Grist for The Matrix
by MikeGeneIt will be fun to discuss something like this from within The Design Matrix:
Microtubules, essential structural elements in living cells, grow stiffer as they grow longer, an unexpected property that could lead to advances in nano-materials development, an international team of biophysicists has found.
["¦]
To the surprise of the scientists, they found that the longer the filament, the more rigid it became.
Florin and his coauthors attribute the microtubules' unique properties to their molecular architecture. The nanometer-sized filaments are hollow tubes made of tubulin proteins that bind to each other in ways that give them the ability to be both flexible and stiff. Flexibility is important for microtubules as they grow and change in cells, while rigidity is important when cells need support.
"Microtubules are optimally designed to give the maximum of mechanical performance at a minimum cost for the cell," said Francesco Pampaloni, a physical chemist at EMBL.
The new finding about the microtubules' properties could provide insights into using the filaments as models for the development of nano-materials.
July 12th, 2006 at 2:17 am
""Microtubules are optimally designed to give the maximum of mechanical performance at a minimum cost for the cell," said Francesco Pampaloni, a physical chemist at EMBL. "
What? "Optimal design???"
Well, we can at least be certain of one thing: "evolution" "designed" this optimal design.
Comment by Ilion — July 12, 2006 @ 2:17 am
July 12th, 2006 at 9:28 am
No. No. No. This cannot be evolution. It's that small little word "to" that causes all the problems. It's a placeholder, you know. Seemingly innocent. But what does it mean in the context of what is stated?
Microtubules are not optimally designed to do anything at all. They just happened, that's all (or rather their precursors did). Sheer, blind, dumb, luck. And they (on their way to becoming microtubules) just happened to provide some sort of advantage which could be reflected in reproduction, thanks to the fact that their appearance on the scene just happened to be in an environment conducive to their just happening to confer a reproductive advantage. And this reproductive advantage just happened to operate over an extended period of time. And the population(s) carrying the fortuitous new mutant strain just happened to not go extinct. And by some lucky accident, the process repeated itself, over and over. Luckily. Until today we have, what we call microtubules. After which, evolution seems to have come to a halt. Having just happened to have stumbled upon this "optimal design." Can someone tell my how to distinguish this fortuitous sequence of events from a miracle?
Of course, I could be wrong about one thing. perhaps they just happened to have spread through the sheer dumb fortuitousness of random genetic drift. We just don't know.
And you're going to tell me design isn't a better explanation? What sort of explanation is "it just happened, that's all?"
However, I am willing to grant for the sake of argument, that in a world of sheer blind random dumb happenstance there will be people who think this was all the result of sheer blind random dumb happenstance, rather than design.
Comment by Mung — July 12, 2006 @ 9:28 am
July 12th, 2006 at 10:24 am
Can someone tell my how to distinguish this fortuitous sequence of events from a miracle?
We can't observe the process directly, so we'd need to guess based on what happens today.
First we count the number of times that we see similarly-complex natural structures springing into existence in a single generation due to the intervention of some unknown designer. Next, we count the number of times that we see non-optimal complex structures changing into more-optimal forms due to mutation and selection.
So if we see, say, 60 incidents of design and 40 incidents of evolution, then we can say that it's 60% likely that cellular microtubules were designed. Of course this is just a first attempt at a guess. It might be that design incidents were more common or less common in the past. At some point we'll want to get information about the designer so that we can understand what sort of features are likely to get designed.
Comment by chaosengineer — July 12, 2006 @ 10:24 am
July 12th, 2006 at 10:48 am
Hi Mike,
Could you please offer a definition of 'optimal' as you ascribe it to biotic structures? I'm wondering how we determine that something is so perfectly formed that it cannot be improved upon. What is the criteria?
Comment by chunkdz — July 12, 2006 @ 10:48 am
July 12th, 2006 at 12:28 pm
chaos:
"Process?" Surely you don't mean trying to envision a Neodarwinian acquisition [via RM-NS] for these particular structures [alpha-beta tubulins, MT associated proteins, operative depolymerization enzymes, etc. - which are evolutionarily conserved and necessary to such functions as oogenesis and embryonic development. Because the current "best guess" on origin in eukaryotic cells is symbiosis, not RM-NS [Margulis, 1975; Margulis and Sagan, 1995].
Check out current database particulars at iHOP, evolutionary conservation for microtubule architecture, MT enzyme conservation and listed sub-references. Microtubules have been studied for a relatively long time (genetically/structurally and functionally speaking), so a lot is known.
This is a case of a biological design that is in fact a design, in that the functions served can only be served by the particular design - variation is not well tolerated (because sterile and/or never-born organisms don't contribute to evolution). Microtubules thus qualify as 'optimal' designs.
Comment by Joy — July 12, 2006 @ 12:28 pm
July 12th, 2006 at 1:07 pm
Chuckdz:
It wasn't Mike who used either of the words: 'design' or 'optimal.'
To wit:
Comment by Ilion — July 12, 2006 @ 1:07 pm
July 12th, 2006 at 1:11 pm
Besides which, 'process' is YET ANOTHER "design-centric" term.
You know, if 'ID Critics' ever actually do make the effort of use words appropriate to their claims, they'll be speachless.
Comment by Ilion — July 12, 2006 @ 1:11 pm
July 12th, 2006 at 1:51 pm
"(because sterile and/or never-born organisms don't contribute to evolution)"
Certainly they do. Or, rather, certainly they can when the 'modern evolutionary theorists' need them to be able to. Just consider how "fitness/differential reproductive success" can so easily be disregarded when the problem-to-be-explained happens to be "explaining" how the human karyotype (2n=46) "evolved" from the ape karyotype (2n=48).
Comment by Ilion — July 12, 2006 @ 1:51 pm
July 12th, 2006 at 2:01 pm
BTW Mike, I'm all for discussing MTs from within a "Design Matrix." But since I haven't yet ordered your book (tight around here due to summertime travels and entertaining), and even if I had I wouldn't have read it yet, can you please put your definition into a paragraph or two so we're all working with the same concept?
I can readily imagine your thrust, but I don't know if my imagination covers your bases. What I do know is that in all complex, multicellular eukaryotic life forms, MTs and all associated regulators, expressors, enzymes and adjuncts (including those originating from genes in other symbiant structures, like mitochondria) are conserved in evolution. The structures themselves are so vital to so many necessary cellular functions - including mitosis/meiosis, communications and transport - that mutations in these genes that effect binding patterns, polymerization and depolymerization, signal transduction, etc. are non-viable. Resulting mutants are occasionally born, but are sterile. Most aren't born at all.
…which, if you think about it, makes these particular structures (and the genes related to them) apparently necessary to complex, multicellular organisms. From yeast to mammals and everything in between. Why, there's even a model of consciousness out there right now that postulates MTs as the physical/neural correlates (Roger Penrose's quantum gravitational model of cosmology united with Stuart Hameroff's model of MTs as the primary targets of medically useful anesthetics).
Because let's face it… if consciousness has anything to do with life and evolution of life over time, it's intelligently designed. On a relative scale, of course…
The Penrose-Hameroff "Orch-OR" Model of Consciousness
Comment by Joy — July 12, 2006 @ 2:01 pm
July 12th, 2006 at 2:57 pm
Ilion (in two posts):
I for one hope the resident critics will go ahead and join this subject, in as much as I am of the opinion [at this point in time] that there's something here to be closely examined from a design point of view. Lynn Margulis is the current champion of symbiosis, which has gained wide support in evolutionary biology over a couple of generations because it "defers the question" of actual origin for structures that apparently had to originate full-blown in order for life to develop the active mechanisms of evolution over time - including sexual reproduction (which speeds the clock and complexity in an exponential fashion).
But very recently some new questions have been brought to bear, which also impact the development of non-darwinian theoretics based on incoming evidence. For instance, the apparent uber-symbiosis between MTs and mitochondria. MTs form such useful constructs as flagella, centrioles (cellular sensory processors), and even neural synapses and dendritic connections in brains in addition to cellular cytoskeletons. It is now being suspected by a growing number of researchers that prokaryote cells - those that do not come with nucleus, cytoskeleton or MT organelles - are a branch off of what would be the original eukaryote cells. IOW, something lost rather than something gained.
Which would tend to indicate that MTs may well have come with the original package, thus aren't acquired symbiants. All complex, truly multicellular organisms are eukaryotic. Prokaryotes do exist, but they don't evolve into dinosaurs or bugs or anything. Perhaps because they can't. MTs don't spontaneously generate in raw cells (at least, not over the ~4.5 billion years we've got to work with), and apparently the coding for them isn't available for acquisition horizontally either (or prokaryotes would be in way short supply). MTs (basic components and structure) fulfill the criteria for irreducible complexity, even though these same structures have been deployed in a progressive manner toward increasing complexity in the evolution of life forms all the way to us. IOW, there is cumulative, self-organized benefit toward meeting life's adaptational developments in the game of life (natural selection).
It has occurred to me - and to Mike, obviously - that life just might be both intelligently designed (engineered) and front-loaded toward the production of independent intelligent agents. It's an intriguing possibility definitely NOT ruled out by what's real on the sub-cellular and genetic levels. Much of which really can't be explained by RM-NS. Which is why working biologists don't emphasize that bit of pablum much anymore - too many unrelated mechanisms and processes have been identified, including symbiosis and HGT.
It's just the ideology that comes attached as baggage to the RM-NS pablum that is threatened by new knowledge about the cellular milieu as something way more than "blobs of goo." They can be expected to go down kicking and screaming all the way, but if science is to remain a useful investigative tool for humanity at large it cannot submit itself to anything approaching a metaphysical "orthodoxy."
Comment by Joy — July 12, 2006 @ 2:57 pm
July 12th, 2006 at 8:53 pm
Microtubules are not optimally designed to do anything at all. They just happened, that's all (or rather their precursors did).
When a biologist says that a feature of an organism is "designed to" do something, they are merely engaging in a kind of shorthand for "evolved because that particular function enhances fitness."
Comment by trrll — July 12, 2006 @ 8:53 pm
July 12th, 2006 at 8:56 pm
Why would they want to? You are talking about the most successful (based on numbers or biomass) creatures on the planet. At one time, there was clearly opportunity for the mutant cell that could do some things that bacteria can't easily do, but those jobs are long since filled by highly optimized creatures who do them very well. Novices need not apply.
Comment by trrll — July 12, 2006 @ 8:56 pm
July 12th, 2006 at 9:03 pm
In truth, when a biologist (or a mere Defender of Science) says that a feature of an organism is "designed to" do something, but in fact he really means "it just happened," the technical term for what he's merely doing is 'equivocation.' It's not 'shorthand,' it's 'equivocation.'
In general, we can say this about uses of 'equivocation:' either 1) it is an indicator of muddled thinking on the part of the speaker/writer; or 2) it is intended to foster muddled thinking on the parts of the listeners/readers; or 3) both.
Comment by Ilion — July 12, 2006 @ 9:03 pm
July 12th, 2006 at 9:23 pm
trrll:
Um… and what, precisely, would be the "particular function" of MTs that enhances fitness? Just so we'll know what they evolved to do and all. Thanks.
Comment by Joy — July 12, 2006 @ 9:23 pm
July 12th, 2006 at 11:18 pm
Hi Joy,
I should have posted this blog on my DM site, as it really is nothing more than a mental note to return to this topic once the book is out. When that happens, I'll gladly throw out a paragraph or two that encapsulates the Matrix. In the meantime, I'll probably do future "Grist for the Matrix" posts the DM site.
Hi chunk,
I'm not sure how these researchers defined optimality in this case, as I would have to read the paper. While that comment is certainly worthy of consideration, it was not the thing that caught my eye.
Comment by MikeGene — July 12, 2006 @ 11:18 pm
July 13th, 2006 at 9:57 am
Hard to know. Something like a rod or girder has so many uses that it is difficult to guess what was important first. Structural, to give a cell shape or mechanical integrity? Linking things together? I'd imagine the "railroad track" functions evolved later. It's one of those things whose evolution seems almost inevitable, like an eye. Oligomerizing into helical rods is a fairly basic property, after all–even carbon molecules can do it. It's a pretty simple symmetry.
Comment by trrll — July 13, 2006 @ 9:57 am
July 13th, 2006 at 10:02 am
No, it is simply an abbreviated way of referring to a highly developed and mathematical theory, supported by huge masses of biochemical and molecular biological data. How natural selection optimizes cells and parts of cells to serve particular functions is rather well understood, so when biologists use the word "design," they all understand it to be in an evolutionary context.
Comment by trrll — July 13, 2006 @ 10:02 am
July 13th, 2006 at 10:07 am
trrll:
Then why don't they say so? Perhaps because that would be false, and "designed to" is closer to the truth.
Notice now how the effect becomes the cause. The effect, increased reproductive success (fitness), has caused the evolution of the function. Notice also the lack of any mention of the required precursors.
lol. Ken Miller criticises ID theorists for not accepting the inevitability of the biological world and all it encompasses while he himself is only willing to go so far as to say it is "almost inevitable." See UD.
Comment by Mung — July 13, 2006 @ 10:07 am
July 13th, 2006 at 10:43 am
trrll:
Sorry trrll, it was a trick question. General consensus at this point is that MTs are symbiants. Meaning they were independently existing organisms (or perhaps virus) before they became the 'brains', central processors and functional GCs of eukaryote cells.
Some think they were invented and developed in-house, but that would suggest eukaryotes came first. While we know quite a bit about form and function, we're not clear about origin. You seem very confident that you know what no one else does. You should publish and share your knowledge with the rest of biological science.
Comment by Joy — July 13, 2006 @ 10:43 am
July 13th, 2006 at 11:10 am
But very recently some new questions have been brought to bear, which also impact the development of non-darwinian theoretics based on incoming evidence. For instance, the apparent uber-symbiosis between MTs and mitochondria.
The strength of evidence wrt symbiosis is different for mitochondria and microtubules, so they probably shouldn't be lumped together. The endosymbiosis model is widely accepted for mitochondria, and recent genome sequencing projects have all supported the idea that mitochondria are derived from alpha-proteobacteria.
For instance, this review:
Gray et al. (2001)The origin and early evolution of mitochondria. Genome Biology 2: 1018.1-1018.5
It's free in pubmed central here:
http://www.pubmedcentral.gov/a...
AFAIK, the endosymbiosis hypothesis is much more controversial for flagella/microtubules, and Margulis' original candidate for the symbiont, a spirochete, seems to be a non-starter, because spirochetes do not have tubulin. But, see the following for a more recent hypothesis:
Li, J.Y. and Wi, C. F. (2005) New symbiotic hypothesis on the origin of eukaryotic flagella.
Li and Wu propose that eukaryotic flagella (and microtubules) are derived from endosymbiosis of verrucomicrobia, bacteria which do have microtubule-like proteins and which are ectosymbionts on some protists. In phylogenies based on sequence, the verrucomicrobia tubulins branch from the base of the tree, with the eukaryotic tubulins clustering together. Li and Wu also discuss and give references to the hypothesis that tubulin is ultimately derived from archaebacterial FtsZ protein.
The references in the Li and Wu paper may be of interest to anyone who wants to read up on the latest research regarding microtubule origin.
It is now being suspected by a growing number of researchers that prokaryote cells - those that do not come with nucleus, cytoskeleton or MT organelles - are a branch off of what would be the original eukaryote cells. IOW, something lost rather than something gained.
Would you give me a reference for that hypothesis, please? In the case of mitochondria/alpha-proteobacteria, that would imply that the alpha-proteobacteria are derived from mitochondria that somehow escaped from the eukaryotic cell and managed to grab all the necessary genes from the eukaryotic nucleus. That seems even less likely than the reverse direction and isn't consistent with the molecular phylogenies of mitochondrial and bacterial genomes.
Comment by Nick — July 13, 2006 @ 11:10 am
July 13th, 2006 at 11:44 am
Sorry, I just realized that I truncated the Li and Wu reference. It is
Li, J.Y. and Wu, C.F. (2005) New symbiotic hypothesis on the origin of eukaryotic flagella. Naturwissenschaften 92:305-309.
Don't be scared off by the name of the journal. The article is in English.
Comment by Nick — July 13, 2006 @ 11:44 am
July 13th, 2006 at 11:52 am
Nick:
Can evolution make things less complicated? - [Becky Ham, AAAS]
Discussion here at TT on this subject: Another Big Example of Reductive Evolution?
More discussion from Mike Gene's website: Extreme Evolution…
The Simple and the Primitive: Some Cautionary Tales
Comment by Joy — July 13, 2006 @ 11:52 am
July 13th, 2006 at 12:07 pm
Surely you don't mean trying to envision a Neodarwinian acquisition [via RM-NS] for these particular structures [alpha-beta tubulins, MT associated proteins, operative depolymerization enzymes, etc. - which are evolutionarily conserved and necessary to such functions as oogenesis and embryonic development.
Oogenesis and embryonic development are unlikely to be primitive functions of microtubules, even under an ID/front loading paradigm, for the simple reason that single-celled eukaryotes (e.g. protists) have neither oocytes nor embryos.
Also bear in mind that symbiosis and RM + NS are not necessarily competing hypotheses. The Li and Wu paper referenced above hypothesizes that the original function of microtubules was a structural one: they formed extrusions or "spikes" on the cell membrane to protect the organism from predation. This is apparently the role of microtubules in modern verrucobacteria that are ectosymbionts on ciliates (and one species is an endosymbiont). The more complex functions of eukaryotic microtubules were then acquired in a gradual stepwise fashion after the initial endosymbiosis.
Comment by Nick — July 13, 2006 @ 12:07 pm
July 13th, 2006 at 12:49 pm
Thanks. I would have preferred a link to the Gray et al review that Ham uses for her news report, but I was able to track back to it.
The Gray et al review is interesting, and it argues fairly forcefully that eukaryotes are not derived from fusion of archaebacteria and eubacteria. However, it does not provide much evidence that the earliest common ancestor was a eukaryote. As the authors point out, their analysis is unable to distinguish between genes present in the ancestor but lost by prokaryotes, and those evolved in eukaryotes after divergence from the ancestors of modern eubacteria and archaebacteria.
Interestingly, the paper does fit nicely with the Li and Wu hypothesis for the origins of eukaryotic microtubules. Gray et al. propose that "streamlining" of prokaryotic genomes was driven by natural selection, in the form of unicellular predators. This is exactly the same selective pressure that Li and Wu propose for the endosymbiotic origin of microtubules.
Comment by Nick — July 13, 2006 @ 12:49 pm
July 13th, 2006 at 12:52 pm
There are quite a few interesting and semi-interesting hypotheses out there related to MTs and their useful constructs/functions. But the fact of the matter is that science doesn't know where they originated or how they got into the business of enabling the development of complex multicellular life forms (and, apparently, sexual reproduction for the collective).
In fact, since the question of MT origin isn't answerable at this point in time, there isn't any particularly compelling reason to assume they are in fact symbiants or that eukaryotes are derivative. They could be original equipment.
It's just stories we tell as we try to imagine things we don't know. Different starting points of view will naturally develop different plot lines. The truth is (as usual) "we don't know."
Comment by Joy — July 13, 2006 @ 12:52 pm
July 13th, 2006 at 1:16 pm
In truth, when a biologist (or a mere Defender of Science) says that a feature of an organism is "designed to" do something, but in fact he really means "it just happened," the technical term for what he's merely doing is 'equivocation.' It's not 'shorthand,' it's 'equivocation.'
I think a better word would be "anthropomorphism". We've got a rich vocabulary for explaining human activity, so we'll sometimes borrow from that when we want to describe complex processes, even if they had an inanimate cause.
Examples:
- Nature abhors a vacuum.
- Water seeks its own level.
- Mountains are built by plate tectonics.
Just last month I described a computer bug by saying, "The operation failed, but the computer thinks that it succeeded." Obviously the computer didn't think that, the program didn't think that, and the original programmer didn't think that. If I'd wanted to be accurate, I would have said, "The operation failed but the error indicator wasn't passed back to the calling routine, so the calling routine executed the code associated with successful completion."
Do you see how the inaccurate "anthropomorphic" explanation is more helpful than the longer-but-more-accurate version? The only time I'd use the long version would be if I was talking to some crackpot who thought that this computer was really capable of thinking, and if I thought he'd take my words out of context and use them to support his nonsense.
I hope no one thinks that I was equivocating.
Comment by chaosengineer — July 13, 2006 @ 1:16 pm
July 13th, 2006 at 1:39 pm
It's just stories we tell as we try to imagine things we don't know. Different starting points of view will naturally develop different plot lines. The truth is (as usual) "we don't know."
That's what a hypothesis starts out as, certainly. Different starting points lead to different hypotheses, but it doesn't need to end there. Li and Wu suggest a series of experiments that could "confirm, replace, or refine" their hypothesis. It would be nice if ID biologists did the same with their hypothesis of microtubule origins.
Simply shrugging shoulders and saying its "unanswerable" isn't particularly helpful. You did ask "critics" to weigh in, after all. Why should we bother if you'll just say it's all unanswerable? At the very least, you could address specifics of Li and Wu's hypothesis and show what about their model is not compelling. From my point of view, it has the admirable qualities of referring to characteristics of actually existing organisms (e.g. defensive protrusions, ectosymbionts, endosymbionts).
Comment by Nick — July 13, 2006 @ 1:39 pm
July 13th, 2006 at 2:34 pm
Nick:
I'm not aware of any "ID biologist" who has proposed a hypothesis of MT origins, so that might go a long way toward explaining why there's no "ID hypothesis" of MT origins to test. Perhaps one of these years "ID biologists" will be allowed to develop and test "ID hypotheses" from within mainstream science, and be able to publish them in scientific journals just like "Orthodox Neodarwinian" scientists do. That would be a big step forward, I think.
Do let us know how the series of experiments Li and Wu are planning turn out. I for one will be interested. I'd also be interested in seeing the results of any series of experiments Margulis and Sagan conduct which would "confirm, replace or refine" their hypothesis as well. Heck, even a single finding from anybody's lab that a prokaryote cell turned itself into a eukaryote cell just by hanging around with other kinds of prokaryote cells in a solution would strongly suggest the hypothesis is sound.
In lieu of that confirmation, all our hypotheses are mere stories about 'how the leopard got his spots' - six of one, half a dozen of the other, nobody knows. I am more interested in the function of consciousness itself toward purposeful contributions to evolution. Questions about whether or not evolution proceeds exclusively by means of RM-NS are moot, since we already surmise with fair confidence from evidence available to us from the fields that it does not.
My interest in MTs and their functions is related to the hypothesis that they are the physical/neural correlates of consciousness. Because if the Penrose-Hameroff model is taken at face value (and its face is expansive), the underlying reality is that some version of protoconsciousness is a fundamental parameter in the matrix itself. That does take reductionism well beyond where biologists wish to go with it (they generally aren't fond of physicists or philosophers of science), but if they want to rely upon reductionism to sell their wares, they can't legitimately impose an arbitrary cut-off on how far down we can go looking.
Comment by Joy — July 13, 2006 @ 2:34 pm
July 13th, 2006 at 6:49 pm
I was intrigued as anybody when I first heard Margulis lecture and saw her pictures of eukaryotic cells apparently being pushed around by spirochetes. Nevertheless I don't believe that there is any such general scientific consensus on an endosymbotic origin for microtubules. Nor do I think that you will find many biologists who will agree that microtubules are the "brains" of eukaryotic cells, although they clearly have crucial structural and transport roles.
But the question of what the selective advantage of microtubules was to the cell in which they first evolved is quite distinct from the question of their subsequent history, and whether they were acquired by other cells by vertical inheritance, horizontal gene transfer, or symbiosis.
I'd still put my money on an initial structural role.
Comment by trrll — July 13, 2006 @ 6:49 pm
July 14th, 2006 at 12:41 am
Nick:
Epixenosomes are cool. But what "series of experiments" do Li and Wu propose to "confirm, replace, or refine" their hypothesis?
Comment by MikeGene — July 14, 2006 @ 12:41 am
July 14th, 2006 at 9:23 am
Hi Mike,
> what "series of experiments" do Li and Wu propose to "confirm, replace, > or refine" their hypothesis?
Primarily additional sequence analysis of tubulin and Ftsz genes in verrucomicrobia and and other organisms:
"(1) determining whether the FtsZ gene exists in verrucomicrobia. If these bacteria obtained tubulin genes by gene transfer, then they should have their own ftsZ genes. If these genes evolved from their own ftsZ gene, verrucomicrobia would no longer have the ftsZ gene, unless it had already multiplied before this point in evolution; (2) determining whether tubulin genes exist in various genera of verrucomicrobia and related groups, such as chlamydia and planctomycetes; and (3) performing phylogenetic analyses among verrucomicrobial tubulin genes, bacterial ftsZ genes, archaeal ftsZ genes, and eukaryotic tubulin genes whenever verrucomicrobial tubulin genes of other general are sequenced."
I guess I would add cell biological studies of verrucomicrobia to see if microtubule assembly, etc, is similar to that of eukaryotes, of it is more simple. Also, wide ranging sequence analysis to see if any additinal genes that bridge the phylogenetic distance between ftsZ and verrucomicrobial "tubulin" can be identified.
Comment by Nick — July 14, 2006 @ 9:23 am
July 14th, 2006 at 9:33 am
I'd also be interested in seeing the results of any series of experiments Margulis and Sagan conduct which would "confirm, replace or refine" their hypothesis as well.
With regard to mitochondria hypothesis, research from numerous labs has supported Margulis and Sagan's hypothesis to the point where I think it can be considered "confirmed" as well as anything in science. Margulis's lab apparently did do a lot of work to "confirm, replace, or refine" the spirochete/microtubule hypothesis, and the result seems to be "replace," since spirochetes don't contain the necessary genes. That's how we get to Li and Wu.
I'm not qualified to comment on Penrose and Hameroff's hypothesis, beyond noting that what you have described doesn't seem incompatible with reductionism or NS+RM. My money is still on electrochemical gradients mediated by ion channels, but even if some sort of quantum effects related to microtubules is required for consciousness in higher animals, that doesn't imply that the same was true of microtubules in single-celled organisms from which animals evolved.
Comment by Nick — July 14, 2006 @ 9:33 am
July 14th, 2006 at 10:42 am
And while endosymbiosis for mitochondria is supported superficially by the simple fact that these organelles remain enclosed within the eukaryote cell, aren't tubulin genes are found in the nuclear DNA (rather than mitochondria)? This would superficially suggest to me a horizontal transfer rather than a symbiosis.
The binding proclivities of tubulins, post-production modification by mRNA, and chirality of the construct would suggest that the structure of MTs is a matter of self-organization. MTs are multi-dynamic, assemble and disassemble like Magneto's metal bridges, enclose ordered water molecules interior and incite gel-phase cytoplasmic exterior, and for information processing functions appear to be superconductive (as chromatin pi-stack also appears to be).
Perhaps tubulin genes were one of those "inventions" Woese talks about in the flea market of the "HGT field" in promiscuous early life forms. I don't know origins, wait to see the hypotheses tested. I've been paying more attention to form and functions, tubulin genes code for alpha and beta (and gamma), but once in place - particularly in neurons and channel transport - the buggers are notorious state-switchers.
At the level of molecular constructs quantum effects are significant - state-switching is just one of the actions arising from quantum forces interior to the molecule. No way around it. MT signal transduction is efficient and related to information incoming and state-specific - communication intra and extra cellular, and this allows the phenomenon of cell differentiation which is required for differential gene expression patterning… complex multicellular organisms.
I don't doubt that MTs have been put to specialized uses in multicellular organisms that they do not perform for single-celled organisms. I think it's nifty they're so amazingly useful to the designs of ever more complex and intelligent life forms.
Comment by Joy — July 14, 2006 @ 10:42 am
July 14th, 2006 at 6:03 pm
Many genes for mitochondrial proteins are found in nuclear DNA. The interpretation is that mitochondrial genes have gradually moved into the nucleus.
Most of these are nothing all that special. Helical oligomerization reflects a fairly basic symmetry. Assembly of protein subunits is normally reversible, so dynamic assembly and disassembly is the rule rather than the exception. Water molecules will be ordered inside any narrow lumen surrounded by protein. All sorts of fibrillar molecules are capable of producing gels. And I don't believe that they are superconductive (can you supply a reference providing evidence for this claim?).
What is the experimental evidence for this? Lots of molecules exhibit state-switching that is understandable in classical terms. What, specifically, about state-switching in microtubules is dependent on quantum effects? For example, is there evidence that tunneling plays a major role in switching kinetics?
I haven't come across any data demonstrating that MT participate directly in signal transduction, as opposed to providing general structural and transport support for receptor-based signal transduction. Do you have any references to experimental work that supports this idea?
Comment by trrll — July 14, 2006 @ 6:03 pm
July 14th, 2006 at 6:04 pm
Hi Nick,
So what "additional sequence analysis" result would confirm Li and Wu's hypothesis and what would falsify the hypothesis?
Comment by MikeGene — July 14, 2006 @ 6:04 pm
July 14th, 2006 at 7:04 pm
trrll, if you want to know, here are some excellent papers [via Stu's site]. More recent research reports have been posted to the LANL pre-print server, accessible whereas journal pubs often are not.
BBC Video of Penrose-Hameroff Orch-OR:
Orch-OR Model
Quantum Computation in Brain Microtubules?
- Philosophical Transactions, Royal Society.
…Decoherence and Biological Feasibility
- Scott Hagan, Stuart Hameroff and Jack Tuszynski, Physical Reviews E.
Conduction Pathways in Microtubules
- Stuart Hameroff, Alex Nip, Mitchell Porter and Jack Tuszynski, Bioenergetic organization in living systems.
Ferroelectric behavior in microtubule dipole lattices
- Jack Tuszynski, Stuart Hameroff, MV Sataric, B. Trpisova, MLA Nip Journal of Theoretical Biology.
A Bio-Polymer Transistor: Electrical Amplification by MTs
- Avner Piel, Arnolt J. Ramos, Jack Tuszinski, Horacio Cantiello.
Decoherence Time of a Microtubule
- Takashi Hiramatsu, Tetsuo Matsui, Kazuhiko Sakakibara.
Wave>Diffusion Transition in Microtubules
- Miroslaw Kozlowski, Nanina Carciak-koslowska.
Information Processing in Brain Microtubules
- Jean Faber, Renato Portugal, Luiz Pinguelli Rosa.
There's more (the whole Penrose end is being tested as well, but that's a horse of a different color). This will keep you busy for awhile. Happy reading!
Comment by Joy — July 14, 2006 @ 7:04 pm
July 15th, 2006 at 1:07 am
These all seem to be either theoretical papers or studies of isolated microtubules under highly nonbiological conditions. I have little doubt that it is possible to contrive conditions in which it is possible to observe quantum behavior with just about any biological molecule. What I'm asking for is experimental evidence that such quantum behavior plays a role in any kind of cellular signal transduction.
Comment by trrll — July 15, 2006 @ 1:07 am
July 15th, 2006 at 11:03 am
trrll:
You too can go to Google.com and input some pertinent key words. Or to arXiv and use their search function (which will return all pertinent files on any of the NL preprint servers). Van der Waals forces, quantum coherence, binding, biophoton generation and state superposition are some of the behaviors you'll want to look out for.
Comment by Joy — July 15, 2006 @ 11:03 am
July 15th, 2006 at 1:38 pm
If eukaryotes came before prokaryotes, wouldn't that mean that the the last common ancestor of eukaryotes had a full nucleus, and perhaps even capable of meiosis?
Comment by Guts — July 15, 2006 @ 1:38 pm
July 15th, 2006 at 6:39 pm
Hi, Guts. It was presumed prokaryotes came first for several pretty good reasons. First, traces of microbial life in fossils predates multicellular organisms by at least 3 billion years (via extrapolation on suspicion, not evidence). Second, eukaryotes have inclusions (nucleus, organelles) with their own membranes, whereas everything in prokaryotes is sort of lying around loose. Much "simpler" by comparison. Of course, now there's a whole other class of "originator" [archaeon], and even Carl Woese says an HGT Field doesn't sort the kinds adequately.
None of which means Margulis' endosymbiotic theory wasn't considered heretical when it came out. Qualified acceptance is relatively recent. There is no actual fossil evidence for life prior to ~1.6 billion years ago, when eukaryotes already existed. If rock dating is accurate.
No one knows what's 'true' (small-t) because things like membranes and DNA and RNA don't fossilize. What is fairly surmised from the evidence is that life didn't really start cooking on the cooperative scale until ~1.6 billion years ago, and didn't start self-organizing into multicellular uber-organisms until a billion years ago or so. And those didn't spawn whole phyla until just about 600 million years ago. All of the vast non-microbial biodiversity we see or have evidence of has originated and run its course in just that amount of time.
Obviously something happened ~1.6 bya, and something else happened ~600 mya. We aren't clear on what those happenings were - so we guess. The situation is confused enough that some luminaries in the biological world subscribe to the notion of "seeding," or panspermia. We've no real reason at this point in time to suspect that earth is the sole harbor of life in the universe, so there's no real reason to believe life originated here at all. Six of one, half a dozen of the other.
Scratch the surface and you'll find emotional/metaphysical investment by whoever's doing the asserting. It has always been thus. There's no good reason to impose a particular consensus so long as we honestly don't know. It's all a game of favorites.
Which makes the fields interesting to those of us watching. They all want us to swear allegiance to their hypotheses, but I see no reason to do so. Maybe real evidence will tip the scale someday. Until then, I'm just enjoying the show.
Did Consciousness Cause the Cambrian Evolutionary Explosion?
Comment by Joy — July 15, 2006 @ 6:39 pm
July 16th, 2006 at 5:12 pm
Yes, I've searched Google and also Medline. So far, all I've found are theoretical speculation and some very nonbiological studies of microtubules in isolation. Which is why I asked whether you were aware of any experimental evidence that such quantum behavior plays a role in any kind of cellular signal transduction. From your response, I take it that the answer is "No."
Comment by trrll — July 16, 2006 @ 5:12 pm
July 17th, 2006 at 11:00 am
So what "additional sequence analysis" result would confirm Li and Wu's hypothesis and what would falsify the hypothesis?
Hi Mike,
See the quote from the paper in my previous post. Li and Wu spell it out.
Various alternatives to Li and Wu's hypothesis include a) horizontal transfer of tubulin from eukaryotes to verrucomicrobia, b)independent evolution of eukaryotic and verrucomicrobial tubulins from ftsZ genes, c) tubulin possessed by an ancestral "eukaryote" that was lost from most prokaryotes but independently retained by modern eukaryotes and verrucomicrobia, or d) endosymbiotic origin of eukaryotic tubulin involving some prokaryotic group other than verrucomicrobia. These alternatives all assume common ancestry, but so do front loaded evolution variants. Obviously, these experiments won't tell us anything if YEC is true, but we can probably ignore that possibility for other reasons.
Li and Wu's hypothesis implies a phylogenetic structure for tubulin genes something like this:
(ftsZ(other microbial "tubulins"(verrucomicrobial tubulin(eukaryotic tubulins))))
The eukaryotic tubulins cluster and are most closely related to verrucomicrobial tubulin. The "other microbial tubulins" are hypothetical, and determining whether they exist is one of the experiments that Li and Wu suggest.
Alternative a) would give us:
(some eukaryotes (verrucomicrobial tubulin (other eukaryotes)))
The verrucomicrobial tubulin nests within the eukaryotic tubulin closest to the eukaryotic tubulin from which it is derived.
Alternative b) would give us:
((ftsZ a (verrucomicrobial tubulin))(ftsZ b (eukaryotic tubulin)))
the verrucomicrobial tubulin and eukaryotic tubulin are most closely related to different ftsZ genes
Alternative c) would be similar to Joy's "original equipment" hypothesis. It would probably give a morphology similar to alternative a, since it implies that prokaryotes are descended from a branch of the eukaryotes.
Alternative d) would probably look like:
(ftsZ (verrucomicrobial tubulin (other microbial tubulin (eukaryotic tubulin))))
This is different from Li and Wu's model, because the eukaryotic tubulin is closest to some non-verrucomicrobial prokaryote.
Obtaining the predicted tree would support Li and Wu's hypothesis. Obtaining any of the alternative trees would be evidence against Li and Wu's hypothesis.
You can probably think of more alternatives. If they predict a tree different than that predicted by Li and Wu's hypothesis, then they are testable by sequencing. If they predict the same tree, then you'll need to come up with a different method to test them.
Comment by Nick — July 17, 2006 @ 11:00 am
July 17th, 2006 at 11:45 am
trrll:
I'm not sure why you would insist that quantum 'behaviors' don't play any role in something as basic to biology as signal transduction, since fold configurations as well as binding proclivities are very much quantum mechanical even if you were to ignore the quantum mechanical properties of cytoskeletal MTs and their role in the process.
You have displayed a rather surprising lack of understanding of basic Neodarwinian theory, thus of "Modern Evolutionary Theory" [MET] as it is developing upon new evidence about the mechanisms of variation, the relative efficacy of selection (lots of mutations are now known to be selectively neutral) and the dynamic, intricately patterned and directly responsive processes of expression. In fact, you have asserted that mutation is a 'mechanism' of selection! So your ignorance of biophysics isn't surprising.
Please don't waste everyone's time on pretense.
Comment by Joy — July 17, 2006 @ 11:45 am
July 17th, 2006 at 7:50 pm
And I'm not sure why you would insist that I am "insisting" anything, when I merely asked a question: Is there any actual experimental evidence that such uniquely quantum behavior plays a role in any kind of cellular signal transduction? I'm not aware of any such evidence, but I'm just a simple experimentalist in the field; the literature on signal transduction is huge and I don't pretend to know it all. I was hoping that you'd put me on to something that I'd missed.
It is from your repeated dodging of the question that I infer that the answer is "No." Actually, I think that's too bad–I think that the idea that quantum phenomena might play a non-trivial role in biological signal transduction is an intriguing one, and I am disappointed if after so many years there is still no solid experimental evidence to support it.
Comment by trrll — July 17, 2006 @ 7:50 pm