Fords are now pretty much extinct. Natural selection even works on things designed by intelligent agencies.

The point you don't yet grasp is that selection can operate independently from random mutation. The environment selects the most fit. That's so true it's almost just a tautology.

How can you deny selection, both natural and human, is beyond me.

As for the random -- well, if mutations aren't at least sometimes random then your designer God purposely gives horrible genetic diseases to many men and animals.

What Wells did with Berra was a dishonest form of quote mining.

Berra's analogy of the corvettes was used at the end of a section on human evolution and discussion of how evolutionary biologists piece together the fossil evidence to generate the hypothesized lineage of descent of homo sapiens. He used the Corvette as an example of how cars can be very similar or very different.

Here's the last paragraph from Berra's "Evolution and the myth of creationism" (just before the Corvette figure):

"...the accelerating pace of hominid fossil discoveries is truly dazzling. In darwin's time, only a few neanderthal remains were known, and they were misunderstood. today we have a whole cast of characters in the drama of human evolution. these fossils are the hard evidence of human evolution. they are not figments of scientific imagination. if the australopithecines, homo habilis and h. erectus, were still alive today, and if we could parade them before the world, there could be no doubt of our relatedness to them. it would be like attending an auto show. if you look at a 1953 corvette and compare it to the latest model, only the most general resembleances are evident, but if you compare a 1953 and a 1954 corvette, side by side, then a 1954 and a 1955 model, and so on, the descent with modification is overwhelmingly obvious. This is what paleoanthropologists do with fossils, and the evidence is so solid and comprehensive that it cannot be denied by reasonable people. there are quibbles about individual relationships, but each new discovery helps fine-tune our increasingly detailed knowledge of human evolution."

Regardless of whether think Berra made a "blunder" or not, what point do you think he was trying to make with the analogy?

Blast wrote:

"Please point out to me ONE such "enlightened response." Just one."

Post# 52001, 51989, 51934, 51933.

Just because you disagree with them does not make them invalid or "unenlightened".

Just because you disagree with them does not make them invalid or "unenlightened".

— shenda

Many species of bacteria are DNA scavengers, receiving new pieces of DNA via horizontal gene transfer. Some take these up easily--they are said to be "naturally transformable." With others, it's more difficult for new DNA to get in. In many cases, bacteriophages may bring new genes in when they infect a bacterium. However they're introduced, this sharing of genes in bacteria is an extremely common phenomenon. Anyone who is familiar with the phenomenon of antibiotic resistance knows that one way this can spread among organisms is via horizontal transfer of these genes, often on little bits of DNA called plasmids.

It's an appeal to use the "microbial" world to demonstrate "transitional" forms----------BUT.........., "the "species" definition is only weakly applicable to bacteriology in general." Do you see the contradiction here? Bacteria have all kinds of "transitional forms"; but a "transition" to what-------since you can't define a "species."

It's annoying for someone to imply that what science might explain someday can't be explained at all.

— Blast

Yes, science is an "all knowing" god.

So if a PATTERNED sequence of 1,000 nucleotides doesn't change a bacterium into something else, then how will a "single-nucleotide" change make a difference?

Second problem: This process cannot be totally random. Yes, there's a random element to it; viz., that the genetic material that is swapped from one particular bacterium with another bacterium is done at random. However, this process is deterministic---it follows some rules.

Third problem: Bacteria---I read this somewhere---have 80% of their genome that is stable, while 20% is constantly changing. If you suppose that NS is functioning to maintain the 80% stable, then what is happening to the other 20%? If NS is acting, then what is its verdict? What final form is the "best-suited" given the environment?

Fourth problem: If 20% of a genome is in constant flux, then it would appear that be the most likely candidate for evolving into a new, and different "life-form." And yet, bacteria remain bacteria, millenium after millenium. If one of the most simple of life-forms, with 20% of its genome constantly changing, can't "evolve" under the influence of NS, then what of more advanced and complicated life-forms?

the "possibility" of random sequence space---without chemically pre-ordained stopping points (i.e., without "favored" places in the probability space of bacterial genomes, as Dawkins imagines)---is indeed demonstrated

Your error is in believing that's a problem for evolution. It's not. It's a big problem for the Biblical concept of "kinds" though, isn't it?

— CJ O'Brien

See, your basline assumption is that, in order for there to be evolution, there has to be a "target," another species, that a given one is evolving "toward." But that's not the case. Organisms change. Lineages diverge.

— CJ O'Brien

Meanwhile, Blast seems to be saying "NS either explains ALL we see, or it explains NONE of it. Since it clearly doesn't explain everything, it is a useless illusion, QED."

— Flint

A single nucleotide change in the right place can in fact make the same difference.

— CJ O'Brien

"NS functioning to maintain..." simply means that alterations to that 80% are not selected for, meaning that a change in the genome at certain loci is almost certainly deletrious. We see the same effect in "higher" organisms and the conservation of early developmental pathways. NS "functions" by differential survival and reproduction. That's it. It's always operative where diversity exists that contributes to differential reproductive success. And again you're locked into "kinds." There is no "final form." Lineages diverge. Some are more fecund in a given environment. The descendants of those lineages will come to predominate in that environment. Rinse and repeat.

— CJ O'Brien

Bacteria are hugely successful organisms.

— CJ O'Brien

You lost me. I need a clarification of your objection here.

— CJ O'Brien

Good old Blast. Everytime he runs into an obstacle, he ignores it, bounces off, and heads off full tilt for the next obstacle, which he will smack into and ignore. He never actually gets anywhere, of course, but he sure does expend a lot of energy converting momentum into acoustic vibrations.

No one expects bacteria to suddenly mutate--in one micro or macro step, so don't do your usual dance with those prefixes, please!--into NONbacteria. Anymore than--to use the useful (for almost anyone but Blast, but then we're not really talking for his benefit) analogy of Berra's given above--we would expect the carts or chariots of old to suddenly change into elegant 17th Century French carriages or 1954 Corvettes. Or cats to turn into dogs.

What we do expect is what we actually see: 1954 Corvettes becoming 1955 Corvettes. Wild grasses becoming heavier-stalked wild strains becoming--over hundreds and thousands of years--domesticated grains. Bacterial strain A differentiating into strains A1-A8, and then into A1a-g, and then into ...

Does Blast really think the first archaic bacteria that started differentiating into eubacteria got there all in one step? Of course not, and somewhere in the cobwebbed attics of his mind, at least a few of his neurons must realize this. But a strain of archaic bacteria became a slightly-more-eubacteria-like strain. And, later, a strain of eubacteria became slightly more yeast-like. Or proto-yeast like, or whatever terminology jogs your jets.

(All without "knowing" where they were headed, or whether they were ever gonna get there, in a contingent universe, can we grok that simple idea, and hold it in mind with these two or three other simple ones, and then also try to juggle with the concept that two or three simple mechanisms interacting and reiterating, can generate highly complex resulting patterns? Or is that too much for the cobwebbed neurons?)

And then one strain of proto-yeast or proto-algae mutated to become a tad more like something that was going to eventually, after many more mutation and selection events, become something more like a multicellular plant or animal.

At this point, though, I always feel like someone shouting very slowly and very futilely at someone who speaks some different language entirely. We of course know, after many earlier replays of these same sorts of conversations with Blast, that no amount of evidence and no amount of explanation or argumentation, will ever drag those few mutinous neurons of his to the forefront of his mind.

Why? Not because the evidence is lacking or because the argumentation is, among reasonable open-minded persons, unconvincing. But because Blast is engaged, within the arena of his own mind, in a process of actively and incessantly suppressing what some few of his neurons, and the grat weight of the outside evidence, are trying to tell him.

And after a period of bafflement, internal struggle, and suppression, back Blast will come, like a windup toy surrounded by blocks he can't quite fit between, to begin bouncing off them all over again.

The entertainment value of watching this has begun to pall. It would simply be pitiful--and mean to make fun of--if it wasn't for that element of willful suppression of thought.

No, it's not a problem at all---it's "one" kind, i.e., bacteria, under many different forms.

without a target, bacteria just change, and change, and change---and they don't become gorillas.

A year ago I was quite comfortable thinking that NS could explain "microevolution." I'm no longer comfortable with that explanation.

can science "explain" why gravity exists? Science knows that it does exist. It can explain how it works. It can predict what it might do. But whence gravity? In a billion years, will science be able to determine whence gravity?

if an elephant produces only a small number of babies over its long lifetime, then how did it ever evolve when bacteria, that reproduce constantly, still remain bacteria.

in terms of fitness, if a mother with Tay-Sachs disease has seven children, and an Olympian athlete has two, who's the more fit?

(Of course, if you don't accept NS, then this argument fails. And hence his argument is ciruclar

But the fact that bacteria can't seem to "find" any such preferred sequences (i.e., the 20% keeps changing) implies that no such preference exists. You see, in fact you do need teleology.

'Course, then at least YECs retreat to "but they're still bacteria!," so apparently all bacteria are of one "kind" despite the extreme diversity at the DNA level, while humans and chimps, despite near 100% DNA identity, are obviously different "kinds."

— Tara Smith

And yet, here we have whole "genes" (1,000 nucleotides on average) being swapped, taken into an organism, and it's still a BACTERIUM!

— Blast

What if we define "kind" to mean all the descendants from a distinct abiogenesis event?

(Should I say "abiogenesis" or just "biogenesis" in that question?)

Henry

But two questions: if an elephant produces only a small number of babies over its long lifetime, then how did it ever evolve when bacteria, that reproduce constantly, still remain bacteria. And in terms of fitness, if a mother with Tay-Sachs disease has seven children, and an Olympian athlete has two, who's the more fit?

*slaps forehead* I've had meetings all day and have another one to get to in an hour, but thanks to everyone else for dealing with Blast's, um, "challenges."

— Tara

Blast, you know what "fitness" means, right? It's an average over a population.

— CJ O'Brien

Except, of course, for the once-bacteria that over a couple billion years DID become gorillas. But we won't count those. How about those bacteria that became eukaryotic at all? We won't count those either. This is like arguing that nobody ever leaves Dallas, because those who do aren't in Dallas anymore, and therefore don't belong to the population under discussion!

— Flint

Evolution by natural selection is a statistical phenomenon.

— Flint

And once more for the world! The bacteria that are still bacteria, are still bacteria. Those that were once bacteria but are no more would flat refute this repeated blind spot, which is probably why you simply refuse to credit this process. Nobody has EVER left Dallas, because 100% of the people in Dallas right now are STILL THERE! Absolute proof, according to Blast.

— Flint

Darwin didn't know about population genetics, and his was the "survival of the fittest." So, obviously, fitness also applies to individuals.

We know that eukaryotes and gorillas exist, and that bacteria exist. What we don't know is that RM+NS brought this about.

ID is a statistical argument refuting neo-Darwinism.

Dawkins effectively argues that this isn't possible, and that it isn't possible because preferences exist throughout this space, preferences---along the lines of your favorite analogy---allow organisms to "get out of Dodge." This finding about this type bacteria challenges Dawkins views---and his arguments about such space.

neo-Darwinism insists that single-nucleotide mutations can eventually bring about macroevolutionI must have missed that lesson in neo-Darwinist indoctrination camp. Can you cite a reference for that?

neo-Darwinism insists that single-nucleotide mutations can eventually bring about macroevolution

Russell beat me to it. Where on earth did Blast get that notion? It belies any tenuous claim he might have had that he knows something about the theory he criticizes. But as Casey Luskin and his leaders teach us, that's not a necessary qualification to shoot off one's mouth about evolution.

RBH

No, it's not a problem at all---it's "one" kind, i.e., bacteria, under many different forms.

Where in Genesis does it say God made bacterial kind? Genesis only talks about two groups (two kingdoms), plants and animals.

Where do you draw the line between bacterial kind and some other kind that's not bacterial? What makes this "kind" a kind distinct from another kind?

Ever wonder where the moniker "BlastFromThePast" might come from? My current hypothesis: It's Dave Cerutti (sp?) again, reliving the fun he had with "Admonitus".

OK, Dave. "Blast" has run his course. We've got to that Phil Hendrie moment where the fake assertions can't get any more absurd, and the audience either gets the joke, or it doesn't.

Just picked up on this thread, and in my haste to post a comment perhaps I've missed where this has been addressed....

Anyway, going back to Blast's original post:

The degree of genetic diversity is a problem for evolutionary theory how???

Did evolutionary theory ever claim to place an upper limit on the amount of diversity? Or does ID, um, "Theory" make a prediction as to how much diversity should be present? And if so, does it provide a better explanation of the phenonenon than does evolutionary theory?

Did it ever occur to you that the amount of diversity observed may be a consequence of the local variation in selective pressures operating at any given time? I guess not - BAM! It's instantly evidence for design, right?

It's obvious, Blast, that you didn't learn much in your school days, that is, if you indeed hold the degrees you claim. Possession of impressive-sounding credentials does not necesarily make for good thinking. Look at Duane Gish, my personal favorite poster child for Well-Credentialed Nincompoop.

As for the snideness of the comments, I (we) make no apologies. You are a moron and you deserve them.

Oh, and by the way, Blast:

Just how the hell do you define a "kind"?

What is the metric for deciding how far apart, genetically, two organisms must be before they are considered different "kinds"???

Or don't you bother with such a "pathetic level" of detail?

Spin this one, Blast:

http://www.msnbc.msn.com/id/9686843/
Reuters 10/23/2005:
Mysterious microbe retrofits itself with plant
One-celled organisms capture algae, perhaps taking evolutionary leap

Fondly, SP.

Oh, and a side note to Michael Behe, this new little beasty is--guess what!-- a flagellate! In fact, both the new bacteria and its algal symbiote are flagellates, and when one engulfs the other, the latter loses its marvelous little tail. How very odd!

Yes, this indeed appears to be your very, very most favorite "unevolvable" biological mechanism, captured in the midst of, um, evolving.

Of course, Mr. Behe, I'm sure the well-funded DI will now divert a little of its cashflow from PR and lawsuits, and will send you off pronto to do some actual scientific research into this interesting new development. Right?

Do keep us here at Panda's Thumb posted on the progress of the funding and outfitting of your research expedition (heck, I'm sure you wouold have already told us about this yourself, but you're probably too busy getting geared up--hey, we understand, this must be a pretty exciting moment for you!).

Of course, Blast, we here at PT realize that this newly-discovered bacteria--strange and novel as it seems at first glance--is still just one of that large and varied, but basically unitary, bacterial "kind". I mean, we certainly realize that, struggle as they might to evolve into something different and novel, bacteria are destined forever to remain just bacteria.

...However much this particular bacteria may enjoy giving its impression of simultaneously being a member of the, um, algal "kind".

But, what the heck, algae, bacteria, they're probably all members of that well-known super-"kind": bALGteria. Or is it bactALGAEia?

Well, anyway, I'm sure you know the kind I'm talking about.

Steviepinhead wrote: "Spin this one, Blast:...One-celled organisms capture algae, perhaps taking evolutionary leap."

If there ever is a new theory that accounts for the diversity of life and replaces Darwinism it won't be called "Intelligent Design," it will be called Margulism, after Lynn Margulis.

Figure out what that means, Blast - if you haven't run off.

Mysterious microbe retrofits itself with plant
One-celled organisms capture algae, perhaps taking evolutionary leap

Oh my god, that's so cool. I dig the microphotographs.

I must admit that, as a geologist/mostly geochemist/hard rock type, my biology is pretty basic, but I did take a biological oceanography class in grad school. We got one class period on whales and fish. I was shocked --- shocked! --- to find out that 90% of the class was about little planktons and bacteria because most of the biology in the oceans is about the tiny guys (not just eubacteria and archea but also the eukaryotic phytoplankton, and, well, we do have to count in the multicellular zooplankton). I recall getting very confused about how biologists can divide bacteria into species at all once I learned that they "share" genetic information back and forth within generations, i.e. that a bacterium could change its genome by snugging up to another bacterium and swapping some DNA. The new genome, then, is not the result of mutation but is passed to future generations. Am I recalling this correctly? Does this make the definition of species sort of irrelevant for bacteria?

I was also really horrified to find out that viruses leave their disgusting DNA in other people's cells (people being used in the sense of "kind", i.e. an arbitrarily sized grouping of organisms, in this case all cellular life).

Hanging around with biological oceanography types I have also over-heard them say things like "We've found more unknown bacteria in the last five years than all known marine bacteria, and we have no idea what they're doing out there." If I recall correctly, this is because hunting the wily bacterium is truly hit-and-miss as far as reproducing populations. Instead what they do is pull up a jug of water and look at all the DNA. Huge numbers of DNA sequences are recognizable as belonging to bacteria, but not known bacteria, and are sufficiently different from one another to be considered different species. Any general comments from the biologists?

If there ever is a new theory that accounts for the diversity of life and replaces Darwinism it won't be called "Intelligent Design," it will be called Margulism, after Lynn Margulis.

— Norman Doerring

Norman, would you like to read my copy of Acquired Genomes?

In fact, the kind of scenarios that Margulis talks about are fully consistent with ID.

ID doesn't say evolution didn't happen; it says that Darwin didn't get it right.

Lenny -- I should have guessed! This really is one of your favorite haunts, isn't it?

If there ever is a new theory that accounts for the diversity of life and replaces Darwinism it won't be called "Intelligent Design," it will be called Margulism, after Lynn Margulis. Figure out what that means, Blast - if you haven't run off.

Woops! Sorry. Misunderstood the conversation. Many apologies, Norman!

I guess that is what I get for coming-in in the middle.

Timothy Chase wrote: "It will be called just what it is called today --- the science of evolutionary biology."

Of course, I didn't replace that term -- I said Margulism would replace Darwinism. Mostly because Lynn Margulis might deserve an equal place of honor.

Question for all of you -- Is Darwin's "Origin of Species" even worth reading these days as a biology text (granting its an important historical text). Darwin was arguing without a lot of the information we now have and we can all point to more evidence that Darwin ever had. Don't we have better books now?

How far has the modern synthesis moved away from Darwin?

Lenny --- I should have guessed! This really is one of your favorite haunts, isn't it?