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Author
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Topic: Does Darwinism Predict the Absence of Irreducible Complexity?
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Argon
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Member # 276
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posted 27. September 2002 13:45
Yersinia wrote: [...]
Are you saying that you don't think there are any nonmotile microbes? Or perhaps, that there is no such thing as an ecological niche where motility would be selected against? [...]
Josh replies:
Why don't you cite a few? [...]
E. coli grown for many generations in shaker cultures tend to lose their flagella. Under such conditions this system is unnecessary and can impose a selectable cost to produce and maintain.
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yersinia
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Member # 324
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posted 27. September 2002 14:20
Hey Josh,
Well, that is a bit clearer. Presumably you are then arguing that nonmotile microbes exist because were not able to evolve the necessary IC structures? (Many of these guys are descended from microbes with flagella etc., so you would still have to explain why the loss occurred if you continue to maintain that motility is universally advantageous)
As per your request, here is one experiment where a nonflagellar form of motility (yes, nonflagellar motilies are quite common) was selected for in a certain environment and selected against in another environment.
This is a problem I and others have been trying to identify in this thread: selective advantage is not some abstract quality that is the same in all environments and which can be determined by thinking about it over breakfast -- rather, it is a relationship between a specific environment and organism which requires at least a bit of consideration of both in order to start drawing even tentative conclusions. Saying that natural selection should do X is like saying that the wind should do Y -- except at a very general level ("natural selection favors traits that maximize relative reproduction of the organism's genes" or for wind: "wind flows from high pressure to low pressure") more information is going to be needed to make predictions (both wind and natural selection are predictable in this latter fashion).
And of course, experiments are far better:
quote:
Velicer GJ, Lenski RE, Kroos L. Rescue of social motility lost during evolution of Myxococcus xanthus in an asocial environment. J Bacteriol. 2002 May;184(10):2719-27.
Replicate populations of the social bacterium Myxococcus xanthus underwent extensive evolutionary adaptation to an asocial selective environment (liquid batch culture). All 12 populations showed partial or complete loss of their social (S) motility function after 1,000 generations of evolution. Mutations in the pil gene cluster (responsible for type IV pilus biogenesis and function) were found to be at least partially responsible for the loss of S motility in the majority of evolved lines. Restoration (partial or complete) of S motility in the evolved lines by genetic complementation with wild-type pil genes positively affected their fruiting body development and sporulation while negatively affecting their competitive fitness in the asocial regime. This genetic tradeoff indicates that mutations in the pil region were adaptive in the asocial selective environment. This finding was confirmed by experiments showing that defined deletions of pil gene regions conferred a competitive advantage under asocial conditions. Moreover, an amino acid substitution in an evolved genotype was located in a region predicted by genetic complementation analysis to bear an adaptive mutation.
yersinia
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Josh
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Member # 405
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posted 27. September 2002 16:57
Frances-
"Intelligent design so far can explain anything and thus nothing. Unless ID can be restricted in some form or fashion it will not be able to produce workable and testable hypotheses."
--Since everyone here actively listens to the ID community, I guess we can wait to see how they do. Until then, I personally think they can explain something.
Argon
"E. coli grown for many generations in shaker cultures tend to lose their flagella. Under such conditions this system is unnecessary and can impose a selectable cost to produce and maintain."
This follows well with yersinia's posted article... see below.
"Well, that is a bit clearer. Presumably you are then arguing that nonmotile microbes exist because were not able to evolve the necessary IC structures?"
--I would be more inclined to say nonmotile microbes exist because God designed and created them to be up front. To give proof of this would be not possible at this point (besides other more qualified people are devoted to the problem), so I enjoy brainstorming on the idea. Within the specific context of my statements I would say that unless you can provide a niche that either negatively selects flagella/ IC motility systems, or does not offer any positive selection force for the adaptation of motility, you're statements are mere speculation. See below for discussion on the reference...
(Many of these guys are descended from microbes with flagella etc., so you would still have to explain why the loss occurred if you continue to maintain that motility is universally advantageous)
--How do you know this? References?
"As per your request, here is one experiment where a nonflagellar form of motility (yes, nonflagellar motilies are quite common) was selected for in a certain environment and selected against in another environment."
--The Key here is to consider exactly WHAT environment. See below.
"This is a problem I and others have been trying to identify in this thread: selective advantage is not some abstract quality that is the same in all environments and which can be determined by thinking about it over breakfast -- rather, it is a relationship between a specific environment and organism which requires at least a bit of consideration of both in order to start drawing even tentative conclusions. Saying that natural selection should do X is like saying that the wind should do Y -- except at a very general level ("natural selection favors traits that maximize relative reproduction of the organism's genes" or for wind: "wind flows from high pressure to low pressure") more information is going to be needed to make predictions (both wind and natural selection are predictable in this latter fashion)."
--True, so all current explanations have failed to take into consideration an extremely wide range of factors. Assuming the conditions I suggested and the proposed selective advantage of Motility IC structures, my conclusions are not unreasonable, even if early. In the end, we should be both unsatisfied with current explanations, and also remain equally open to competing theories!!!!
Velicer GJ, Lenski RE, Kroos L. Rescue of social motility lost during evolution of Myxococcus xanthus in an asocial environment. J Bacteriol. 2002 May;184(10):2719-27.
"Replicate populations of the social bacterium Myxococcus xanthus underwent extensive evolutionary adaptation to an asocial selective environment (liquid batch culture)."
--The question is, what kind of "selective environment" is "liquid batch culture" since both Argon and Yersinia like this experiment? Well, to look back at the material methods in the paper that described the original selection experiment (PNAS 95, 12376-12380, 1998):
"Selection Experiment. Six replicate clones of strain S and six of strain R were inoculated into flasks with 10 ml of CTT liquid (a rich medium composed mainly of free amino acids and short peptides) (30). These 12 lines were grown to stationary phase (32°C, 120 rpm) and diluted 100-fold into fresh medium. Such dilution transfers were performed daily, with the resulting regrowth requiring 6.6 (= log2 100) generations of binary fission per day. Culture samples from each line were stored frozen (80°C in 5% glycerol) after 1,000 generations (150 days) of growth."
These conditions match exactly what I previously referred to when discussing selection of motile organisms (quoting earlier post):
"Non-motile organisms must exist because either 1. They have unlimited resources from which to thrive, 2. Motility issues play no selection on them whatsoever. 1 is obviously not true and 2 makes no sense since it seems intuitive by the reasoning applied for the initial development of cilia and flagella: organisms gain benefit by being motile. Unless you describe ecological niches that gain no benefit by IC motility systems and correlate those niches to the organisms that occupy them (i.e. niche requires motility and contains only/predominantly motile organisms), your premise is highly speculative."
Here, the "rich medium composed mainly of free amino acids and short peptides" satisfies condition (1) that never exists in nature (unless you can provide references). At least I don't know of an ecological niche that is infinite in resources (cells grown to stationary phase and passaged daily into fresh rich medium can be called an "infinite resource" because these cells are replenished in a great abundance of rich resources every day!) These cells have become big fat slobs. Ask them to clean their act up, get a hair cut and a real job in the real world of competition and they'll lose (i.e. place them in a real ecological niche found in nature and they'll die- they aren't advantageous over anything than a situation only real in a laboratory controlled experiment designed by humans.) I would say they purposely designed the experiment this way going into this, their results are both unsurprising and expected. In fact ask the first cell to (literally) get a hair cut and a real job by evolving into a human over 4 billion years under these conditions and you will get nothing. Why do anything at all except the very basic functions required to grow and divide if all your supplies are given in a richly membrane-diffusable fashion? You don't even have to get off the couch to get the remote, much less swim anywhere. SURPRISE!! These organism divide faster and compete against one another more readily when they no longer have to take the resources required to produce motility structures. This is not impressive evidence for adaptation to an ecological niche, because the niche is manufactured.
Finally, a quote of the paper you posted illustrates my greater point clearly:
"Unfortunately, the ecology of M. xanthus in the wild is not well characterized. What are the precise contributions that M. xanthus social behaviors make to evolutionary fitness under various natural conditions? We know that, in the laboratory, social motility allows faster swarming on soft surfaces than does adventurous motility (36), but under what specific natural conditions does such gregarious motility confer an advantage (or disadvantage)? Also, what is the evolutionary benefit of maintaining a complex process of fruiting body formation when mutants exist (as we have found) that can sporulate without undergoing such development? Although these questions are beyond the scope of this study, our results do have some ecological implications. It is reasonable to assume that different natural populations of M. xanthus experience environments that differ in their growth regimes and physical structure. Our results suggest that natural populations which frequently encounter abundant resources or physically unstructured conditions are likely to exhibit lower levels of social cooperation than do populations that have adapted to resource scarcity or more structured habitats."
Notice that we can discuss the EVOLUTION of this organisms' ability to be motile without understanding anything at all about how the environment around it provides selective pressures that are overcome by whatever processes are being analyzed. So, assuming evolution everything else follows. I particularly enjoy the statement "our results suggest that natural populations which frequently encounter abundant resources or physically unstructured conditions..." which never happens to occur in nature (they supplied both conditions simultaneously, remove either condition and I'll place a bet that the results won't lead to the same conclusion). Not assuming evolution, what do we have here, perhaps a well-designed organism? Proposterous, I know! Hence my openness to ID theory and skepticism of evolution. Future data would change my mind, but now it doesn't seem like there's a convincing answer anywhere in sight (and the motility of this organism doesn't appear to be based upon some defined IC structure like the flagella).
Josh
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rafe gutman
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Member # 134
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posted 27. September 2002 17:01
quote:
by josh:
The conclusion I am leading to is that evolutionary "mechanisms" lack as much explanatory power as ID does when people complain about the fact that Dembski et al. won't say that God does X, Y, Z to install design into biological systems. Evolution refuses in many areas to identify X, Y, Z- just offers speculations and "This Must Be" because we exist, because non-motile and motile organisms exist, etc.
really? did you check out this thread? i, and several others put up probably a few pages of original text on what we thought was going on in the origin of the immune system. what explanations did the IDists offer in turn?
quote:
dembski:
As for your example, I'm not going to take the bait. You're asking me to play a game: "Provide as much detail in terms of possible causal mechanisms for your ID position as I do for my Darwinian position." ID is not a mechanistic theory, and it's not ID's task to match your pathetic level of detail in telling mechanistic stories. If ID is correct and an intelligence is responsible and indispensable for certain structures, then it makes no sense to try to ape your method of connecting the dots. True, there may be dots to be connected. But there may also be fundamental discontinuities, and with IC systems that is what ID is discovering.
this line of argumentation is getting tiresome. if you think that ID has explanatory powers equal to evolution, then why won't IDists propose models for the origin of molecular systems? it's clear they flatly refuse.
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yersinia
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Member # 324
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posted 27. September 2002 18:06
Josh,
This discussion is again becoming unfocused and turning into "general under-informed critique of evolution". E.g. ISCID poster and IDist Mike Gene would readily accept that many nonmotile microbes are descended from motile ones, so why should we go over such basic ground here?
E.g. the phylogenetic tree posted at Ken Jarrell's webpage clearly shows that the distribution of aflagellate archaea is scattered:
...and as losing structures is quite easy in evolution, the parsimonious assumption is that these losses have occurred multiple times, rather than the almost-exact-same flagellum has originated independently numerous times.
Since you will probably now question phylogenetic tree reconstruction, you should read this.
Regarding environments, sure, experiments are artificial by definition. But have you really thought very carefully about:
quote:
Here, the "rich medium composed mainly of free amino acids and short peptides" satisfies condition (1) that never exists in nature (unless you can provide references). At least I don't know of an ecological niche that is infinite in resources (cells grown to stationary phase and passaged daily into fresh rich medium can be called an "infinite resource" because these cells are replenished in a great abundance of rich resources every day!)
[...]
This is not impressive evidence for adaptation to an ecological niche, because the niche is manufactured.
Obviouly human experimenters aren't really infinite providers of resources either. What we're talking about is a regular mixing and replenishment of food. You may not be able to think of such a case happening naturally, but for a biologist it is a trivial question to answer: seashore ecosystems. The tides and waves wash in new nutrients at regular intervals. And probably, the same forces wash out loose bacteria. In such situations it is pointless to lolly-gag about wasting energy with flagella, it is much better to just secret some sticky glue and attach to a rock. Unsurprisingly, these kinds of situations are just where we find bacterial mats and slime and algae layers (which, last time I checked, did not spend a lot of time slithering around). I suspect there are a zillion other such cases -- e.g., soil in places where regular rainfall washes down nutrients.
Regarding understanding in-the-wild microbial ecology, I would readily agree that it is in a primitive state (for two main reasons: (1) microbiology is dominated by the study of diseases in organisms, not the study of free-living critters, and (2) you can't observe bacterial behavior by going for a walk in the woods with your binoculars; their small size almost requires study via experiment). However, you exagerate when you say that "nothing" is known. There is, for example, a large literature on microbes that assemble into group fruiting bodies and the conditions under which this occurs (e.g., starvation).
quote:
I particularly enjoy the statement "our results suggest that natural populations which frequently encounter abundant resources or physically unstructured conditions..." which never happens to occur in nature (they supplied both conditions simultaneously, remove either condition and I'll place a bet that the results won't lead to the same conclusion).
Again, not really true. Ever heard of cyanobacteria blooms? They happen in open water infused with nutrients, e.g. an upwelling current. Cyanobacteria IIRC don't have flagella, they keep from sinking by a passive method involving internal floats made of proteins that exclude water and thus lower density. Another exception to the "Motility is Always Good" supposition being promoted in the thread.
One more piece of evidence that microbial motility is not always advantageous is based on the physics of Brownian motion: turns out that if you're too small, it's impossible to overcome the jostling of brownian motion:
quote:
Dusenbery DB. Minimum size limit for useful locomotion by free-swimming microbes. Proc Natl Acad Sci U S A 1997 Sep 30;94(20):10949-54
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA. david.dusenbery@biology.gatech.edu
Formulas are derived for the effect of size on a free-swimming microbe's ability to follow chemical, light, or temperature stimuli or to disperse in random directions. The four main assumptions are as follows: (i) the organisms can be modeled as spheres, (ii) the power available to the organism for swimming is proportional to its volume, (iii) the noise in measuring a signal limits determination of the direction of a stimulus, and (iv) the time available to determine stimulus direction or to swim a straight path is limited by rotational diffusion caused by Brownian motion. In all cases, it is found that there is a sharp size limit below which locomotion has no apparent benefit. This size limit is estimated to most probably be about 0.6 micron diameter and is relatively insensitive to assumed values of the other parameters. A review of existing descriptions of free-floating bacteria reveals that the smallest of 97 motile genera has a mean length of 0.8 micron, whereas 18 of 94 nonmotile genera are smaller. Similar calculations have led to the conclusion that a minimum size also exists for use of pheromones in mate location, although this size limit is about three orders of magnitude larger. In both cases, the application of well-established physical laws and biological generalities has demonstrated that a common feature of animal behavior is of no use to small free-swimming organisms.
I'd say that this is game, set, and match on this particular issue. Active motility, like just about everything else, is not a Universal Good for microbes.
quote:
and the motility of this organism doesn't appear to be based upon some defined IC structure like the flagella
If flagella are IC, then twitching motility is also because the twitching system has the same basic components as the archaeal flagellum.
yersinia
PS Josh: One reason this discussion is confusing is that you're not using quote tags...if you want to quote stuff to reply to, type (quote) before and (/quote) after the quote, except use square brackets instead of round ones. Why UBBs don't use [q][/q] I don't know...
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Argon
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posted 27. September 2002 18:19
Regarding Yersinia's post about M.xanthus and the conditions necessary for selecting non-motility in bacteria:
Josh wrote: [...]
quote:
These conditions match exactly what I previously referred to when discussing selection of motile organisms (quoting earlier post):
"Non-motile organisms must exist because either 1. They have unlimited resources from which to thrive, 2. Motility issues play no selection on them whatsoever. 1 is obviously not true and 2 makes no sense since it seems intuitive by the reasoning applied for the initial development of cilia and flagella: organisms gain benefit by being motile. Unless you describe ecological niches that gain no benefit by IC motility systems and correlate those niches to the organisms that occupy them (i.e. niche requires motility and contains only/predominantly motile organisms), your premise is highly speculative."
Here, the "rich medium composed mainly of free amino acids and short peptides" satisfies condition (1) that never exists in nature (unless you can provide references). At least I don't know of an ecological niche that is infinite in resources (cells grown to stationary phase and passaged daily into fresh rich medium can be called an "infinite resource" because these cells are replenished in a great abundance of rich resources every day!) [...]
Josh,
E. coli lose flagella in chemostat cultures as well. That is, they'll lose their motile ability in minimal, nutrient-limited growth conditions as well as in "rich" media. The common factor in the cases of E.coli & Mixococcus losing their motility is actually growth in liquid culture, not "unlimited resources". Non-motile bacteria are distributed among all the major banches of the eubacteria (similar to the archaebacterial example provided by Yersinia) and so this is nothing shocking to find in these two instances. What is interesting is that M.xanthus and E. coli are both gram-negative bacteria of the Purple group (M.xanthus is in the Delta purple subgroup while E.coli is in Gamma purple supgroup). M.xanthus has apparently aqcuired a new mechanism for active movement since these groups split.
Why use so "rich" a medium for M. xanthus? Well, that's what they need to reproduce. Many bacteria are rather finicky about what they'll eat. Most remain unculturable today. But far from being something that never exists in nature, short peptides, amino acids and complex polysaccharides are found in many organic environments. Take any decent soil (under some trees is pretty good), perform an extraction and run the extract through an amino acid analyzer. You'll see peaks corresponding to amino acids and peptides. Free amino acids and peptides are also what you'll find when you lyse and digest bacteria, fungi & algae -- Which is exactly what Mixococcus does. One of the social behaviors of M.xanthus is to "hunt" other micro-organisms for food. When they can't find bacteria to munch they still secrete all sorts of hydrolyses to break down the various organic polymers found in their typical environment. Give Thomas Brock's _Biology of Microorganisms_ a read sometime.
And now a M.xanthus digression:
Several years ago a couple grad students at Stanford U. decided to stage a Celebrity Death Match-like event between C. elegans (a worm) and M. xanthus. Both these organisms hunt bacteria for food and these students, obviously with too much time on their hands, decided to see which species would "win" if they put both in the same petri dish.
They dropped a small culture of M.xanthus in one side of the plate. Then they placed some C. elegans on the other side. After waiting for a very long time (neither of these organisms are particularly speedy), they observed the C. elegans worms trying to flee from the petri dish.
As one of the students described the results: Dude, Mixo rules!!!
[ 27. September 2002, 18:25: Message edited by: Argon ]
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Jesse
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posted 27. September 2002 21:01
It seems to me that we don't have to go to "ancient" systems to find things that qualify as irreducibly complex. In fact irreducible complexity seems pretty ubiquitous--virtually any novel complex system could probably be seen as qualifying. One example that I've seen which I like a lot is the venus flytrap, a biological "mousetrap" if ever there was one. In this case it seems to have evolved through loss of redundant parts (sometimes called 'scaffolding', although that term is a bit teleological-sounding)...probably the venus flytraps' ancestors used "glue" to catch insects as well as the leaf-snapping mechanism, which meant that even a poor leaf-snapping mechanism would not prevent the ancestors from surviving because the glue would still capture insects. But once the glue disappeared, the system looks irreducibly complex, because any venus flytrap that does not snap its leaves shut very quickly would almost certainly not catch enough insects to survive.
I think virtually any other complicated innovation could probably be seen as irreducibly complex, given the correct choice of function and parts. I've argued on ARN that wings are irreducibly complex--without the preexisting system of bones, muscles, nerves and circulatory system that originally evolved for more forgiving tasks than flight, like paddling in the water and shuffling on land (co-option) it is very hard to imagine evolving wings from scratch in a gradual way, since early stages would not be able to fly at all. Likewise all sorts of organ systems, like the respiratory system or the circulatory system, are probably irreducibly complex in the sense that if you removed certain "parts" from the system in an adult organism, the system would simply fail and the organism would die. Even certain symbiotic relationships seem to be irreducibly complex, like flowers which are only capable of pollinating with the help of insects. This again seems to have occurred partly through loss of function, since there are other flowers that pollinate using the wind, but these flowers have lost the ability since they don't need it (just like the venus flytrap and glue). And of course co-option was also involved, since flying insects that like nectar just happen to have provided some advantage to wind-based pollinators.
Finally, there are a number of genetic algorithms which seem to have resulted in irreducibly complex structures. Here are some pages on an interesting experiment by Adrian Thompson, using evolving circuits that learned to discriminate between two tones, eventually resulting in a system with very few components, each of which was essential to the functioning of the system:
http://classes.yale.edu/math190a/Fractals/CA/GA/GACircuit/GACircuit.html
quote:
Thompson's FPGA has 100 logic cells, and the best program has each of the cells doing something. But only 32 were doing something necessary to distinguish the signals. (Note there was no fitness benefit for a smaller circuit.) This is about 1/10 the number of logic cells used by the most efficient human-designed discriminators. The circuit still worked if the other 68 were removed. However, 5 of the 32 were not directly connected to the output, but when any one of these was removed, the circuit stopped working. The program appears to have discovered a subtle inductance effect between logic cells, an effect not used by human designers.
(probably the route to IC here was based mostly on loss of redundancies, but there also seems to have been some co-option in the way the system took advantage of an 'inductance effect' which originally was just a 'spandrel' of the way the logic cells were built)
Some other pages on this experiment:
http://www.newscientist.com/hottopics/ai/primordial.jsp
http://www.cogs.susx.ac.uk/users/adrianth/ascot/paper/paper.html
http://www.glendhu.com/ai/neuralchips/sussex.html
And another similar experiment with evolving logic cells resulted in a circuit that functioned as a radio, also based on co-option (it was supposed to function as an oscillator, but it did so by picking up oscillating signals from a nearby computer):
http://www.newscientist.com/news/news.jsp?id=ns99992732
In short I don't think IC should be seen as some sort of special or unusual result of Darwinian evolution...in fact it seems to be fairly inevitable and commonplace. The main thing that's notable about "ancient" systems like the flagellum is not that they're IC, but just that we have less idea about what possible precursors to the system could have looked like, unlike in cases such as bird wings or venus flytraps.
[ 27. September 2002, 21:07: Message edited by: Jesse ]
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Mike Gene
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posted 28. September 2002 09:05
Argon: E. coli grown for many generations in shaker cultures tend to lose their flagella. Under such conditions this system is unnecessary and can impose a selectable cost to produce and maintain.
Could you please cite some references for this. I'd really enjoy looking at this in more detail.
Andy and RBH,
It will be my pleasure to respond to your lasting postings. I just never have the time these days so my reply might be posted anywhere from tomorrow until 3 months from now. ![[Smile]](smile.gif)
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Argon
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posted 28. September 2002 09:47
Argon: E. coli grown for many generations in shaker cultures tend to lose their flagella. Under such conditions this system is unnecessary and can impose a selectable cost to produce and maintain.
Mike Gene:
Could you please cite some references for this. I'd really enjoy looking at this in more detail.
Frederick C. Neidhardt, personal communication, approx. 1991 (at the 1st E. coli Genomic Meeting in Madison, Wisconsin). Fred is very approachable and is the closest thing to a walking encyclopedia on E. coli I've encountered. Contact info here. I think there could be other conditions in which E. coli flagella are selected against but I can't recall (viral attachment?).
Since you are interested in flagellar references and sequence variability, here's an interesting one I just ran across wrt Campylobacter. The authors found that Campylobacter carry two sets of flagellin genes, possibly for antigenic phase variation ("stealth mode").
Meinersmann RJ, Hiett KL. Concerted evolution of duplicate fla genes in Campylobacter. Microbiology. 2000 Sep;146 ( Pt 9):2283-90. PMID: 10974116
[ 28. September 2002, 09:56: Message edited by: Argon ]
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Mike Gene
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posted 29. September 2002 21:18
Hello Andy,
You originally wrote: I think the difficulty in labeling things as "machines" is that one can get into knots working out what the "parts" are, and whether some combination of "parts" within a "machine" represent a "machine" in their own right. For example, an automobile is a machine by at least one of the above definitions, but consists of a whole series of different sub-machines as well. An automobile is clearly not IC - the engine can function perfectly, even if the brakes are shot - so how do we define "machine" such that machines "are IC by definition"? I hope Mike can share his feelings on this issue.
Well, I don't have any feelings to share. But I can try to clarify what I meant. Perhaps I should not have suggested that "machines are IC by definition." A better way to put it is that embedded in all functional machines is some type of IC-core. Let me expand on this.
Yes, defining things can often tie us into knots. Whether it's 'life,' 'species,' 'homology,' 'evolution,' 'science,' 'design,' or 'machine,' we often find ourselves in fuzzy domains when certain specific questions are put to any definition. Nevertheless, and for starters, we can work with Albert's description from his 1998 Cell essay:
quote:
But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules.
The key word is "assembly." Molecular machines are protein assemblies (which is not to say that all protein assemblies are molecular machines). Like machines invented by humans, the components are first synthesized and then assembled into a whole. The assembly itself is the key, as it entails a meaningful fit of multiple parts, where meaningful can be thought of as the specific assembly that confers functional output. The key is the functional output is assembly-dependent. This is the IC core.
Go back to your car. If the function of the car is to transport people safely over certain distances and for certain periods of time, then it becomes clear that embedded within the car is an IC system. Take away the wheels and the engine and transmission function fine. Yet as far as the core function is concerned, a car without wheels works as well as a car without wheels, engine, and transmission. You say that a car is not IC because the engine functions well even if the brakes don't. But the engine is not the car.
I'm not quite sure why any of this would be controversial. The point is simply that machines do specific things because they integrate multiple, independent parts. This machine function is then dependent on all parts working together. Take away any one "cog" in the machine and it breaks down. And yes, we can quibble about what parts mean, but unless this quibbling leads us all to embrace a one-part machine, I don't see its relevance to my point (i.e., my response to Frances' claim).
The discussion about myoglobin/hemoglobin is interesting in its own right, as if the fact that the type III system probably evolved from the flagellum. But I'm afraid I don't see their relevance to my point either (and I don't have the time to spin off in various different directions, although I would enjoy this tremendously).
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andyg
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posted 30. September 2002 14:46
Quoth Mike Gene:
quote:
The discussion about myoglobin/hemoglobin is interesting in its own right, as if the fact that the type III system probably evolved from the flagellum. But I'm afraid I don't see their relevance to my point either (and I don't have the time to spin off in various different directions, although I would enjoy this tremendously).
The whole point of labeling something as IC is to suggest that it is unlikely to have evolved, and/or to suggest that it was likely designed. If the concept of IC has any other use, I'd be interested to hear what it is.
My point in raising haemoglobin and myoglobin was to show that we have two systems, both arguably IC, and compelling molecular phylogeneitc evidence that one evolved from the other. That seems to cut to the heart of whether IC is a useful concept in thinking about the origin of biochemical systems.
The issue of the flagellum and secretory systems was meant to address your point that
quote:
That is, structural constraints that come from participating in a particular machine may prevent that component from playing any other meaningful biological role.
Regards,
AndyG
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Josh
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posted 30. September 2002 17:06
Here I will try to practice the quote technique (thanks for the tip)...
quote:
Again, not really true. Ever heard of cyanobacteria blooms? They happen in open water infused with nutrients, e.g. an upwelling current. Cyanobacteria IIRC don't have flagella, they keep from sinking by a passive method involving internal floats made of proteins that exclude water and thus lower density. Another exception to the "Motility is Always Good" supposition being promoted in the thread.
--You are arguing a strawman, I never said there aren't counter-examples to the claim that "motility is always good." In fact I was questioning the existence of these counter examples and my argument was constructed quite differently. I asked the reason for these examples to exist and for correlative evidence supporting such an argument, you have provided nothing along those lines. Skip microbial size issues, etc. I understand well that there are non-motile creatures.
quote:
If flagella are IC, then twitching motility is also because the twitching system has the same basic components as the archaeal flagellum.
I was referring to M. Xanthus, I thought it was crawling and using social behaviors to move, did I miss something?
quote:
But far from being something that never exists in nature, short peptides, amino acids and complex polysaccharides are found in many organic environments. Take any decent soil (under some trees is pretty good), perform an extraction and run the extract through an amino acid analyzer.
Another strawman, I never suggested that amino acids and short peptides cannot be found in nature. If you think soils are an equivalent environment to this experiment, I have nothing to say about it anymore.
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Several years ago a couple grad students at Stanford U. decided to stage a Celebrity Death Match-like event between C. elegans (a worm) and M. xanthus. Both these organisms hunt bacteria for food and these students, obviously with too much time on their hands, decided to see which species would "win" if they put both in the same petri dish.
Perhaps C. elegans are picky eaters and didn't like the taste of M. xanthus? ; )
Anyways, Does any of the evidence y'all are posting convince you that evolution has the capability of producing apparent IC structures whenever they are needed, which is something I expect from the theory itself. Nothing that has been said shows me that billions of years and generations of organisms should not have produced a plethura of IC systems for any given task the cell needs to perform, as opposed to evolution deriving structures that appear IC in nature, but are highly adaptable for numerable tasks in each organism available.
Josh
[ 30. September 2002, 22:29: Message edited by: Josh ]
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Mike Gene
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posted 01. October 2002 08:39
Andy: The whole point of labeling something as IC is to suggest that it is unlikely to have evolved, and/or to suggest that it was likely designed. If the concept of IC has any other use, I'd be interested to hear what it is.
My argument was a reaction to a specific claim proposed by Frances. Simply reread the context of my reply.
Andy: My point in raising haemoglobin and myoglobin was to show that we have two systems, both arguably IC, and compelling molecular phylogeneitc evidence that one evolved from the other. That seems to cut to the heart of whether IC is a useful concept in thinking about the origin of biochemical systems.
First we'd have to establish that hemoglobin and myoglobin are IC. But we can sidestep
this issue by simply focusing on the evolution of the former from the latter. Essentially, gene duplication, followed by adaptive tweaking, turned an oxygen-binding protein into a somewhat more complex oxygen-binding protein. Are you suggesting all IC machines are expanded (by duplication), complex versions of a simpler one-gene core, where the original stem gene carries out the same basic function as the 10-part machine? Unless that is where you are going, I'm afraid the example you provide is a very blunt cutter that gets nowhere near the heart.
The issue of the flagellum and secretory systems was meant to address your point that "That is, structural constraints that come from participating in a particular machine may prevent that component from playing any other meaningful biological role."
Yes, I said such constraints may prevent this. One counter example does not really address my point.
Besides, your counterexample is interesting. Already embedded within the flagellum is a secretory machine, such that the type III system (which likely evolved from the flagellum) can be viewed as a stream-lined flagellum. It is interesting that the example you chose to address my point actually seems to underscore it, as the meaningful role played by the type III systems is already inherent in the flagellum - there is evidence that flagella themselves secrete virulence factors.
What is the typical fate of flagellar genes when one gene is rendered functionless by a mutation?
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andyg
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posted 01. October 2002 16:44
Quote from Mike and Andy:
quote:
Andy: My point in raising haemoglobin and myoglobin was to show that we have two systems, both arguably IC, and compelling molecular phylogeneitc evidence that one evolved from the other. That seems to cut to the heart of whether IC is a useful concept in thinking about the origin of biochemical systems.
Mike: First we'd have to establish that hemoglobin and myoglobin are IC. But we can sidestep
this issue by simply focusing on the evolution of the former from the latter. Essentially, gene duplication, followed by adaptive tweaking, turned an oxygen-binding protein into a somewhat more complex oxygen-binding protein. Are you suggesting all IC machines are expanded (by duplication), complex versions of a simpler one-gene core, where the original stem gene carries out the same basic function as the 10-part machine? Unless that is where you are going, I'm afraid the example you provide is a very blunt cutter that gets nowhere near the heart.
I hope the moderator will indulge me a post in which I quote the above and append a simple question. I am doing this to refocus the discussion:
Mike, why do you consider IC to be a useful concept in thinking about the origin of biochemical systems?
AndyG
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Argon
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Member # 276
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posted 01. October 2002 17:05
Josh writes (to me - Argon):
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Another strawman, I never suggested that amino acids and short peptides cannot be found in nature. If you think soils are an equivalent environment to this experiment, I have nothing to say about it anymore.
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Equivalence was not the issue. The question I addressed above was whether one finds "natural" growth conditions rich in free amino acids and short peptides.
Specifically, Josh wrote earlier:
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Here, the "rich medium composed mainly of free amino acids and short peptides" satisfies condition (1) that never exists in nature (unless you can provide references). At least I don't know of an ecological niche that is infinite in resources (cells grown to stationary phase and passaged daily into fresh rich medium can be called an "infinite resource" because these cells are replenished in a great abundance of rich resources every day!) These cells have become big fat slobs.
Note: Condition (1) was: "They have unlimited resources from which to thrive"
Points of fact:
- Mixococcus xanthus is indeed found in areas rich with organic matter (and prey bacteria) -- including dung heaps. An environment rich in amino acids and short peptides is definitely something that may be found in nature. Cells in nature are indeed passaged through stationary phase and replenished with fresh media (or in this case, warm doo-doo). If this ever failed to happen, M.xanthus would go extinct.
- M.xanthus *requires* those particular medium components for growth.
- Those cells were not "big fat slobs". They were under fairly stringent selection -- competing *directly* against each other. For continuous cultures of growing cells, it is pretty easy to calculate that those cells with even slight advantages in reproduction eventually "take over" the culture.
Finally Josh writes:
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Anyways, Does any of the evidence y'all are posting convince you that evolution has the capability of producing apparent IC structures whenever they are needed, which is something I expect from the theory itself.
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Sorry for any confusion but this wasn't the point of my replies in this thread. I was discussing a rather narrow issue. Josh requested information about niches where motile systems could face negative selection. Those were provided.
[ 03. October 2002, 19:23: Message edited by: Argon ]
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