text:
Talk:Microtubule

Microtubes and Alzheimer's
Can there be some paragraph on this. topic.--69.150.170.49 (talk) 10:03, 20 September 2011 (UTC)

http://www.youtube.com/watch?v=NjgBnx1jVIU&feature=related

Removing Penrose/Moving
I had a conversation with a friend of mine this past weekend about this article, and because of the Penrose section he pointed out that this was a perfect example of why Wiki articles really can't be trusted for information beyond pop culture. Frankly that's the last straw for me since I feel like I've added evidence against Penrose as if I'm arguing with him when he really doesn't have any knowledge of microtubules. So I've decided that this information needs to be removed from this article. If anyone disagrees I'd like you to consider moving the section to the article about Penrose, since this theory is more about Penrose's personal philosophies about the nature of consciousness than about any actual scientific studies done on the topic. Kablamo2007 21:27, 26 February 2006 (UTC)

I've removed the section again after it was readded. While Roger Penrose's speculation on quantum consciousness are famous they are in no way authoritative, widely accepted, conform to the evidence, or have ever been empirically tested. In short, don't belong in an encyclopedia. For specifics see my post from a long time ago at the bottom of the talk. If you would like to include the topic in an article on Penrose or his theories then that is the appropriate place. Please, discuss this topic on the talk page before readding the section. 132.162.208.59 Kablamo2007 20:36, 18 October 2006 (UTC)

Perhaps some link to the Orch-OR article would be in order? Any discussion can take place there. I propose this because I wanted to review Penrose's theory and had some trouble locating the Orch-OR article: both this article and the Roger Penrose one didn't link there. I'll fix it for the Penrose one, but leave any modification of this page up to you guys and gals. --tijmz 14:59, 8 December 2006 (UTC)

Can something be said about the rebuttal of Max Tegmark's argument? I find it unusual that someone would post an isolated rebuttal of Hameroff's calculation, while neglecting what Hameroff has said about Tegmark's calculation. --DoYouKnow 3:00, 3 January 2007 (UTC)

I'm going to continue to work on this article, I don't research microtubules myself (which is good, because that might skew my vantage point for contributing), but I'm in biology/biochemistry... I separated a "structure" section from "organization" ... I'll be back to work on it more later... The so-called "theory of consciousness" has no business in this article... it should be removed entirely or reduced to a very small statement linking to a stub pertaining to it.IlliniWikipedian 17:34, 19 December 2005 (UTC)

a GDP-bound tubulin in the middle of a microtubule cannot spontaneously pop out.

This is incorrect. Microtubules are known to have the ability to subunit exchange within the polymer, but the occurence of these exchanges are infrequent enough to not endanger the stability of the polymer. -- user:Kablamo2007

Microtubules radiate from the centrosome.

The organization centres that microtubules come from are sometimes called centrosomes, but I think that's more often restricted to the centrioles. These only give rise to microtubules involved in mitotic division, and not those in flagella and axopodia, or those supporting the cell. There could be a connection, but some cells don't even have centrioles, e.g. plants. I'm going to err on the side of caution and remove it unless some better description is given. -- Josh

Actually where a centrosome is present it is the dominant site of microtubule nucleation and it is definitely fair to say that microtubules radiate from the centrosome. The centrosome organises a microtubule array in both mitosis and interphase in animal cells. AND the microtubules of the axoneme are nucleated and organised by the basal body, which is a modified form of the centrosome. The centrioles are a component of both the centrsome and the basal body.

Basal bodies are related to the centrosome, but in most books they aren't the same thing. The centrosome page flatly states that plants don't have centrosomes, and they do have microtubules. As such, making it look like all microtubules come from centrosomes is a mistake.

...however there is growing experimental evidence for a connection between quantum effects in microtubules and the mechanisms of consciousness.

Could we get a reference for this? It really sounds questionable to me. ---

move this to talk.

...however there is growing experimental evidence for a connection between quantum effects in microtubules and the mechanisms of consciousness.

At least mention what the evidence is.

Roadrunner 01:51, 3 Apr 2004 (UTC)

shrinkage vs retraction:

I changed "retraction" to "shrinkage". Depolymerizing microtubules do not usually retract. Depolymerization is the loss of monomers from one end, whereas retraction is a backward movement (or shifting/sliding) of the whole microtubule - an event which is not usually associated with depolymerization. In other words, microtubules can for example depolymerize and protrude at the same time, and it would appear, as if the microtubule would not change at all. However, all kinds of behavior (retraction vs. protrusion and depolymeriztion vs polymerization) can be disected and visualized by a technique called fluorescent speckle microscopy. Another often used expression to describe depolymerizing microtubules is the word "shortening"

This article is categorized under organelles, which microtubules are not. Should we change it? And, oh yeah, the consciousness thing is VERY questionable. --Delldot 22:48, 8 October 2005 (UTC)

 * I have no objection to removing this article from Category:Organelles. The "consciousness thing" is already marked as being on the scientific fringe. However, it is a famous proposal and I think it has a place in this article. Fringe ideas serve useful functions in science. There is nothing wrong with wikipedia showing that scientists can "think outside of the box" and that science does not break down when controversial ideas are discussed. Once in a while, a fringe idea even turns out to be correct. --JWSchmidt 01:29, 9 October 2005 (UTC)

 * Fringe is one thing. Penrose really knows nothing about how microtubules work.  He started out with a conclusion in mind, that quantom effects could explain conciousness, and searched for something he could fit to his already made conclusion.  That is psuedoscience to start with your conclusion in mind and fit the evidence to it.  I stil think that the info should be left up with sufficient evidence that the strong scientific consensus is that it is dead wrong.  Always good to openly debunk the talking heads for this kind of "science".  I mean the fact that so many people take What the Bleep Do We Know!? seriously is reason enough to be worried for the future of science as a public endeavor in this country.Kablamo2007 06:10, 4 November 2005 (UTC)

 * What about Hameroff's reb

 * I agree that it is far better to explain why most scientists think microtubules are not central to consciousness than to ignore the issue. In my view, a hypothesis can only really become part of a pseudoscience if it is not subjected to critical analysis. The microtubule article should have some references for the "Microtubules and theory of consciousness" section. There should be discussion of the content of references that contain published microtubule-related quantum consciousness proposals and discussion of the content of articles that critically evaluate those microtubule-related quantum consciousness proposals. --JWSchmidt 13:20, 4 November 2005 (UTC)
 * Unfortunately I've never seen a concise single argument against Penrose published. Mostly I think this is because scientists in the field see it as immediately nonsense and see no reason to respond to something published as popular science.  Penrose's idea has never been in the peer reviewed literature where they would feel compelled to respond (mostly because a reviewer would never let something like that through).  I'll put all the reasons why I can see it doesn't work here and you decide if they belong in the article:

 * A Refutation of Penrose's Gödelian Case Against Artificial Intelligence (2000) http://citeseer.ist.psu.edu/320350.html This is watertight, and the fact that it destroys his central argument makes the rest of his musings unravel as irrelevant.

 * (Yes, I know, talk pages should never be edited..) Link is dead. New link and full citation:  This article is also referenced by the following 2002 paper, which appears to argue against Bringsjord & Xiao:

 * In my view, a hypothesis can only really become part of a pseudoscience if it is not subjected to critical analysis. -- This "view" is clearly wrong--quite a bit of pseudoscience has been subjected to critical analysis. And you seem to be arguing for the opposite--it looks like "not" is a typo--but that too is clearly wrong ... there is vast amounts of pseudoscience that is not taken seriously, for good reason. Also, it's "pseudoscience", not "a pseudoscience"--pseudoscience is rarely organized and coordinated into fields of study the way the sciences are.
 * There should be... -- no, there shouldn't; that would go against WP policy. There's a single link to Penrose & Hameroff's "theory", which is more than adequate. Jibal (talk) 19:17, 1 July 2023 (UTC)

1. Microtubules are too large for quantum coherence. The inside of a microtuble is large enough to allow many water molecules and even some drugs such as the cancer medication taxol bind inside the microtubule. Right there is an obvious example of why microtubules don't produce conciousness. If quantum coherence inside the tubule could even occur then someone taking a drug like taxol should exhibit problems with cognitive functions of conscious.

2. While tubulin has two possible conformations, these conformations are not equally likely throught the microtubule. In fact the entirety of the tubule except the outside ring is one state while the outside ring is the other. Without the ability of the microtubule to click through these two states (the 1's and 0's of quantum computing) there is no basis for quantum consciousness.

3. Microtubules are present in all cells and in all eukaryotes. If they are the source of consciousness than why is yeast not conscious in the same sense that we are.

4. Finally, Penrose's argument is only based on the fact that he decided long before picking on the microtubule that consciousness must be a quantum phenomenon. While this may or may not be true, he has targeted the microtubule not out of real understanding of how it functions, but because it was the first thing that he could find that might fit his already formed theory. That's just bad science. Kablamo2007 07:57, 5 November 2005 (UTC)

 * The Penrose hypothesis, even though it is highly improbable (and most probably wrong) SHOULD be mentioned in the entry. Why? Because it exists (i.e. it was published and people can read it). An encyclopedia should cover as much content as possible. Someone who is reading Penrose's book could then consult Wikipedia, read the Microtubule entry, and learn that the scientific community has largely rejected Penrose's arguments. With references to authoritative work/opinions on the question. What's the point of not covering scientific work just because it is wrong? Then, shouldn't we remove coverage from famous hoaxes and scientific errors such as the Piltdown man, the Ptolemaic system or Lamarckism? This would be a dangerous path to follow. Hugo Dufort 05:43, 20 November 2006 (UTC)
 * By your reasoning, the page for Joe Biden deserves discussion of the contents of his son's laptop simply because Trump keeps trying to smear him by saying there's something nefarious about it. Like with Piltdown man, Penrose's musings have indeed generated enough controversy to warrant its own page, and indeed it already exists as Orch OR. That does not mean that it deserves a link in the content of a page about the biological molecule he picked beyond the see-also section where it currently resides. Cutelyaware (talk) 04:45, 26 May 2022 (UTC)

 * And by the way, it IS possible to find refutations of Penrose's hypothesis coming from PhDs and experts. For instance, the following article has been published : http://psyche.cs.monash.edu.au/v2/psyche-2-03-klein.html So merely saying that Penrose's theory is "untouchable" by serious researchers is not a sufficient argument for totally ditching Penrose's theory out of the Wiki. It deserves to be criticized. -- Hugo Dufort 06:06, 20 November 2006 (UTC)

 * With reference to the citeseer link, the argument is not quite so clear cut. The authors argue that Penrose has not made his case. However, in the final paragraphs of the paper, the authors start to attack some proponents of strong AI (LaForte, Hayes and Ford) for demonstrating the same weaknesses as Penrose and failing to prove the consistency of Strong AI and Godel. In the final paragraph one of the two authors, Selmer Bringsjord, comes out of the closet as being 'in complete and utter agreement with Penrose that it is possible to drive the denial of Strong AI from Godelian facts'. Persephone19 21:27, 27 October 2007 (UTC)

MT and consciousness??
I strongly object putting a half-cooked theory into a encyclopedia. It has make its way to the textbook first. The molecular or even neuronal nature of consciousness is still a big controversy. Or even the definition of consciousness itself. And I found here stating that it came out of a nanotube? Objection!

11:11, 16 December 2005 (UTC)Jumpingrat

I'd agree with you, but JW Schmidt has said that because of the fame of Penrose that it should be addressed. I would like you to look at my earlier post in the talk about the reasons why it's a crackpot theory. I have yet to try to incorporate them into the article, because they're not something I can really site.... its just what I know is obvious from having undergraduate biology courses. If you could help by writing a good rebuttal paragraph and adding sources I think it would be nice. I do think this article needs to address and firmly rebut Penrose sense I've had a smart friend who's a neuroscience major interested in cognition come to me thinking this theory was "it" and myself having worked with a tubulin-like protein having to explain the reasons why penrose doesn't understand the microtubule. A well written paragraph explaining those points would be good for any readers of Penrose coming here for more information. Kablamo2007 04:34, 25 December 2005 (UTC)

 * As someone with a 10 year old BSc, but never done biology since high school, I got to this article when a non-scientific friend pointed me to the Hameroff site and asked me if it made sense to me. Being me, I looked him up here and one of the first links in the Hameroff article is to here. I learned 10x more from the explanation that Kablamo2007 wrote than I got from the main page. IOW, yes, lay people come here wondering if the science is credible. I think it would be appropriate to have a section about why microtubules aren't a QC thing. And I think it would be better to put it and mark it citation needed than to have nothing there. Ricky 13:10, 22 August 2006 (UTC)

Microtubules and quantum consciousness
Information is being regularly reverted about this subject, even though one editor actually acknowledges the subject is well known. The subject gets 66,900 Google hits from many proper sources, so there is no reason to continually remove the subject entirely. This will have to go to mediation if other parties continue their blanket removal of the subject. wikipediatrix 00:31, 19 October 2006 (UTC)

Neutrality of the quantum conciousness section
Okay, this section currently reads something like "Yeah, it exists, and it's completely wrong". There should be at least a small blurb about what the theory proposes, and any evidence that does in fact support it, if anyone feels qualified to do that.Nathanww 03:00, 22 February 2007 (UTC)

At this time there is no lab science in support of the theory. No microtubule researchers are interested in the topic at all since most don't see how it could work given the present knowledge about microtubules. The current "evidence" for the theory is just the theoretical requirements for quantum coherence which are addressed in the Orch-OR article and as of now there are theoriticians who have said they could never work for the time-scale, size/temperature of microtubules. Besides that fact is that microtubules don't work the way the theory assumes with two equally likely states... the states are not equally likely. I'm fine with the section being tagged... its my opinion that it should go, but it keeps coming back Kablamo2007 16:38, 28 February 2007 (UTC)

I'm just a biology student and I haven't really put any research into this matter, but the section about "Microtubules and consciousness" seems awfully misplaced and I don't understand what it's doing in this article. 130.243.248.239 15:42, 22 March 2007 (UTC)

Keep it, but be skeptical
I think the point is that the Penrose story is pretty much the only logically coherent story of consciousness that science has so far proposed -- sure it's way beyond the fringes and wacky and very very speculative -- but it is the /only/ story we have. Surely every living person on the planet is interested in what consciousness is, and unless they walk away from science altogether and sign up for some religious or new-age fiction then this is the best we currently have to offer. It's wacky, far-fetched, and not accepted by anyone, but its still currently the only, and therefore best, theory we have. —The preceding unsigned comment was added by 84.51.150.211 (talk) 08:53, 6 April 2007 (UTC).

 * You are entirely incorrect. "the Penrose story" is not any sort of explanation of consciousness, and there are in fact good coherent explanations. Also, people being interested in what consciousness is (and no, only a relatively few people actually are) has no relevance to this article on microtubules. Jibal (talk) 21:07, 1 July 2023 (UTC)

I think you should mention the Penrose theory and link to another page where a more thorough examination of it can be made aside from this main article on MTs. I would do the same for any other notable past or present theory that relates or refers to the MTs.

 * Only theory? Whatever happened to intracellular electrical discharge triggering the release of chemicals from brain cells, that are sensed by other brain cells? Doesn't that count as such a theory, especially given the observation that drugs that alter, disrupt, or enhance this process produce observable, frequently repeatable changes in the emotional status of human beings? If microtubules were going to play any role at all, I'd be much more interested in hearing how they serve to alter the propagation of charge down the length of a neuron! 70.162.81.229 19:54, 24 July 2007 (UTC)

I just stumbled over this article looking for some info about microtubules and must say, that the Penrose-part is really irritating. I think you should mention that a theory, not supported by the scientific community exists and link to it, that should keep the conspiracy theory people from deleting it. (I'm not doing it myself as i'm no biochemist and do not really know much about this topic) As for presenting far-fetched, wacky theories as "science", it think that is a really bad idea and i would more likely associate that with new age-fiction than with science. --134.76.210.206 08:19, 25 July 2007 (UTC)

Penrose again
The microtubule/quantum consciousness thing has no place here, I've removed it. It is a wild speculation unsupported by anything. The statement that "the Penrose story is pretty much the only logically coherent story of consciousness that science has so far proposed" is absolutely not true (see the Wikipedia page on consciouscness for logically coherent theories of consciousness that are actually supported by evidence). We may as well say here that unicorn horns are made of microtubules. 137.132.243.141 —Preceding comment was added at 03:25, 17 October 2007 (UTC)
 * Why not make a link to quantum mind? --JWSchmidt 03:31, 17 October 2007 (UTC)

 * So, I just re-added the Penrose section. Not to be troublesome, I promise! Actually, I agree that it should NOT be part of this article. The theory is bunk, and at most should get a VERY SKEPTICAL article of its own, or maybe be resigned to a reference in the Penrose article. Before we delete it, I just want to make sure that most of the people CURRENTLY working on this page agree with the decision (since this seems to be the standard way to do things around here). --AaronM 02:46, 18 October 2007 (UTC)

 * There are dozens if not hundreds of fascinating, well-researched things microtubules ACTUALLY DO IN REALITY that are not part of the article (which contains very little on actual microtubule function). Including the most far-fetched and unsupported function for microtubules ever published (though never in a peer reviewed forum) is severely distorting. Having one piece of quackery claiming a function for which there is no evidence is ridiculous. It's like like having an article on radios that says "Radios make sound. Although many are skeptical, the government might be using them to read my mind."137.132.243.141 08:40, 18 October 2007 (UTC)

 * The Penrose/Hameroff take on microtubules lies well within the Wikipedia guidance for inclusion of non-mainstream of fringe theories. This says that the theory should be referenced extensively, in a serious manner and in mainstream publications. In particular debunking or disparaging comments, which are legion for this theory are in fact adequate to establish notability of the theory. The fact that many scientists reject or ridicule the theory is not really relevant in this context, so long as it is made clear that it is speculative. I think a few sentences giving a more detailed explanation of the processes proposed should be added. A paragraph on the various refutations could follow this, but in the interests of neutrality, attempts to reply to these refutations should not, as is common in the popular literature, be totaly ignored, for instance the Hagan, Tuszynski, Hameroff response to the better known Tegmark article on decoherence. Persephone19 21:04, 27 October 2007 (UTC)

 * The point is not whether it is allowable, the point is that it makes it a bad article. The entries should strive to accurately and concisely represent what is known and understood about microtubules. This entry is severely unbalanced, because it omits the many things microtubules DO do and gives space to something that a tiny number of people speculate, with no evidence, that they MIGHT do.24.252.32.54 22:54, 12 November 2007 (UTC)

 * The answer would seem to be to expand the main part of the article, which does seem skimpy for such an important component of cells. It goes without saying that the article should fully describe the known mechanism and function of the microtubules. However, I can't see that this precludes discussing speculative material. Given the widespread, if mainly critical coverage given to the Penrose'Hameroff proposal, many readers may access the article with the hope of getting more information on the theory. If anything it could do with fuller discussion, for instance the reasons for scepticism, as part of a more comprehensive article. Persephone19 11:18, 13 November 2007 (UTC)

Motor proteins and MAPS affecting MT dynamics
I think the article is a bit sparse on describing motor proteins interacting with MT, and should definitely give some space to microtubule associated proteins (MAPS) that can influence the dynamics of microtubules. Such MAPS can favour either a catastrophe or rescue state. Examples of these are numerous, such as XMAP215 (a MT 'polmymerase') and XKCM1 (a MT 'depolymerse'). In general, MT polymerases and depolymerases play important roles in enabling MT dynamics to be altered depending on the requirements of a particular cellular process. —Preceding unsigned comment added by 131.111.244.145 (talk) 08:12, 12 September 2007 (UTC)

Eukaryotes only?
As components of the cytoskeleton, does this mean that microtubules are found only in eukaryotic cells? --EncycloPetey (talk) 05:20, 7 January 2009 (UTC)

 * see e.g. Shih YL, Rothfield L (2006). The bacterial cytoskeleton. Microbiol. Mol. Biol. Rev. 70 (3) 729–54. Plantsurfer (talk) 10:04, 7 January 2009 (UTC)

 * Microtubules are found in some bacteria (Prosthecobacter). I added a description of their structure.Eikosi (talk) 21:44, 16 November 2015 (UTC)

Polarity
Microtubules are generally referred to as polar. Is this a polarity in the acid/base sense or merely a recognition of the orientation of subunits? Akita86 (talk) 17:19, 23 January 2009 (UTC)

 * You are correct - the polarity of the microtubule has to do with the subunit orientation. Each subunit is a dimer of alpha and beta tubulin, and all subunits within a microtubule all "face" in the same direction. Thus, one end of the microtubule has the alpha tubulin facing outward, while the other end will have the beta tubulin facing outward.--AaronM (talk) 14:35, 24 January 2009 (UTC)

 * Thank you. In that case, it ought to be pointed out in the page that the MT subunits are not polar in the way water is. Akita86 (talk) 20:28, 24 January 2009 (UTC)

Quality of Citations??
I would just like to comment that all of the "citations" for the microtubule entry are garbage. They all cite papers from a very narrow faction of microtubule weirdos (outside of mainstream research), and none is actually a citation of the primary research that originally demonstrated experimentally the particular fact being cited. Citations in scientific articles should cite either the original primary literature or reviews that cite the material, not unrelated primary articles that reference the information in the background or introduction section of the paper.

It appears as if someone from the tribe of "microtubule quantum consciousness" wanted to fool lay readers into believing (1) that they have contributed to the field by discovering some very important basic biological aspects of microtubules (false, these were discovered by others) and (2) their published speculation about quantum consciousness, etc is somehow true and/or commonly accepted (also false).

Just as an example, the microtubule entry correctly states that "the tubulin dimers polymerize end to end in protofilaments," but it cites a 2008 article by Vahid Rezania and Jack A. Tuszynski ("A first principle (3+1) dimensional model for microtubule polymerization"), which is a recent mathematical modeling of microtubule dynamics paper, not the original series of biological experiments that proved this (many years before). The paper cited doesn't prove anything at all, let alone that "tubulin dimers polymerize end to end in protofilaments."

I don't have to continue. The citations are all equally vacuous. Someone with more patience than me should clean it up. Better no citations than false attribution of credit, in my opinion.

I'd hate to believe that peer-review and scholarship in the field are so poor that pseudoscientists are even making a living hallucinating about microtubules, but it might be so... —Preceding unsigned comment added by 69.181.184.55 (talk) 08:35, 27 May 2009 (UTC)

UPDATE: Another user has changed the citations since the above commentary was posted. The new citations are appropriate. More citations may still be desirable however. —Preceding unsigned comment added by 69.181.184.55 (talk) 05:34, 1 June 2009 (UTC)

 * I am worried that the last para. of the May 27 posting could be a bit near the line in terms of libel. Most researchers dislike quantum consciousness theory, but the posting could be taken to imply that Tuszynski & Rezania are themselves hallucinating pseudoscientists, when they are in fact affiliated to the Dept. of Oncology at Alberta University, and Tuszynski has a career stretching back to 1980. Perhaps a slight rewording is in order. Persephone19 (talk) 20:29, 14 September 2009 (UTC)

 * The article itself is very informative, which is great! However, more citations are needed if the article itself is going to improve. Each claim needs a verification Kfh123 (talk) 08:20, 16 August 2012 (UTC)

Body
Small but expandible. —Preceding unsigned comment added by 216.186.77.139 (talk) 17:57, 17 December 2009 (UTC)

Microtubules and Consciousness: The Debate Reborn
So a new section on the Penrose theory has been added to the page. This topic was long the bane of this talk page, and that alone causes me to feel unease at its return. The inclusion of a Microtubules and Consciousness section was debated until its removal on: 20:57, 22 January 2008 by user 198.70.211.246. In the absence of any newly emerged reasons as to why this section should be a part of this article, I am going to defer to precedent and remove the section. --AaronM (talk) 15:28, 23 December 2009 (UTC)

The consciousness section has no place here. I have spent two decades performing research on microtubules and what this page needs is a lot of work, not Penrose pseudoscience. Could a new entry be made were all this quantum consciousness speculation can be stuffed? (Microtubules (talk) 01:54, 31 August 2011 (UTC))

 * I think it's rather ridiculous to accuse someone like Penrose of pseudoscience here especially considering that Bandyhopadhyay confirmed that qubits exist in microtubules anyway. Even if controversial, the work being done to connect consciousness with microtubules should be mentioned in the page. --jfraatz

 * What you think is not relevant, especially when in the form of a fallacious argument from authority. The microtubules and consciousness stuff is pseudoscience, regardless of Penrose's formidable credentials and contributions to physics. BTW, your characterization of what Bandyopadhyay showed begs the question because it assumes the Orch-OR model in the first place. -- Jibal (talk) 20:59, 1 July 2023 (UTC)

 * This is a tricky one and I'm not sure how best to proceed. We (Cancer Research UK) have linked here from a recent press release and this paragraph's existence has been subsequently flagged as a concern by a member of the public. While we are keeping the link for the time being (the rest of the information is sufficiently useful to warrant this) I just thought I'd flag up these wider implications to other editors. All that said, I do agree with some of the other arguments - that Penrose's paper exists, as does the controversy around it, and that an Encyclopaedia should try to be comprehensive. On balance I think I'd be more comfortable with the suggestion of creating a new page on Quantum Consciousness and hosting this info there. Any other thoughts on the matter? HenryScow (talk) 14:15, 5 September 2011 (UTC)

 * I agree. The Quantum Consciousness should be on a separate entry. It should absolutely not be in the Microtubule section. Orangutans (talk)

I came here looking for information about the quantum effects which they claim supports their theory so that I may evaluate the evidence in a neutral environment. While controversy clearly makes a lot of people's neocortex malfunction there is no reason for why those results too should be censored. - nos 84.248.91.157 (talk) 19:53, 8 October 2020 (UTC)

 * Nothing is being "censored". Jibal (talk) 21:01, 1 July 2023 (UTC)

Removing Dynamic mechanism
The section on "Dynamic mechanism" is an odd one. First, it is unmotivated, incomplete and off-topic. Furthermore, considering the vast literature on MTs, both experimental and theoretical, including reference to this largely esoteric result is really inappropriate. A look at the talk page of the author of the section is informative. It appears as though the author has a habit of self-citation (see the revision history of Graph theory for a good example). Web of Science confirms my impression that the referenced paper is a small fish in a very big pond. Of its 37 citations, the only citing papers that are about MTs are from the consciousness crowd (Hameroff, Tuszynski et al.) which, in my view, does not exactly bolster its relevance here. I removed the section once (readded by AaronM) and will do so again shortly unless someone posts a reasonable defense of it's inclusion. -- Cytryn (talk) 16:29, 28 August 2010 (UTC)

 * Agreed. Wikipedia is not the place to publicize yourself. I reverted the removal before as a reflex, since I didn't see any discussion on it and figured it might just be a vandal deletion (since it was by an unnamed user at the time). But now having re-read it, I agree that this level of detail does not belong in the article and should be removed. --AaronM (talk) 01:25, 31 August 2010 (UTC)

Error
I think there's an error here: "This complex acts as a scaffold for α/β tubulin dimers to begin polymerization; it acts as a cap of the (−) end while microtubule growth continues away from the MTOC in the (+) direction."

How come the image shows the cap at the + site, whereas it says it's at the - site?

In the image, the green b-tubulin are at the + site, and it says the 2 b-tubulin subunits shown are the cap site. However, in the quotation, it says that the YtRC acts as a cap of the - site, contradicting, thus, the image explanation. Besides, it says this complex acts as a scaffold for POLYMERIZATION [from + site].

I dont get it — Preceding unsigned comment added by 200.106.164.193 (talk) 01:15, 18 July 2012 (UTC)

Mercury Amalgam, Microtubulin, Alzheimer's AND University of Calgary Team
It would be good to have a section on Mercury Amalgam and its effects on microtubulin in the brain at low levels (found in those with amalgam fillings). This is on youtube which shows the work of the University of Calgary team as relates to microtubulin in the brain.

AnInformedDude (talk) 00:42, 10 October 2012 (UTC)

Persinger
There is a statement in "Postulated role in consciousness" that reads thus:

"While at least one researcher, Michael Persinger, claims otherwise, Jeffrey Gray states ... that tests looking for the influence of electromagnetic fields on brain function have been universally negative in their result."

While I agree that Michael Persinger has shown the influence of magnetic fields on cognition, I am not aware of him making "claims" about consciousness itself. Persinger's experiments have altered the content of consciousness, but as far as I know he does not claim that he is altering the fact that consciousness is present. For this reason, I added a "citation needed" in the text. Timothy Campbell (talk) 18:30, 17 June 2013 (UTC)

Removing Penrose/Moving (again)
Please can this section be removed from the page. As an active researcher in the microtubule field, I don't see how an unsubstantiated theory that is not well accepted by the scientific community should be included in an encyclopaedia entry. — Preceding unsigned comment added by 133.1.233.36 (talk) 02:19, 23 July 2013 (UTC)

 * Agreed. This is an extreme minority viewpoint, and falls under the domain of WP:FRINGE. The mathematical and scientific basis of Orch-OR is almost universally rejected by mathematicians and scientists. It doesn't merit its own section in Microtubule. Not even a subsection. Even a See also link is unduly generous.
 * Between his accusations of vandalism and dishonesty, 24.192.195.236 declares that "This is an actual hypothesis" and "... it is a scientific case nevertheless". But that's not the point. It's a hypothesis advocated by an extreme minority, with no supporting evidence, and crippling evidence against it.
 * Someday, new evidence may lend credence to Orch-OR. But until it progresses beyond a minority theory in poor standing, it is inappropriate to present the Orch-OR hypothesis in this context, in this fashion. To do so gives Orch-OR WP:UNDUE weight.
 * "Views that are held by a tiny minority should not be represented except in articles devoted to those views (such as Flat Earth)... Even plausible but currently unaccepted theories should not be legitimized through comparison to accepted academic scholarship." – WP:NPOV
 * — wing  gundam  01:06, 5 August 2013 (UTC)

 * Agreed some more ;) This has been discussed so many times in the talk above, until the objections above are no longer valid this section should not be on this page Fisman (talk) 06:05, 5 August 2013 (UTC)

 * Remove the section. As someone who has studied MTs for the past few decades, (and as I've stated before in this page), no work has been done to support this wild speculation. Microtubules (talk) 19:56, 5 August 2013 (UTC)

 * Excuse me, but quite a lot of work has been done. The articles listed were out-of-date (Tegmark's paper was from 2000 and the Jeffrey Gray reference from 2004, before the quantum bio stuff on microtubules appeared), and it is not "fringe" in the way that flat-Earth theories are. It is falsifiable, and criticisms like Tegmark's have been addressed quite directly several times, either directly by Hameroff or even by Danko Georgiev! The statement that the criticisms are "crippling" is not quite right, either. I have been in correspondence with Hameroff quite a bit, and said that though the A- vs B-lattice distinction was a mistake, Orch-OR can still work with it. This isn't ad-hoc, it just wasn't necessary in the first place. Also, I'm not sure how much merit Georgiev's claims have. I've looked at some of the Hameroff papers and again, dendritic lamellar bodies were considered at one point, but weren't essential to the hypothesis as a whole. I'm not sure Hameroff (and his team) mismodelled the DLBs either, since he never required them to be as close as Georgiev said they needed to be. This might help: http://www.quantumconsciousness.org/biosystemselsevier.htm. Hameroff et al. even REFERENCE de Zeeuw's paper! 24.192.195.236 (talk)

 * There are no known or proposed mechanisms by which microtubules could become entangled or support for Penrose's theory in any other respect. The notion of tubulin condensates was introduced ad hoc to provide a mechanism for Orch-OR, and it has been discredited. If there is some other mechanism, then that should be put on the appropriate page if any evidence is found. But until then, it doesn't belong on an encyclopedia, and it certainly doesn't belong on the page on microtubules. Eebster the Great (talk) 01:23, 6 August 2013 (UTC)

 * Also, entanglement of microtubules is still being tested by the Bandyopadhyay group in Japan. 24.192.195.236 (talk) 12:56, 6 August 2013 (UTC)

 * I really don't know or care who the Bandyopadhyay group are. But if this testing is still ongoing and hasn't been published, then it still doesn't belong in this article. It may belong in the article on Orch-OR. Eebster the Great (talk) 05:20, 7 August 2013 (UTC)

 * "I have been in correspondence with Hameroff quite a bit..." — Then you may want to refrain from editing articles related to his theories. Some editors will view this private communication as a significant risk of WP:POV. — wing  gundam  02:27, 6 August 2013 (UTC)

 * "Then you may want to refrain from editing articles related to his theories. Some editors will view this private communication as a significant risk of WP:POV." I thought it would be best to get the response from the horse's mouth, knowing how controversial this debate is and how much of a conflict of interest there is from both rival models and AI groups. I don't see how that's "violating" anything. Also, the Bose-Einstein and Frohlich condensates were BOTH considered from the start, and Orch-OR is fine with weak condensation. I don't think there was anything in the older papers that contradicted this, so it doesn't seem ad hoc. Also, Orch-OR was open to change from the start, but the central hypothesis of topological quantum computing in microtubules remains the same. It's not ad hoc at all. Also, the JoC reference was NOT Hameroff's response. His response was first presented at TSC 2010, and I think he is working on a peer-reviewed response with commentary by Reimers and McKemmish as well. 24.192.195.236 (talk) 12:32, 6 August 2013 (UTC)
 * how much of a conflict of interest there is from both rival models and AI groups
 * That's not conflict of interest. OTOH, you seem to have some. Jibal (talk) 20:27, 1 July 2023 (UTC)

 * I've been forced to full-protect this article because some editors--even non-new ones (i.e., "you should know better!")--seem unable to contain their enthusiasm pending this discussion's outcome. DMacks (talk) 01:41, 6 August 2013 (UTC)

 * As a researcher in the field I will say that the wild speculations by Penrose et al., have not been validated and are based on zero experimental evidence. Can supporters of this unvalidated idea provide links to any empirical evidence? In contrast, until yesterday the microtubule page was missing information on the capture search model, one of the most important theoretical developments in microtubule biology (Kirschner et al. Cell 1986, http://www.ncbi.nlm.nih.gov/pubmed/3516413) cited 975 times! I think that this reflects that much of the page was eddited by non-experts. The journal Nature had made a collection of the most important milestones in cytoskeletal reseach: http://www.nature.com/milestones/milecyto/full/milecyto01.html. The Penrose model is not part of the list. In contrast dynamic instability and the search and capture model of microtubule function is milestone 14. Microtubules (talk) 12:04, 6 August 2013 (UTC)

 * I understand, but you're just asserting that there's "no evidence" when there IS evidence to support quantum processes related to microtubules. I'm also not sure what citing those articles from 1986 and 2008 have to do with anything. The evidence for the Orch-OR hypothesis and its plausibility are only starting to perk up from quantum bio. — Preceding unsigned comment added by 24.192.195.236 (talk) 12:42, 6 August 2013 (UTC)

 * Please provide links to published peer-reviewed articles that provide EMPIRICAL evidence. This evidence should consist of the verification of falsifiable hypotheses that stem from this work and tested with microtubules either in vitro or in vivo. 13:00, 6 August 2013 (UTC) — Preceding unsigned comment added by Microtubules (talk • contribs)

 * Well, I am a layman, but I think I have some stuff. Freeman and Vitiello showed that global gamma synchrony requires some kind of intra-neural quantum mechanism (they suggested quantum field theory): http://sulcus.berkeley.edu/wjf/ff%20freeman-vitiello%20qft.pdf. In addition, Karl Pribram published a great deal of material on how the brain behaves like a holonomic system (this seems to be a good summary): http://www.scholarpedia.org/article/Holonomic_brain_theory. Sahu et al. have found conductance in a single microtubule at room temperature that seems to be above Tegmark's limit (already published), and Bandyopadhyay has presented preliminary evidence for topological qubits in microtubules (yet to be published, but presented at various TSC conferences). Here's his talk: https://www.youtube.com/watch?v=VQngptkPYE8/, and the paper: http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=6487877&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D6487877. I hope this helps. 24.192.195.236 (talk) 13:38, 6 August 2013 (UTC)

 * There's this paper (Op-Ed?) by Nick Navromatos which is a nice overview of how this quantum bio stuff relates to microtubules: http://iopscience.iop.org/1742-6596/329/1/012026/pdf/1742-6596_329_1_012026.pdf/. Also, quantum computer scientist Scott Aaronson, an avowed skeptic of Penrose's ideas, also admits there's some truth to there being quantum information in the brain: https://www.youtube.com/watch?v=tMMBaC7QRO0. 24.192.195.236 (talk) 13:53, 6 August 2013 (UTC)

OK, after going through these two papers, I can summarize what they found and give you an analysis. In Sahu et al., they applied various AC or DC currents to an isolated microtubule and measured conductivity (Figure 2e, f). Microtubules conduct current and there seems to be two types (resistance of 1–10 MΩ and ~300 MΩ). In Figure 3 various electric fields are applied to the MT and the conductance changes, although no rigorous statistics are shown. In Figure 4 the authors claim that changes in applied voltage change the shape of the microtubule as seen under atomic force microscopy. The second paper by Mavromatos is purely theoretical. He claims that microtubule polymers may again adopt two forms (analogous I suppose to the two conductive forms) and goes over some ideas of conductance and integrates this with models that the microtubule lattice may help to order water in the microtubule lumen.

 * I understand that. I even indicated that in my response to you. 24.192.195.236 (talk) 22:48, 6 August 2013 (UTC)

Leaving aside some of the factual errors in each paper (microtubules did not appear 3.5 million years ago, there is no Ca2+ imbedded in the microtubule protofilaments ...),

 * They said 3.5 billion years, when the first prokaryotes appeared. And where did they bring up Ca2+ again? 24.192.195.236 (talk) 22:48, 6 August 2013 (UTC)

 * Perhaps the 3.5 million years was a typo on their part. The Ca2+ is in Mavromatos paper, page 3. Microtubules (talk) 00:10, 7 August 2013 (UTC)

 * It says 3.5 billion on my copy, dude. It seems like Tegmark and Navromatos think it to be common knowledge. Why do you say otherwise? 24.192.195.236 (talk) 01:14, 7 August 2013 (UTC)

 * From Sahu et al. "Figure 1a shows tubulin protein and the protein made microtubule, a 25 nm wide and 200 nm to 25 μm long nanowire that appeared in the living cell for a mysterious reason, nearly 3.5 million years back." Microtubules (talk) 02:33, 7 August 2013 (UTC)

 * Look at the abstract... 24.192.195.236 (talk) 04:21, 7 August 2013 (UTC)

I would say that the authors of the first manuscript provide some data supporting the idea that microtubules have some electrical properties (however other groups have also shown this) and these properties may display some features that depend on dipole moments that may be in some entangled state. So what? How does this translate to any physiological effects? How does it impinge on neuronal behavior?

 * You're making these discoveries a great deal less important than it really seems. From where I've looked, all of this is a relatively new group of discoveries. Also, it would probably impinge on neuronal behavior by providing a mechanism to mediate gamma synchrony. 24.192.195.236 (talk) 22:48, 6 August 2013 (UTC)

 * Microtubules monomers have dipoles that may interact within the polymer - is that surprising? Nucleotide base pairs along the DNA axis also have dipole moments that interact with each other, likely with much higher ΔGs. Microtubules (talk) 00:10, 7 August 2013 (UTC)

 * OK. 24.192.195.236 (talk) 01:14, 7 August 2013 (UTC)
 * You're making these discoveries a great deal less important than it really seems.
 * What an ironic comment. "really seems" to whom?
 * For reasons that clearly escape you, your comments make a strong case for not including this stuff here, and other editors inclined to include it can be pointed toward your comments as to why it shouldn't. Jibal (talk) 20:44, 1 July 2023 (UTC)

If these effects are used to perform computations, how does data input occur in vivo (what is the source of the data? what writes the data?) and then how is the output read in vivo. The authors do not even attempt to come up with a plausible scenario for how biological molecules perform data input/output on microtubules.

 * That's because others have done so, including Hameroff as well as Shi et al. The input is provided by other proteins and microtubules. The tests have been performed at ambient room temperature. Also, Hameroff has said that the Japanese group is testing for resonance transfer between separated microtubules. Do you think the Sahu et al. results are close to the quantum limit? 24.192.195.236 (talk) 22:48, 6 August 2013 (UTC)

In contrast Mavromatos points to other systems where quantum effects do play a role in biological processes. For example in photosynthetic process, where we have an exact understanding of how energy states are transferred between molecules and how this is leads to the production of a proton gradient across a membrane. The gradient is then disipated by F1 ATPase to regenerate ATP. In this case, the underlying mechanism is clear – quantum states translate to the movement of protons. However I am puzzled by the statements being made with respect to microtubule function, such as microtubules “compute”. What does this mean? What is the mechanism that reads and writes? How could this possibly affect physiology? In short, there is no there there. Indeed Navromatos writes “I believe that very interesting future experiments can be done with MT, which could shed light on the above aspects of MT as quantum devices, which presently belong to the realm of science fiction.”

 * Again, please see Hameroff's and others' papers for more. I'm still trying to make head and tail of all this, but the computing power of microtubules, including the input-output power of proteins like CaMKII and protein orchestration, seems to be being discussed in detail in the literature. Also, Navromatos was waiting for further experiments to be done, and they ARE being done and published. Finding what we have regarding Frohlich condensation is a pretty decent development, if you ask me! 24.192.195.236 (talk) 22:48, 6 August 2013 (UTC)

 * If you are referring to this: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002421 that's just more speculation.

 * I wasn't specifically referring to that, but fine... 24.192.195.236 (talk) 01:14, 7 August 2013 (UTC)

 * If you are aware of any other data, send it my way and I will try to give you my 2 cents. Microtubules (talk) 19:04, 7 August 2013 (UTC)

 * From the abstract "Using molecular mechanics modeling and electrostatic profiling, we find that spatial dimensions and geometry of the extended CaMKII kinase domains precisely match those of MT hexagonal lattices. This suggests sets of six CaMKII kinase domains phosphorylate hexagonal MT lattice neighborhoods collectively". That's nice, but so what? The entire paper is based on modeling, i.e. speculation without empirical data. They don't know if it binds or phosphorylates microtubules in vivo. In fact they write: "Wandosell et al. [34] showed that free, unpolymerized α- and β-tubulin are phosphorylated by activated CaMKII on or near the C-terminal region (beyond residue 306), resulting in tubulin conformational change, inhibition of assembly and inability to bind MT-associated protein 2 (MAP2)." So if anything CaMKII phosphorylation would cause microtubule disassembly based on this in vitro result. (Note that kinases are notorious for being promiscuous in their ability to phosphorylate substrates in vitro, and many times the results do not match what occurs in vivo).

 * Er... I'm not sure it would result in that. Wouldn't CaMKII result in assembly AND disassembly? That was the impression I got from the paper, but I could be wrong. 24.192.195.236 (talk) 01:14, 7 August 2013 (UTC)

 * "inhibition of assembly" = disassembly. Microtubules (talk) 02:30, 7 August 2013 (UTC)

 * Thank you, Captain Obvious. I know that's what the passage you quoted talks about, but it indicates there might be other possible things for what CaMKII can do that we haven't heard before. Also, what did you think of Bandyopadhyay's talk? 24.192.195.236 (talk) 04:21, 7 August 2013 (UTC)

 * Please. If you are going to use this tone, I will halt this discussion. Biochemical reactions under a set of conditions will head towards equilibrium. If CaMKII mediated phosphorylation inhibits assembly (i.e. pushed the molecules to a new equilibrium where monomers are fovored over polymers) then the same reaction cannot also promote assembly. Microtubules (talk) 05:04, 7 August 2013 (UTC)

 * I apologize. I've had to deal with some of the most patronizing people you can imagine, and I jumped too soon. What I meant was that it can aid assembly in other locations, as I gathered from the paper. By the way, you keep getting hung up on this when it wasn't the only thing I presented to you. 24.192.195.236 (talk) 14:06, 7 August 2013 (UTC)

 * In any case, why would this particular phosphorylation event matter? Again the authors speculate without providing empirical data. Does depleting or inhibiting CaMKII disrupt consciousness? microtubule function? Just like any kinase, there are commercial inhibitors available (Merck sells a compound called CK59), this would be easy to test, but where is the empirical data? Again if there are any other publications, send them my way. Microtubules (talk) 00:10, 7 August 2013 (UTC)

 * Well, from what I can tell, they think that CaMKII matches up with the proteins of a microtubule "perfectly", and can assist in information transfer between microtubules and gap junctions, as far as I can tell (15:38-20:06): https://www.youtube.com/watch?v=Mm6Mt9BoZ_M&list=PLA425A0C01A9082DD Here's the previous paper. I think the paper you read was building off this: http://www.quantumconsciousness.org/documents/membytespublished.pdf This is also interesting: http://jcb.rupress.org/content/198/6/1055.short 24.192.195.236 (talk) 01:14, 7 August 2013 (UTC)

 * Models are a dime a dozen in biology. As an experimentalist, my lab has come up with many beautiful ideas only to see them go down in flames. That's why biologists really insist on empirical data. Even when structure biologists propose some model based on 3D information, it is usually understood that they should test it empirically. Microtubules (talk) 02:30, 7 August 2013 (UTC)

 * Excuse me, but I wouldn't be so quick to dismiss all of this as "just modeling". I have a feeling that you're just dismissing this for no good reason. This is a plausible model that accords with what we know. Tests are underway by many scientists, not just one tiny lab, and it seems likely that it will work. AND it's separate from Orch-OR. It's more of a side project that may or may not affect the main hypothesis. 24.192.195.236 (talk) 04:21, 7 August 2013 (UTC)

 * I am dismissing it bacause it is not rigorous. I'm sorry to say but science is tough. I spent 10 years of my life making models and understanding microtubule dynamics. It is one thing to come up with models, but hard data is another thing. After years of work I learned how cells organize their microtubule arrays. But it took a long time and a lot of experimental work. To just come in and line up some 3D models is nice but unless there is empirical data it is all just speculation. If people are testing these, great! When the data is out and they present a convincing case then we'll look at what they have to say, but untill then it is just a nice idea. Microtubules (talk) 05:04, 7 August 2013 (UTC)

 * I presented it to you in the first place because you asked for a mechanism on how a microtubule can receive its input if it were a computer. I was honoring the request. 24.192.195.236 (talk) 14:06, 7 August 2013 (UTC)

 * I'm glad that you pointed out this work. I would rather discuss data then have some ethereal argument. But realize that it is incumbent on those who make the case for quantum effects in microtubules to bring forward pieces of experimental evidence. It is also important that you listen to our criticism. People claim that scientists are conservative. That is missing the point. As an experimentalist, especially in biology, you learn very quickly to be careful. 99% of the time the underlying mechanisms are only discernible after much experimental work. This is what many physicists who enter biology fail to understand, mostly out of a lack of experience dealing with biological systems. Microtubules (talk) 16:53, 7 August 2013 (UTC)

So all of this work is very speculative, and I do not think that the few investigators studying quantum effects on microtubule function have made a compelling case for their physiological relevance. In contrast, many more labs are investigating the post-translational modification of microtubules (for a recent review see Janke & Bulinsky in Nature Rev MCB (2011) - with 186 references, http://www.fbmc.fcen.uba.ar/materias/qbiia/teoricos-2012/teorica-4-bibliografia-de-apoyo-de-graciela-bocaccio/micotub%20PTM%20by%20cloe%20bulinsky.pdf), yet until yesterday this extremely active area of research was not even mentioned on the microtubule page. Microtubule modifications are known to affect how motors interact with tubulin and how organelles are transported along the microtubules. In this case there is physiological relevance. And findings from this very active area are published in Science (http://www.ncbi.nlm.nih.gov/pubmed/15890843), Nature (http://www.ncbi.nlm.nih.gov/pubmed/12024216) and Cell (http://www.ncbi.nlm.nih.gov/pubmed/19524510)! I point this out to contrast the two fields, the first is speculative and thus far does not seem to be conected to physiological relevance (but was included on the microtubule page), the second is a very active field (but until yesterday was not even mentioned). Microtubules (talk) 21:57, 6 August 2013 (UTC)

 * Again, I get how great research on microtubules is doing. You do not need to remind me. Nevertheless, I appreciate the discussion. 24.192.195.236 (talk) 22:48, 6 August 2013 (UTC)

 * Microtubules are one of the most studied cellular components. There are MANY theories and speculations as to what they do. This page should be about what has been established. Microtubule modifications have been studied for close to 40 years, and is a well established field that has given us insights into how cell polarity is generated. Quantum effects on the microtubule lattice is at the level of speculation and has yet to been established, let alone provide any novel insights. Microtubules (talk) 00:10, 7 August 2013 (UTC)

 * I know the page should talk about things that have been established. But it was labeled "postulated" for a reason. It's not "bad science" and it's certainly not "fringe" in the way flat-Earth "theories" are. I find that to be a straw-man. Is there a way to compromise and say that it's postulated but convincing evidence has yet to show up? It's hardly "bad science". You could even say "It was considered, but there's been a lack of development." I'm not even sure about there not being any development whatsoever, but you don't need to cut it out completely. 24.192.195.236 (talk) 01:14, 7 August 2013 (UTC)

 * You have to realize that my main critique is that these ideas are just speculation. Theories are a dime a dozen, especially in biology. This page should not about speculation but about what is known. This not only applies to Penroses' ideas, but also cytoskeletal tensegrity, tubulin healing, microtubule luminal transport or other speculative ideas that have arisen through the years. Microtubules (talk) 02:21, 7 August 2013 (UTC)

 * OK. I don't have any authority to say anything about this, but I'm starting to think that you're dismissing all of this as "speculation" because you don't like it. This is a very plausible idea, one that has evidence from our knowledge of CaMKII and the computing abilities of microtubules. Also, what about the topological qubits Bandyopadhyay claimed he found, or the Freeman-Vitiello article? 24.192.195.236 (talk) 04:21, 7 August 2013 (UTC)

 * And I wouldn't call it "mere speculation" either. 24.192.195.236 (talk) 04:21, 7 August 2013 (UTC)

 * Look, I'm skeptical for a reason. We currently have good models for how information is conveyed between cells. We have a decent understanding of the principles of how long term potentiation (strengthening of synapses to form new memories) works. We have a good understanding of how microtubules contribute to neuronal function. I'm not talking about plausible theories, but concepts that have been tested and verified. When the model of CaMKII affecting microtubule-driven consciousness has convincing empirical data to back it up (i.e. makes falsifiable predictions that have been experimentally tested), then it will be accepted. This is how science works. Science is not about whether we like or dislike plausible ideas. Microtubules (talk) 05:04, 7 August 2013 (UTC)

 * I understand how science works. It's still a plausible option which has yet to be tested (and is currently being tested). You asked for a mechanism. I gave it to you. 24.192.195.236 (talk) 14:06, 7 August 2013 (UTC)

 * To understand my skepticism, see Philosophic burden of proof. Microtubules (talk) 11:32, 7 August 2013 (UTC)

 * I understand that I have the burden of proof. 24.192.195.236 (talk) 14:06, 7 August 2013 (UTC)

 * I'll give it too you that the CaMKII angle is at least a starting point. But as my thesis advisor once told me, this story is not ready for prime time. Microtubules (talk) 16:53, 7 August 2013 (UTC)

 * The kinase is a candidate for memory sharing and input. It isn't really the quantum-mechanical aspect of the hypothesis. That comes from Bandyopadhyay's work in finding topological qubits in a single microtubule at room temperature, which is a first even if it's in vitro. This stuff is a lot more open than you think, and the people who are promoting it have the academic rigour to back it up. For that reason, I wouldn't call this postulated role in consciousness "pseudoscience". 24.192.195.236 (talk) 20:05, 7 August 2013 (UTC)

 * In fact, I am aware of some of the CaMKII literature as its mRNA is known to be transported to dendrites. The local translation of the CaMKII mRNA on the post-synaptic side of activated neuronal connections has been implicated in LTP (part of my lab currently studies mRNA localization http://biochemistry.utoronto.ca/palazzo/index.htm - in fact I was just at the mRNA localization meeting a month ago where some aspects of CaMKII mRNA transport were discussed). But I think that the data linking it to "reading" or "writing" data on microtubules is at best speculative. Again, when more rigorous data on this is published, feel free to let me know (i.e. post a link in my talk page) and we can discuss the data further. To reiterate, it is not enough to state that data exists, point to the relevant publication and then we can analyze the results. Microtubules (talk) 22:48, 7 August 2013 (UTC)

 * Re:"This stuff is a lot more open than you think, and the people who are promoting it have the academic rigour to back it up." Please provide published refs. Many scientists push their pet ideas, but the degree of "promotion" is not how we evaluate competing theories. Microtubules (talk) 22:58, 7 August 2013 (UTC)

 * OK. Thanks for your time. 24.192.195.236 (talk) 00:42, 8 August 2013 (UTC)
 * So he conceded, then. — wing  gundam  01:13, 9 August 2013 (UTC)
 * No, not even that. From WP:FRINGE:
 * "Wikipedia is also not a crystal ball: While currently accepted scientific paradigms may later be rejected, and hypotheses previously held to be controversial or incorrect sometimes become accepted by the scientific community (e.g., plate tectonics), it is not the place of Wikipedia to venture such projections. If the status of a given idea changes, then Wikipedia changes to reflect that change. Wikipedia primarily focuses on the state of knowledge today, documenting the past when appropriate (identifying it as such), and avoiding speculation about the future."

 * — wing  gundam  02:19, 7 August 2013 (UTC)

This is not a place to discuss the scientific merits of Orch-OR. This is an issue of scientific acceptance, and under WP:NPOV, Orch-OR cannot be mentioned in this article.

Orch-OR departs from mainstream science, and has little scientific support; it is classifiable as a fringe theory in science under WP:FRINGE, and subject to heightened scrutiny. From WP:FRINGE,

 * "Fringe views ... may be mentioned in the text of other articles only if independent reliable sources connect the topics in a serious and prominent way."

In this context, a reliable secondary or tertiary source is required. An acceptable source would be a review article on recent microtubule work in Nature Reviews Molecular Cell Biology that positively highlights Orch-OR's direct implications to the field, or an undergraduate textbook on cell biology that mentions Orch-OR in a serious fashion in connection with microtubules.

There exist no reliable WP:secondary or WP:tertiary sources that do this. Therefore, per WP:ONEWAY, a decent article on microtubules should not mention Orch-OR. — wing  gundam  02:05, 7 August 2013 (UTC)

 * Excuse me, but serious and prominent sources are being considered here. Please realize that. I am not promoting a conspiracy theory. And your saying that it's fringe doesn't make it so. I don't even get that impression from the sources I've been reading. It may be a minority view, but it's a significant enough view that you should at least mention it, since it's been getting quite prominent due in rather respected journals, and there is good reason to think it might be correct. 24.192.195.236 (talk) 04:21, 7 August 2013 (UTC)
 * Fallacious argument from authority. None of your comments here reflect any understanding of either Wikipedia policy or critical thinking. What you are or are not promoting, your impressions, what you think should be done--these are facts about you that have no relevance here. Jibal (talk) 20:20, 1 July 2023 (UTC)
 * I've seen them. Jeffrey Gray had good things to say about it in CONSCIOUSNESS: CREEPING UP ON THE HARD PROBLEM. I've seen some others too. I'll try to bring them around. 24.192.195.236(talk) 04:21, 7 August 2013 (UTC)
 * By the way, to say that Orch-OR has been "universally rejected" is dishonest, as I've told you before. A more accurate description would be "widely-criticized," and understandably so, since half the people you cite either sympathize with Penrose or Hameroff's positions or have a conflict of interest over the hypothesis. All you need to do is read Danko Georgiev's or Solomon Feferman's papers to figure that out. 24.192.195.236 (talk) 04:27, 7 August 2013 (UTC)

 * Per WP:V, the WP:ONUS is on you to prove it has significant scientific traction (i.e. is not fringe). The burden of proof is yours. And you don't appear to understand what constitutes fringe on Wikipedia. PLEASE review WP:FRINGE, WP:NPOV, and WP:RS.
 * And as I said, you must provide reliable secondary or tertiary sources that discuss microtubule biology, and mention Orch-OR. This would include a review article in Nature Reviews Molecular Cell Biology, or a critically reviewed textbook on cell biology, or a mention in Nature's milestones. Yet Orch-OR has none of these.
 * An independently published book (like the Jeffrey Gray) is absolutely not a reliable source in this context. Please provide a peer-reviewed article from a notable journal, that reviews microtubule discoveries, and mentions Orch-OR in a serious, non-critical fashion.
 * "I'll try to bring them around." — If they are like your Gray source, don't bother.
 * "to say that Orch-OR has been "universally rejected"..." — please restrain your comments to this article, to keep down the clutter, and per WP:TALK. If you have an issue with another article, feel free to bring it up on that article's Talk page. But not here.
 * — wing  gundam  05:41, 7 August 2013 (UTC)

I'm really impressed with Microtubules', 24.192.195.236's and  wing  gundam  's  dedication to this discussion. The last time I commented on this talk page, I considered commenting on the Penrose material but noticed how intense people seem to get about it so I dropped it to avoid wasting a bunch of time. Given that Microtubules picked up the banner, I figure I may as well chime in. I've read a bit of Penrose's work (The Emperor's New Mind) but not much about his theories of microtubules and consciousness. As someone who works on modeling of microtubules and FtsZ in cell division, almost entirely theoretical, I can say that I strongly agree with Microtubules concerning the value of models and theories. They are a dime a dozen and should not be included in an encyclopedia article simply because someone famous proposes or endorses them or because they generate controversy in the realm of popularized science. Substantiation is essential. Sure, a controversial topic has a place in an encyclodepia - in an article about the primary topic (e.g. Orch-OR) but not in an article on one of the players invoked in the theory. As to whether Orch-OR is one such theory, consider the principle that "extraordinary claims require extraordinary proof". Orch-OR strikes me as a classic extraordinary theory. It would not attract the interest of non-scientists in the way it does nor would it fail to attract the interest of scientists the way it does if it weren't. I haven't read enough to weaken the adjective on "proof" but it's clear from the few sources I've looked at so far that extraordinary proof is definitely lacking. As such, including reference to it in the articles about its component parts is inappropriate. --Cytryn (talk) 23:06, 7 August 2013 (UTC)

 * I agree with Microtubules' statement that "Models are a dime a dozen", as well. As he mentioned above, there are many unproven conjectures about microtubules, and it would violate WP:NPOV to include any of them in Microtubule.
 * And moreover, this isn't an arbitrary requirement. Orch-OR can't be mentioned in this article for the same reasons it can't be mentioned in General relativity, Quantum mechanics, or Gödel's incompleteness theorems. It is a fringe theory of science, and there exist no reliable secondary or tertiary sources that connect any of these to Orch-OR.
 * This article cannot become a WP:COATRACK for Orch-OR. — wing  gundam  00:56, 8 August 2013 (UTC)

Consensus opinion
Summarizing the consensus opinion, we find that Orch-OR cannot be mentioned in the Microtubule article. Pursuant to this, we hold that the section #Postulated role in consciousness should not be reintroduced. While Orch-OR may turn out to have scientific validity some basis in reality, that is not for us to judge. We merely document the established views of the scientific community, wherein we note Orch-OR is an unproven minority viewpoint and consequentially the subject matter of WP:FRINGE.

As User:Microtubules and User:Cytryn argued, there are many hypothetical models for microtubules, including Penrose/Hameroff's ideas, cytoskeletal tensegrity, tubulin healing, microtubule luminal transport, and others equally speculative. Models like these are "a dime a dozen". To be mentioned in this article, an independently reviewed secondary or tertiary source must directly connect microtubules to some particular model. (e.g. a review article in Nature Reviews Molecular Cell Biology, a critically reviewed textbook on cell biology, a mention in Nature's cytoskeletal milestones). There exist no such sources for Orch-OR. Thus, it would be a violation of WP:NPOV for Microtubule to include any discussion of Orch-OR, however minor.

— wing  gundam  01:48, 9 August 2013 (UTC)

 * Instead of "While Orch-OR may have scientific validity, ..." I would write "While Orch-OR may turn out to have some basis in reality,..." It is my impression that "scientific validity", implies that the theory in question is backed by our current scientific understanding. This is not the case for Orch-OR. It remains in the realm of speculation. Microtubules (talk) 18:17, 9 August 2013 (UTC)

 * Wow quite a long discussion there. May I then just chime in that I also agree with the consensus opinion above. I have searched everywhere for empirical data which supports Orch-OR and found none. As mentioned above, if it is just a model/proposed theory with no experimental (scientific) data to back it up then it is truly WP:FRINGE and should be treated as such until an experiment has been conducted to support it. Fisman (talk) 07:37, 14 September 2013 (UTC)

Organization during cell division
I did a major edit of the section on organization during cell division. I hope I got the centromere/centriole thing correct (had no idea about that before I read the talk page!); feel free to correct that if I got it wrong. Also, I'm not entirely sure I got it right about polar microtubules. From the article on centromeres, it seems like there's a type of microtubule called the polar microtubule which assists in cell division, but there's also the fact that all microtubules are considered to be polar due to the end-to-end orientation of the dimers. And of course both of those definitions have nothing to do with the polarity that exists in some molecules such as water. It's very confusing! Jojojlj (talk) 07:13, 21 October 2013 (UTC)

Electronic properties of single isolated microtubule
This section seems a little out of place and not in keeping with the rest of the article. It's a list of biophysical facts directly taken from one or two papers with no context in particular to any biological application. I  appreciate that other researchers might be looking at microtubules as structures for the development of new computing architectures or explanations for the information processing capacity of the human brain. Yet these viewpoints are held by a minority and I don't believe that an encyclopaedia article should be carrying information on current research that is a minority viewpoint.

Its well known to researchers in the field that the electrostatic properties of tubulin/microtubules are considered to underlie their interactions with various proteins such as MAPs and motors.

Perhaps a section of the physiochemical properties of microtubules/tubulin would better idea?

Image
There is an image with the legend as follows: "This image shows two components of the cytoskeleton, microtubules (green) and actin filaments (red), in an endothelial cell derived from a cow lung. The cystoskeleton provides the cell with an inner framework and enables it to move and change shape."

In my opinion the legend is incorrect. The green structures on this image look like actin fibers, and the red structures look like mitochondria.

--Eszcze (talk) 13:24, 1 March 2015 (UTC)
 * Yes, it seems the two colors were mixed up. The caption was taken from this site. I've contacted the author of the image to confirm it's a mistake and will get back as soon as I hear from her.  SPLETTE  :] How's my driving? 17:01, 17 June 2015 (UTC)
 * I already got a detailed reply from the author of the pic, Tina Carvalho. She explained that the image is problematic for various technical reasons and that it was never meant to be released into the public domain in the first place. It was originally used for a brochure for the NIH and later the NIH decided to also upload the individual image to their website. The caption of the picture is not from the author of the pic but was written by some NIH employee. It is most likely incorrect. Unfortunately, Ms. Carvalho couldn't locate her notes for this particular image (which was created over 12 years ago). She remembers that AlexaFluor 488 was used to stain the phalloidin bound to F-actin and thinks that the red is probably MitoTracker Red and those are indeed mitochondria, not actin!
 * Therefore I am going to remove the pic from the article and replace it with another one, where the labeling is clear. Thanks Eszcze for bringing this up. It's kind of embarrassing that no one else has caught this so far...  SPLETTE  :] How's my driving? 12:28, 18 June 2015 (UTC)

Okay, I started a request for deletion.  SPLETTE  :] How's my driving? 13:05, 18 June 2015 (UTC)
 * Update: Image was deleted from Wikipedia.  SPLETTE  :] How's my driving? 22:26, 29 June 2015 (UTC)

Why don't we add a section (In Culture?) or "See also" part linking to Orch-OR?
Unless so few people know about it. Socialistguy (talk) 17:33, 25 February 2016 (UTC)
 * Agreed. Added to See also.  Thanks, Adrian J. Hunter(talk•contribs) 22:45, 25 February 2016 (UTC)

Assessment comment
Substituted at 23:59, 29 April 2016 (UTC)

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A perfect example of the worst kind of writing in Wikipedia
The article begins with this sentence:

Microtubules (micro- + tube + -ule) are a component of the cytoskeleton, found throughout the cytoplasm.

We can assume that whoever came to read this articles wants to know what microtubules are.

So including the etymology of the word in the first sentence is overloading the sentence with too much extraneous information too soon. (Sure, the etymology is a good thing to include, but not before the reader knows what the word means.)

Next we get to the word "component" which most high school students know, but younger children may not. Why use an unnecessarily advanced word when a word like "portion" or "part" will work?

Then we get to the two worst aspects of this sentence by far: two words — "cytoskeleton" and "cytoplasm" — that are highly unlikely to be in any reader's vocabulary. (Unless of course they are in the small fraction of readers who happen to know the word.)

Such words are entirely inappropriate for an introductory part of an article, and especially the first sentence, above all when simpler words can be used. That is surely true. Do not make the reader click on links in order to know what you are talking about, especially in the very first sentence. There are five links in this first sentence!

I hope the first sentence and paragraph are rewritten by someone knowledgeable about the subject, so that most 9-year-old children can understand it. I see no reason why that could not be the case.108.245.209.39 (talk) 21:14, 14 June 2018 (UTC)

 * These are ridiculous objections. Jibal (talk) 20:08, 1 July 2023 (UTC)

Microtubule diameter
Am I blind, or the information that the diameter of microtubules is 24 nm is not stated in the cited article? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232192 — Preceding unsigned comment added by Vašek Bočan (talk • contribs) 10:01, 22 March 2019 (UTC)
 * Third sentence of the first paragraph. DMacks (talk) 20:38, 22 March 2019 (UTC)
 * This is the third sentence of the first paragraph: "All tubulins evolved from a common ancestor they share with the distantly related bacterial cell division protein FtsZ [5–9], but while eukaryotic a- and b-tubulins evolved into highly conserved tube-forming heterodimers [1,4], bacterial FtsZ presumably continued to function as single homopolymeric protofilaments as it does today [10]." (Not counting the abstract as the first paragraph.) Where is the remark on diameter? Vašek Bočan (talk) 09:27, 24 March 2019 (UTC)
 * Oooh wait, I misread your question. I was thinking you couldn't find the statement in our article (missing WP content), not that you couldn't find support for the WP content in the cited ref. I tagged the ref as being a problem, will research it when I get a chance. DMacks (talk) 14:42, 25 March 2019 (UTC)
 * I have identified primary references for microtubule diameters ranging from 23-51 nm (also different numbers of protofilaments ranging from 10-15). I will add these references to the main text and somehow also include that there is a diversity of structures beyond the "classical" 13-unit protofilaments.Gepasi (talk) 18:15, 22 August 2019 (UTC)

title: Talk:Microtubule


text:
Signal peptide

A signal peptide (sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short peptide (usually 16-30 amino acids long) present at the N-terminus (or occasionally nonclassically at the C-terminus or internally) of most newly synthesized proteins that are destined toward the secretory pathway. These proteins include those that reside either inside certain organelles (the endoplasmic reticulum, Golgi or endosomes), secreted from the cell, or inserted into most cellular membranes. Although most type I membrane-bound proteins have signal peptides, most type II and multi-spanning membrane-bound proteins are targeted to the secretory pathway by their first transmembrane domain, which biochemically resembles a signal sequence except that it is not cleaved. They are a kind of target peptide.

Function (translocation)
Signal peptides function to prompt a cell to translocate the protein, usually to the cellular membrane. In prokaryotes, signal peptides direct the newly synthesized protein to the SecYEG protein-conducting channel, which is present in the plasma membrane. A homologous system exists in eukaryotes, where the signal peptide directs the newly synthesized protein to the Sec61 channel, which shares structural and sequence homology with SecYEG, but is present in the endoplasmic reticulum. Both the SecYEG and Sec61 channels are commonly referred to as the translocon, and transit through this channel is known as translocation. While secreted proteins are threaded through the channel, transmembrane domains may diffuse across a lateral gate in the translocon to partition into the surrounding membrane.

Structure
The core of the signal peptide contains a long stretch of hydrophobic amino acids (about 5–16 residues long) that has a tendency to form a single alpha-helix and is also referred to as the "h-region". In addition, many signal peptides begin with a short positively charged stretch of amino acids, which may help to enforce proper topology of the polypeptide during translocation by what is known as the positive-inside rule. Because of its close location to the N-terminus it is called the "n-region". At the end of the signal peptide there is typically a stretch of amino acids that is recognized and cleaved by signal peptidase and therefore named cleavage site. This cleavage site is absent from transmembrane-domains that serve as signal peptides, which are sometimes referred to as signal anchor sequences. Signal peptidase may cleave either during or after completion of translocation to generate a free signal peptide and a mature protein. The free signal peptides are then digested by specific proteases. Moreover, different target locations are aimed by different types of signal peptides. For example, the structure of a target peptide aiming for the mitochondrial environment differs in terms of length and shows an alternating pattern of small positively charged and hydrophobic stretches. Nucleus aiming signal peptides can be found at both the N-terminus and the C-terminus of a protein and are in most cases retained in the mature protein.

It is possible to determine the amino acid sequence of the N-terminal signal peptide by Edman degradation, a cyclic procedure that cleaves off the amino acids one at a time.

Co-translational versus post-translational translocation
In both prokaryotes and eukaryotes signal sequences may act co-translationally or post-translationally.

The co-translational pathway is initiated when the signal peptide emerges from the ribosome and is recognized by the signal-recognition particle (SRP). SRP then halts further translation (translational arrest only occurs in Eukaryotes) and directs the signal sequence-ribosome-mRNA complex to the SRP receptor, which is present on the surface of either the plasma membrane (in prokaryotes) or the ER (in eukaryotes). Once membrane-targeting is completed, the signal sequence is inserted into the translocon. Ribosomes are then physically docked onto the cytoplasmic face of the translocon and protein synthesis resumes.

The post-translational pathway is initiated after protein synthesis is completed. In prokaryotes, the signal sequence of post-translational substrates is recognized by the SecB chaperone protein that transfers the protein to the SecA ATPase, which in turn pumps the protein through the translocon. Although post-translational translocation is known to occur in eukaryotes, it is poorly understood. It is known that in yeast post-translational translocation requires the translocon and two additional membrane-bound proteins, Sec62 and Sec63.

Secretion efficiency determination
Signal peptides are extremely heterogeneous, many prokaryotic and eukaryotic ones are functionally interchangeable within or between species and all determine protein secretion efficiency.

Nucleotide level features
In vertebrates, the region of the mRNA that codes for the signal peptide (i.e. the signal sequence coding region, or SSCR) can function as an RNA element with specific activities. SSCRs promote nuclear mRNA export and the proper localization to the surface of the endoplasmic reticulum. In addition SSCRs have specific sequence features: they have low adenine-content, are enriched in certain motifs, and tend to be present in the first exon at a frequency that is higher than expected.

Alternate secretion mechanisms
Proteins without signal peptides can also be secreted by unconventional mechanisms. E.g. Interleukin, Galectin. The process by which such secretory proteins gain access to the cell exterior is termed unconventional protein secretion (UPS). In plants, even 50% of secreted proteins can be UPS dependent.

Nonclassical sequences
Signal peptides are usually located at the N-terminus of proteins. Some have C-terminal or internal signal peptides (examples: peroxisomal targeting signal and nuclear localisation signal). The structure of these nonclassical signal peptides differs vastly from the N-terminal signal peptides.

Nomenclature
Signal peptides are not to be confused with the leader peptides sometimes encoded by leader mRNA, although both are sometimes ambiguously referred to as "leader peptides." These other leader peptides are short polypeptides that do not function in protein localization, but instead may regulate transcription or translation of the main protein, and are not part of the final protein sequence. This type of leader peptide primarily refers to a form of gene regulation found in bacteria, although a similar mechanism is used to regulate eukaryotic genes, which is referred to as uORFs (upstream open reading frames).

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

title: Signal peptide


text:
Translocon

The translocon (also known as a translocator or translocation channel) is a complex of proteins associated with the translocation of polypeptides across membranes. In eukaryotes the term translocon most commonly refers to the complex that transports nascent polypeptides with a targeting signal sequence into the interior (cisternal or lumenal) space of the endoplasmic reticulum (ER) from the cytosol. This translocation process requires the protein to cross a hydrophobic lipid bilayer. The same complex is also used to integrate nascent proteins into the membrane itself (membrane proteins). In prokaryotes, a similar protein complex transports polypeptides across the (inner) plasma membrane or integrates membrane proteins. In either case, the protein complex are formed from Sec proteins (Sec: secretory), with the heterotrimeric Sec61 being the channel. In prokaryotes, the homologous channel complex is known as SecYEG.

This article focuses on the cell's native translocons, but pathogens can also assemble other translocons in their host membranes, allowing them to export virulence factors into their target cells.

Central channel
The translocation channel is a hetero-trimeric protein complex called SecYEG in prokaryotes and Sec61 in eukaryotes. It consists of the subunits SecY, SecE, and SecG. The structure of this channel, in its idle state, has been solved by X-ray crystallography in archaea. SecY is the large pore subunit. In a side view, the channel has an hourglass shape, with a funnel on each side. The extracellular funnel has a little "plug" formed out of an alpha-helix. In the middle of the membrane is a construction, formed from a pore ring of six hydrophobic amino acids that project their side chains inwards. During protein translocation, the plug is moved out of the way, and a polypeptide chain is moved from the cytoplasmic funnel, through the pore ring, the extracellular funnel, into the extracellular space. Hydrophobic segments of membrane proteins exit sideways through the lateral gate into the lipid phase and become membrane-spanning segments.

In bacteria, SecYEG forms a complex with SecDF, YajC and YidC. In eukaryotes, Sec61 forms a complex with the oligosaccharyl transferase complex, the TRAP complex, and the membrane protein TRAM (possible chaperone). For further components, such as signal peptidase complex and the SRP receptor it is not clear to what extent they only associate transiently to the translocon complex.

Translocation
The channel allows peptides to move in either direction, so additional systems in the translocon are required to move the peptide in a specific direction. There are three types of translocation: cotranslational translocation that happens as translation happens, and two types of post-translational translocation that happens after translation, each seen in eukaryotes and bacteria. While eukaryotes unfold the protein with BiP and use other complexes to transport the peptide, bacteria use the SecA ATPase.

Co-translational

In co-translational translocation, the translocon associates with the ribosome so that a growing nascent polypeptide chain is moved from the ribosome tunnel into the SecY channel. The translocon (translocator) acts as a channel through the hydrophobic membrane of the endoplasmic reticulum (after the SRP has dissociated and translation is continued). The emerging polypeptide is threaded through the channel as an unfolded string of amino acids, potentially driven by a Brownian Ratchet. Once translation is finished, a signal peptidase cleaves off the short signal peptide from the nascent protein, leaving the polypeptide free in the interior of the endoplasmic reticulum.

In eukaryotes, proteins due to be translocated to the endoplasmic reticulum are recognized by the signal-recognition particle (SRP), which halts translation of the polypeptide by the ribosome while it attaches the ribosome to the SRP receptor on the endoplasmic reticulum. This recognition event is based upon a specific N-terminal signal sequence that is in the first few codons of the polypeptide to be synthesised. Bacteria also use an SRP, together with a chaperone YidC that is similar to the eukaryote TRAM.

The translocon can also translocate and integrate membrane proteins in the correct orientation into the membrane of the endoplasmic reticulum. The mechanism of this process is not fully understood, but involves the recognition and processing by the translocon of hydrophobic stretches in the amino acid sequence which are destined to become transmembrane helices. Closed by stop-transfer sequences and opened by embedded signal sequences, the plug alters between its open and closed states to place helices in different orientations.

Post-translational
In eukaryotes, post-translational translocation depends on BiP and other complexes, including the SEC62/SEC63 integral membrane protein complex. In this mode of translocation, Sec63 helps BiP hydrolyze ATP, which then binds to the peptide and "pulls" it out. This process is repeated for other BiP molecules until the entire peptide has been pulled through.

In bacteria, the same process is done by a "pushing" ATPase known as SecA, sometimes assisted by the SecDF complex on the other side responsible for pulling. The SecA ATPase uses a "push-and-slide" mechanism to move a polypeptide through the channel. In the ATP-bound state, SecA interacts through a two-helix finger with a subset of amino acids in a substrate, pushing them (with ATP hydrolysis) into the channel. The interaction is then weakened as SecA enters the ADP-bound state, allowing the polypeptide chain to slide passively in either direction. SecA then grabs a further section of the peptide to repeat the process.

The ER-retrotranslocon
Translocators can also move polypeptides (such as damaged proteins targeted for proteasomes) from the cisternal space of the endoplasmic reticulum to the cytosol. ER-proteins are degraded in the cytosol by the 26S proteasome, a process known as endoplasmic-reticulum-associated protein degradation, and therefore have to be transported by an appropriate channel. This retrotranslocon is still enigmatic.

It was initially believed that the Sec61 channel is responsible for this retrograde transport, implying that transport through Sec61 is not always unidirectional but also can be bidirectional. However, the structure of Sec61 does not support this view and several different proteins have been suggested to be responsible for transport from the ER lumen into the cytosol.

title: Translocon


text:
Androscoggin

Androscoggin may refer to:

 * Androscoggin people, an Abnaki tribe who lived in what is now Maine and New Hampshire in the US
 * Androscoggin County, Maine
 * Androscoggin Lake
 * Androscoggin Mill, Jay, Maine
 * Androscoggin River in New Hampshire and Maine
 * Camp Androscoggin, a summer camp in Wayne, Maine

title: Androscoggin