User talk:Opabinia regalis/Archive 8

Archive 5

Archive 6

Archive 7

Archive 8

Archive 9

Archive 10

→

Archive 15

And now, for Fvasconcellos' traditional nonsectarian holiday greeting!

Wherever you are, and whether you're celebrating something or not, there is always a reason to spread the holiday spirit! So, may you have a great day, and may all your wishes be fulfilled in 2009! Fvasconcellos (t·c) 14:40, 24 December 2008 (UTC)

Is this a combination of my Christmas greeting from 2006 and my New Year's greeting from last year? Why, it most certainly is! Hey, if it ain't broke...

Netzarim

A user has somehow reverted your edit on Netzarim and Netzarim (disambiguation). Could you revert back to yours. Thanks. --Shuki (talk) 00:33, 8 February 2009 (UTC)

Help your fellow scientists?

Hi, Tim Vickers and I and a few others have been invited to give workshops that may turn dozens of research life scientists into actively contributing Wikipedians. I've been impressed by your Featured Articles for the MCB WikiProject, and I would be grateful if you could help us. Would you be willing to answer a few questions of these nascent editors by private e-mail? I realize that you're de facto retired from Wikipedia, but I don't think it will take much of your time and any help would be at your leisure (i.e., flexible schedule). If you would like to help us, please e-mail me for details. Thanks! Proteins (talk) 23:20, 27 June 2009 (UTC)

Clara Elsene Peck

Thanks for the peer review. Many good points that will help improve the article. Much appreciated. --Scott Free (talk) 23:00, 13 July 2009 (UTC)

FAR Sequence alignment

I have nominated Sequence alignment for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Remove" the article's featured status. The instructions for the review process are here. —Mattisse (Talk) 01:01, 2 August 2009 (UTC)

Hi!

I just ran across a peer review you did and I rushed over here. Every once in a while I check your user talk, but it is always so quiet. I hope you are going to edit less "sporadically" now! :) Awadewit (talk) 14:40, 2 August 2009 (UTC)

Heh, and here I was thinking 'sporadically' would be an upgrade! :) Good to hear from you again though. I've started to get more involved in other 'open science' type efforts, so it seems logical to pick up wiki editing again... or it would, if only I had a few more hours in the day! Opabinia regalis (talk) 20:20, 2 August 2009 (UTC)

Coalesence theory

$P_{c}(t)={\frac {1}{2N}}e^{-t/(2N)}.$

This is going to sort of be out of the blue, this formula does not seem to be correct. Here is an example of the output

N=10

t = 1 to 20

p(1) = 0.047561471

....

p(21) = 0.017496887

Above is an approximation of what the curve should look like. I am not sure but I think the it should be 1/t since the lambda is based on rate which is 1/t. I didn't change the formula, just wanted to know why it is not working.PB666 ^yap 04:51, 27 August 2009 (UTC)

You happen to have caught me at a good time! Hmm, couple of issues here.

1) There is a typo in the formula; should be $P_{c}(t)={\frac {1}{2N}}e^{-(t-1)/(2N)}.$ because we're doing the calculation for generation t.

2) This is a bad approximation for such small values of t and N as in your calculations.Opabinia regalis (talk

Hmm I tried it for 8000 and it, well, it coughed at reality. (at least the reality I was trying to get it to recreate) I'll explain the problem below.PB666 ^yap

3) The equation has the form ${\frac {1}{\beta }}e^{\left(-{\frac {1}{\beta }}\right)}$, where the expectation value is beta ( = 1/lambda = 2N). I don't quite understand your graph - probability of fixation isn't the same as probability of coalescence. Opabinia regalis (talk) 05:29, 27 August 2009 (UTC)

Agreed but the 2N is frequently quoted as the time in generations to the MRCA. I know what the problem is I just dont know how it can be solved. The problem is that the exponential distribution assumes that any individual in a population can produce population size in one generation, which may be true if the population size is small or partuition rates are high. So for example in the graph above there are limits on progeny, producing a single female is 0.5 and two female 0.25. I have done this also were I have extended the distribution outward to as many as 6 female offspring in a balanced distribution, the results are similar to the above. Because there is a finite limit on progeny production (I think the record is 35 females in a population of 6 billion trials) one can create a poisson distribution to estimated the probability of X number of females. Therefore a given trial p(1)~ 0.5, p(2), . . . . p(35) = 0.000000000001 p(50) = 0. IOW for a population of 50 females it is impossible that all females will coalesce to one female in the next generation. For a population of 2500 females it is impossible for that the population coalesce to one female in 2 generations, however with the above formula the highest probability is in the first generation, ergo the formula contradicts observation. I suppose if we had Speckled Trout in a Bay, and a single trout could produce 1 million eggs, and there are less than a 1/2 million female trout in the bay then it is possible. I have tested this with Monte Carlo analysis several years ago (right after Vigilante published) and did a reanalysis after doing some modeling against some stone age life expectancies. The demonstrated that some females needed to produce more than 6 offspring for the population to remain stable in size. The graph above is close even if we extend progeny outward and if one consider 100s of generations the median of the cummulative distribution is at ~2.6N. I can show you a paper where these curves are used. I want to recapitulate the curves for an image, but I can't seem to find the formula (that way I am not WP:COPYVIO). I would hate to have to run a Monte Carlo analysis for 11,000 individuals and 5 million years (heh-heh).PB666 ^yap 16:16, 27 August 2009 (UTC)

This coalescence distribution is asking the question how long before any two random individuals will have the same parent, OK so but for a gene quasi-fixed in the extant population we are asking the question how far back to we have to go such that all extant members share an ancestor, and that is the first ancestor all share together. So that traveling down the tree there is the probability that two individuals are related in the next generation by several probabilities 1, the female had 2 female offspring (lets just say p(0)=0.25, p(1)=0.5), p(2)=0.25 therefore 1/2 of the individuals in the population can be paired to a common ancestor in the previous generation and half cannot, the process continues backwards until we reach the TgMRCA. If we make the assumption that by chance all of individuals have a valid sibling of the same sex in all generations of the lineage then minimum coalescent time is log₂N in generations. The probability of fixation in T generations is p(2)^(Sum_{i=0 to T-1} 2ⁱ) where

N is a value of 2,4,8,16,...... I think you can see what I am getting at.PB666 ^yap 16:25, 27 August 2009 (UTC)

I found the formula, its in Wakely [1]: $f_{TMRCA}(t)=\sum _{i=2}^{n}{\frac {(2i-1)(-1)^{i}n_{[i]}}{n_{(i)}}}{\binom {n}{k}}e^{-{\tbinom {t}{2}}t}$

where

$n_{[i]}=n(n-1)\cdots (n-i+1)$

$n_{(i)}=n(n+1)\cdots (n+i-1)$

This is from Tavare (1984) and BTW if you know what it means or how to convert it to microsoft excel equation it would be greatly appreciated :^) (I think I can figure it out, I'll put that little metal hat on my head and bzzzzz).PB666 ^yap 21:38, 27 August 2009 (UTC)

Don't use the above formula, they have substitute N, population size with n, number of alleles, they have substituted T with t which is the number of branch times. I have tried to applied both versions of the formula and the answer was always 0.PB666 ^yap 16:47, 29 August 2009 (UTC)

NowCommons: File:Transcription label fromcommons.jpg

File:Transcription label fromcommons.jpg is now available on Wikimedia Commons as Commons:File:Transcription label en.jpg. This is a repository of free media that can be used on all Wikimedia wikis. The image will be deleted from Wikipedia, but this doesn't mean it can't be used anymore. You can embed an image uploaded to Commons like you would an image uploaded to Wikipedia, in this case: [[File:Transcription label en.jpg]]. Note that this is an automated message to inform you about the move. This bot did not copy the image itself. --Erwin85Bot (talk) 08:09, 27 September 2009 (UTC)

File:Image-alignment-wycombe.png listed for deletion

An image or media file that you uploaded or altered, File:Image-alignment-wycombe.png, has been listed at Wikipedia:Files for deletion. Please see the discussion to see why this is (you may have to search for the title of the image to find its entry), if you are interested in it not being deleted. Thank you. FASTILY_sock^(TALK) 08:33, 19 December 2009 (UTC)

And now, for FV's traditional last-minute nonsectarian holiday greeting!

Here’s wishing you a happy end to the holiday season and a wonderful 2010. Fvasconcellos (t·c) 15:31, 25 December 2009 (UTC)

Happy New Year!

A noiseless patient spider, I mark'd where on a little promontory it stood isolated, Mark'd how to explore the vacant vast surrounding, It launch'd forth filament, filament, filament, out of itself, Ever unreeling them, ever tirelessly speeding them. And you O my soul where you stand, Surrounded, detached, in measureless oceans of space, Ceaselessly musing, venturing, throwing, seeking the spheres to connect them, Till the bridge you will need be form'd, till the ductile anchor hold, Till the gossamer thread you fling catch somewhere, O my soul." —"A Noiseless Patient Spider" by Walt Whitman Happy New Year Awadewit (talk) 05:53, 31 December 2009 (UTC)

Proposed deletion of Geoffrey Chang

The article Geoffrey Chang has been proposed for deletion because of the following concern:

No indication this scientist is sufficiently notable per WP:PROF

While all contributions to Wikipedia are appreciated, content or articles may be deleted for any of several reasons.

You may prevent the proposed deletion by removing the {{dated prod}} notice, but please explain why in your edit summary or on the article's talk page.

Please consider improving the article to address the issues raised. Removing {{dated prod}} will stop the proposed deletion process, but other deletion processes exist. The speedy deletion process can result in deletion without discussion, and articles for deletion allows discussion to reach consensus for deletion. Rockpocket 05:40, 2 January 2010 (UTC)

GA reassessment of Multiple sequence alignment

I have conducted a reassessment of the above article as part of the GA Sweeps process. You are being notified as you have made a number of contributions to the article. I have found some concerns which you can see at Talk:Multiple sequence alignment/GA1. I have placed the article on hold whilst these are fixed. Thanks. Jezhotwells (talk) 19:33, 28 February 2010 (UTC)

AfD nomination of Wikipedia

An editor has nominated one or more articles which you have created or worked on, for deletion. The nominated article is Wikipedia. We appreciate your contributions, but the nominator doesn't believe that the article satisfies Wikipedia's criteria for inclusion and has explained why in his/her nomination (see also Wikipedia:Notability and "What Wikipedia is not").

Your opinions on whether the article meets inclusion criteria and what should be done with the article are welcome; please participate in the discussion(s) by adding your comments to Wikipedia:Articles for deletion/Wikipedia (4th nomination). Please be sure to sign your comments with four tildes (~~~~).

You may also edit the article during the discussion to improve it but should not remove the articles for deletion template from the top of the article; such removal will not end the deletion debate.

Please note: This is an automatic notification by a bot. I have nothing to do with this article or the deletion nomination, and can't do anything about it. --Erwin85Bot (talk) 01:05, 2 April 2010 (UTC)

Main page apperance

Hello! This is a note to let the main editors of this article know that it will be appearing as the main page featured article on November 23, 2010. You can view the TFA blurb at Wikipedia:Today's featured article/November 23, 2010. If you think that it is necessary to change the main date, you can request it with the featured article director, Raul654 (talk · contribs). If this article needs any attention or maintenance, it would be preferable if that could be done before its appearance on the Main Page so Wikipedia doesn't look bad. :D Thanks! Tbhotch^{Talk C.} 07:03, 9 November 2010 (UTC)

Proteasomes are very large protein complexes inside all eukaryotes and archaea, as well as in some bacteria. In eukaryotes, they are located in the nucleus and the cytoplasm. The main function of the proteasome is to degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds. Enzymes that carry out such reactions are called proteases. Proteasomes are part of a major mechanism by which cells regulate the concentration of particular proteins and degrade misfolded proteins. Proteins are tagged for degradation with a considerably small protein called ubiquitin. The tagging reaction is catalyzed by enzymes called ubiquitin ligases. Once a protein is tagged with a single ubiquitin molecule, this is a signal to other ligases to attach additional ubiquitin molecules. The result is a polyubiquitin chain that is bound by the proteasome, allowing it to degrade the tagged protein. The proteasomal degradation pathway is essential for many cellular processes, including the cell cycle, the regulation of gene expression, and responses to oxidative stress. The importance of proteolytic degradation inside cells and the role of ubiquitin in proteolytic pathways was acknowledged in the award of the 2004 Nobel Prize in Chemistry to Aaron Ciechanover, Avram Hershko and Irwin Rose. (more...)

Suspension of admin privileges due to inactivity

Following a community discussion in June 2011, consensus was reached to provisionally suspend the administrative privileges of users who have been inactive for one year, meaning administrators who have made neither any edits nor any logged actions in over one year. As a result of this discussion, your administrative privileges have been removed pending your return. If you wish to have these privileges reinstated, please post to the Wikipedia:Bureaucrats' noticeboard and the userright will be restored per the re-sysopping process (i.e., as long as the attending bureaucrats are reasonably satisfied that your account has not been compromised and that your inactivity did not have the effect of evading scrutiny of any actions which might have led to sanctions). This removal of access is procedural only, and not intended to reflect negatively upon you in any way. We wish you the best in future endeavors, and thank you for your past administrative efforts. RL0919 (talk) 22:12, 9 July 2011 (UTC)

Main page appearance: RNA interference

This is a note to let the main editors of RNA interference know that the article will be appearing as today's featured article on November 25, 2011. You can view the TFA blurb at Wikipedia:Today's featured article/November 25, 2011. If you prefer that the article appear as TFA on a different date, or not at all, please ask featured article director Raul654 (talk · contribs) or his delegate Dabomb87 (talk · contribs), or start a discussion at Wikipedia talk:Today's featured article/requests. If the previous blurb needs tweaking, you might change it—following the instructions at Wikipedia:Today's featured article/requests/instructions. If this article needs any attention or maintenance, it would be preferable if that could be done before its appearance on the Main Page. The blurb as it stands now is below:

RNA interference (RNAi) is a system within living cells that takes part in controlling which genes are active and how active they are. Two types of small RNA molecules – microRNA (miRNA) and small interfering RNA (siRNA) – are central to RNA interference. RNAs are the direct products of genes, and these small RNAs can bind to other specific RNAs (mRNA) and either increase or decrease their activity, for example by preventing a messenger RNA from producing a protein. RNA interference has an important role in defending cells against parasitic genes – viruses and transposons as well as gene expression in general. The RNAi pathway is found in many eukaryotes and is initiated by the enzyme Dicer (pictured), which cleaves long double-stranded RNA (dsRNA) molecules into short fragments of ~20 nucleotides that are called siRNAs. Each siRNA is unwound into two single-stranded (ss) ssRNAs, namely the passenger strand and the guide strand. The passenger strand is degraded, and the guide strand is incorporated into the RNA-induced silencing complex (RISC). The selective and robust effect of RNAi on gene expression makes it a valuable research tool, both in cell culture and in living organisms because synthetic dsRNA introduced into cells can induce suppression of specific genes of interest. (more...)

UcuchaBot (talk) 00:02, 23 November 2011 (UTC)

File:Antibiotic resistance thick.png listed for deletion

A file that you uploaded or altered, File:Antibiotic resistance thick.png, has been listed at Wikipedia:Files for deletion. Please see the discussion to see why this is (you may have to search for the title of the image to find its entry), if you are interested in it not being deleted. Thank you. Cloudbound (talk) 21:42, 12 March 2012 (UTC)

Vandalism Studies Update - August 2012

Hello, members of the Vandalism Studies Project! As some of us are quite new with the Vandalism Studies project, it would make sense for us to re-read some of the past studies, as well as studies outside the project. Please do so if you have a chance, just so we can get into the groove of things. We're planning on attempting to salvage the Obama study (or possibly simply convert it to a new Romney study), as well as hopefully begin our third study this November. If you have any ideas for Study 3, please suggest them! If you have any questions please post them on the project talk page. Thanks, and happy editing - we can't wait to begin working on the project! --Dan653 (talk) and Theopolisme _:)
11:31, 24 August 2012 (UTC)
_{If you would like to stop receiving Vandalism Studies newsletters, please remove your name from the member list.}

Notice of change

Hello. You are receiving this message because of a recent change to the administrator policy that alters what you were told at the time of your desysopping. The effect of the change is that you will not longer be able to request restoration of the tools because of your prior inactivity. You have until December 30, 2012 to request restoration or else the policy will prevent you from doing so in the future; you would need to seek a new WP:RFA. Until December 30, you can file a request at WP:BN for review by the crats. Thank you. MBisanz ^talk 04:22, 3 December 2012 (UTC)

(delivered by mabdul 23:41, 3 December 2012 (UTC))