User talk:Zaalis

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Hello, Zaalis! Welcome to Wikipedia! Thank you for your contributions. You may benefit from following some of the links below, which will help you get the most out of Wikipedia. If you have any questions you can ask me on my talk page, or place {{helpme}} on your talk page and ask your question there. Please remember to sign your name on talk pages by clicking or by typing four tildes "~~~~"; this will automatically produce your name and the date. If you are already excited about Wikipedia, you might want to consider being "adopted" by a more experienced editor or joining a WikiProject to collaborate with others in creating and improving articles of your interest. Click here for a directory of all the WikiProjects. Finally, please do your best to always fill in the edit summary field when making edits to pages. Happy editing! Jim1138 (talk) 05:33, 22 May 2016 (UTC)[reply]
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Incubator picture.[edit]

Not being sure whether the ping template has worked, this is to let you know I posted my ideas on LTEE's talk page. 79.49.120.161 (talk) 06:16, 26 May 2016 (UTC)[reply]

New User Suggestions and LTEE[edit]

Hi @Zaalis:. I see you are new to wikipedia. There have been some significant improvements to this article by you already, and thank you for that!! However, I think that there needs to be a bit of slowing down. This is an online encyclcopedia and it does have rules about pictures, statements and claims one can make, and also language. One cannot simply express what one wishes since there has to be a consensus established on what belongs on the E. coli long-term evolution experiment article and any other Wikipedia articles while also following wikipedia protocol and policies. Consensus is important here on wikipedia because this cannot become a one piece re-editing of an article. This can lead to "edit warring" (see WP:EDITWAR if there are too many disagreements because one editor wishes to control the contents of an article and other editors are not taken into account.

Also a warning on "reverting" edits on wikipedia, as a rule if you revert people's edits more than 3 times in a day you could be blocked out for some time by administrators. In wikipedia there are people who vandalize and so to stop them from editing or disrupting articles, administrators block them for some time or even permanently. If there is resistance among editors, it is best to discuss the issue on the "Talk page" like was done on the "incubator image". The disagreements should be settled in the Talk page first before making further edits on the article. Some agreement between editors must be established to reduce edit warring.

Please take your time to discuss issues such as pictures, copyright, and content. Become familiar with wikipedia policy such as WP:OR WP:SYN because there are some statements that have been added to the LTEE article that look like it violates wikipedia policy such as the statement "The experiment has so far yielded over 70 peer-reviewed publications, and has provided insight into a wide variety of evolutionary questions and phenomena." The source is just a list of research papers from Dr. Lenski's lab, but the source does not state at all " ...and has provided insight into has provided insight into a wide variety of evolutionary questions and phenomena.". This extra clause is WP:SYN. Also in wikipedia, technically every statement written on any article should be 1) relevant to the scope of an article, 2) have a "reliable source", 3) statement that an editor makes should reflect what the source says, not be interpreted beyond what the source says.

Also, try to abide by WP:NEUTRAL and please see this policy too WP:VERIFIABILITY for info on sources that are permitted.

Finally, Zaalis, it seems you are very intimate Dr. Lenski's research (per what you said in the talk page on the incubator image- I actually work on the project, which is why I can take such photos, post them, and know that they are what I say they are, but proving it to others? and this may raise an issue for wikipedia in terms of WP:CONFLICT. In general, people who are close to the article content, run the risk of bias (over inflating the good an undermining the bad). For instance in biographical articles, the actual person, their family, friends, etc should not edit those articles because of the conflict of interest.

It is a bit delicate but I am just trying to give you a heads up. I am just trying to make sure that we are all aware about how wikipedia works. It is a give and take. Nonetheless, I hope you can make many more contributions since they are quite good. Mayan1990 (talk) 07:33, 26 May 2016 (UTC)[reply]

Hi @Mayan1990:. My apologies for causing any problems. I was originally drawn to the article because information had been added that was incorrect, and then noticed that the article was quite paltry, and slanted toward giving the impression that the citrate work was the bulk of the experiment, when it is not. I have enjoyed it to a degree, though some of Wikipedia baffles me. I am puzzled by two things in what you have said. First, in the statement about the 70 papers, there actually were more than 70 papers listened on the LTEE. Moreover, just reading their titles showed that the experiment had delved into a variety of questions and phenomena, and that the results had been published in peer-reviewed journals. Does there have to be a direct statement synthesizing the apparent for it to be used? (Similar statements about the importance and scope of the work have been made in a number of articles and reviews on the experiment, so if I should try to include it again, I will include those citations.) Second, I do understand the desire to preserve neutrality by keeping those to close to a subject away from it. However, does that not produce a problem that trades neutrality for knowledge? I really have tried to be neutral in my edits, and when I have been in conflict with other editors, it really is because they have either had the facts wrong or their wording just made no sense. (With the photo issue, I can see the point, and I worked it out with the editor. I'm going to see what I can do about ensuring citation in the future. I will note that with any photo or other image I have posted, I have ensured is posted at Wikimedia commons under a free use license.) I know a lot about the project, not simply because I work on it, but because I am familiar with the primary literature, which is important. I have only included details that have been published, as anyone who has read up on the primary research articles and had time to edit would. I have tried not to over blow anything, or to minimize the bad, but have approached it largely as we are required to when writing up scientific papers. Indeed, you will note the section dealing with criticism of the citrate work is still there, even though the critical papers listed make arguments that made no sense, misrepresent the science they are criticizing, and even make some egregious errors of fact. Their inclusion in the article bothers me for those reasons, but I don't see that as reason to exclude them for the article. Honestly, I really just want to improve the article to make it a better educational resource that actually reflects reality, as so many get their first understanding of the LTEE, like so many subjects, from Wikipedia. I will try to do better, and I ask your patience, as well as your forgiveness for any and all mistakes I have made. Zaalis (talk) 14:49, 26 May 2016 (UTC)[reply]
Hi Zaalis, no problem. Most of what you have edited looks fine. I was just giving you some info to keep in mind.
To your questions: I am puzzled by two things in what you have said. First, in the statement about the 70 papers, there actually were more than 70 papers listened on the LTEE. Moreover, just reading their titles showed that the experiment had delved into a variety of questions and phenomena, and that the results had been published in peer-reviewed journals. Does there have to be a direct statement synthesizing the apparent for it to be used? - Hmmm...Anything you write on any article has to be already mentioned in some way in the source you are citing. Otherwise it falls under WP:SYN and WP:OR. For instance, the list of papers from the lab does not mention the importance of the experiment or lack of importance. It makes no claim to its value, so you cannot add value if the source itself does not mention value. If you can find a good source that mentions its value, then maybe it can be added in the body of the article under a relevant section - in fact you already have recognition of the value under the "Implications for evolutionary innovation" section which looks ok.
To your second question about neutrality and truth, check out WP:BUTITSTRUE. Wikipedia, as an encyclopedia, collects diverse sourced opinions and since some sourced opinions are agreeable to some and not agreeable to others, can reduce POV pushing by attributing statements to the sources "According to..." or to just note the "bare facts" from a source while reducing value statements "he is wrong, this is right". Technically only the sources can debate each other, as in the criticism section of LTEE. To say something with value added like "evolutionary biologists have accepted this research" without a proper citation can be an issue since who did a poll on acceptance or rejection? Is it even relevant to the scope of the article? Perhaps if someone got a Nobel prize for it, then it would make sense to mention that somewhere in the article, but if not, then probably best to leave it to the readers to decide. In your case, since you have worked directly with Dr. Lenski's lab, there can be an issue of conflict of interest just because you are too close to the subject. Others like John Roth and Sophie Maisnier-Patin have different opinions on the LTEE and I am sure they would change many parts of this article if they could. I think Wikipedia had issues like this before and so the conflict of interest policy was made to screen out people who may slant an article and commit things like WP:UNDUE. The WP:CONFLICT article has some more relevant info.
So far, the article has been greatly improved by many of your edits!! I think most are good as is, but I am just giving you some advice and pointers since you are new. Keep up the good work.Mayan1990 (talk) 18:14, 26 May 2016 (UTC)[reply]
Thank you most kindly for the clarifications and advice. I'm glad what I have done is largely within bounds and useful. As I said, I am trying to keep it to the facts, though I see your points. I'll try to take it slower and more carefully in the future, as you suggested, but please do keep helping me to stay honest! Zaalis (talk) 19:38, 26 May 2016 (UTC)[reply]
Sure thing Zaalis. Wikipedia is a fun place to make some healthy contributions like you already have. The article looks WAY better with what you have already posted. If you have any questions or need a second opinion on something, please feel free to give me a ping. I can back you up if there is any major issue with other editors.Mayan1990 (talk) 01:30, 27 May 2016 (UTC)[reply]

10,000 transfers[edit]

That's a heck of a precise record! 79.53.226.135 (talk) 21:03, 22 March 2017 (UTC)[reply]

Yup! Not many experiments go that far, either. Zaalis (talk) 01:46, 24 March 2017 (UTC)[reply]
Long term experiments might not necessarily be considered high priorities, for economic reasons, rather than scientific. 79.53.226.135 (talk) 11:07, 26 March 2017 (UTC)[reply]
There are always those who will make arguments like that against scientific work of any kind, but it is very blinkered view. One never knows what the economic impact of a given line of scientific inquiry will be. Even seemingly esoteric science can yield new ideas and findings of enormous value. I don't understand those who look to save by de-funding science. It's akin to saving money by eating your seed corn, really. As for long-term experiments, over any given time frame of a few years, they tend to be fairly cheap. The LTEE, given how simple it is, can't cost much at all. You could run it and many other experiments like it for quite a long time for the price of a single advanced fighter plane, I would expect. Zaalis (talk) 02:36, 27 March 2017 (UTC)[reply]
Hmpf! What was intended as a possible explanation on why the rarity of long just bit me back. It is unfortunate that today's climate skews activities toward short-term results, rather than long-term ones. 79.53.226.135 (talk) 07:05, 27 March 2017 (UTC)[reply]
No worries. I figured you were playing devil's advocate. The emphasis on the short-term does play into why long-term experiments are rare, though I think it's a pretty long-term problem, and I'm not sure the expense is the issue. (Again, long-term experiments tend to have to be pretty simple and relatively cheap.) Lenski, I know, faced push-back on the LTEE in the early days because many thought there wasn't any point to it, that it wouldn't show much, and that it was too exploratory. Another factor is that not many people are patient enough to carry an experiment out so long. In short, I think the rarity of 29-year-old, 10,000th-procedure experiments is just over determined. Zaalis (talk) 13:28, 27 March 2017 (UTC)[reply]

Are there other projects being carried out in the lab other than LTEE, if you don't mind me inquiring? Securing funding seems to require them, given the circumstances. It's personal curiosity, so it's not necessary for you to answer, if you don't feel like it. 79.53.226.135 (talk) 19:36, 27 March 2017 (UTC)[reply]

Funding is always required! The LTEE is cheap, but it isn't free, after all. I don't know off the top of my head what grants there are now, but funding has come at various times from MSU endowments, NSF, NIH, DARPA, EPA, NASA, The Templeton Foundation, The BEACON Center, and various smaller organizations and agencies. (In other words, yes, the environment is very worrisome.) As for projects, yes, there are always a number of projects ongoing in the lab. The LTEE itself spins off a variety of projects that involve using it to answer various questions, or as a source of evolved strains so that the effects of prolonged evolution under a given selective regime can be examined. At present, there are projects related to speciation, the evolution of antibiotic resistance, more on the citrate story, and the effect of long-term evolution under aerobic conditions on fitness under anaerobic conditions. Past work has delved into the evolution of freezing tolerance, the origins of novelty in viruses, social evolution, how resistance to environmental stress evolves, as well as a number of projects involving digital evolution using the AVIDA platform. So the LTEE is the bulk of the work, but not the entirety of it. If you are curious about more, you should contact some of the lab members. They are quite friendly, and I'm sure they would be happy to take questions. Zaalis (talk) 02:58, 28 March 2017 (UTC)[reply]
That's interesting - the "origin of novelty in viruses". I wouldn't have thought the two related, but why shouldn't they?
Seems a good occasion to learn something more about LTEE. I have no easy access to peer reviewed journals, but I'll see what I can do. :) 79.53.226.135 (talk) 07:18, 28 March 2017 (UTC)[reply]
It just means how new viral traits evolve. In that case, how viruses evolve to infect cells through different proteins. If you are interested in learning more about the LTEE, again, email some lab members. I know Zachary Blount answers emails. Also, Lenski has a number of his papers on the LTEE posted on his website, here: http://myxo.css.msu.edu/PublicationSearchResults.php?group=aad
Similarly, Blount has his papers posted at his website: www.blount-lab.org
For those papers not posted, most scientists are happy to email copies if asked :-) Zaalis (talk) 14:07, 28 March 2017 (UTC)[reply]
Will check on them, thanks! 79.53.226.135 (talk) 10:09, 30 March 2017 (UTC)[reply]
Any time! Happy to help! Zaalis (talk) 14:32, 30 March 2017 (UTC)[reply]

Gene duplication[edit]

Zaalis, greetings.

I wonder if I can prevail on you to clarify a point. The way it is written on ltee article, it seems that it is whole genes (or perhaps transcriptional units, as the current preferred term appears to be) that are duplicated, one or more times. This might be true for transposons, but not necessarily otherwise: in the end, it is a stretch of DNA that is duplicated, which may or may not include a whole gene (or number of genes), part of a gene, a promoter, a repressor or a sequence of non-coding base pairs, either as the duplication template or as the inserted strand. Further, even if a gene (or at least a meaningful/acrive strand of DNA) is duplicated, there might be a further stretch of DNA that does not carry any activity when duplicated. Provided I made myself clear, am I correct in supposing this? Thanks! 62.211.109.15 (talk) 17:18, 20 November 2017 (UTC)[reply]

Greetings! I cleaned up some of the language in the section on the cit amplification. Can you tell me if I helped with the confusion there? As to your question, the 2933 bp segment of DNA duplicated and then amplified, going by the LTEE papers, includes both whole genes, citT and rna, contained in the middle of the segment, and fragments of the citG and rnk genes are the ends. I apologize if the portions of the article I wrote indicated that the entire segment contained only whole genes. Duplicated stretches or segments of DNA can, of course, contain any mix of whole coding or regulatory elements, fragments of the same, and other. This means that the effects of a duplication or amplification will depend on the contents of what is amplified. It is certainly possible for a duplication to not have any clear effect on gene activity, phenotype, or fitness. In the case of the cit amplification, it seems that the important thing is that the duplication contained a full copy of the citT gene, and an aerobically-expressing promoter that, because of the head-to-tail tandem orientation resulted in the citT gene copy being under the control of that promoter, altering its expression so that the CitT transporter was produced when oxygen was present. (If, say, only the citT gene had been duplicated, so that there ended up being two or more exact copies of citT right next to each other, it seems that there would have been no phenotypic effect at all, and the Cit+ trait wouldn't have manifested.) Does that explanation make sense? Could I help clarify any better? I sincerely hope I helped! Zaalis (talk) 17:54, 20 November 2017 (UTC)[reply]
Yes to both questions; thank you very much.
Problem with popularization is that so very often it has to oversimplify an explanation, losing quite some detail and yielding a not overtly accurate picture of the situation. English Wikipedia tries to counterbalance this to an extent, but its success is not assured.
Thank you again. 62.211.109.15 (talk) 19:08, 20 November 2017 (UTC)[reply]
I'm glad! And I fully agree with you on popularization and loss of details. I think there's a good balance that can be struck. It's one of the main reasons why I started editing this entry. There's a lot of nifty findings in experimental evolution, and it really is possible to be accurate and understandable at the same time. Thank you for your help in that! Zaalis (talk) 19:40, 20 November 2017 (UTC)[reply]

Happy to be of help! I would also like to ask a follow-up question: is the duplicated DNA segment inserted randomly in the chromosome? Or, perhaps better stated, wherever suitable "adesive" elements, or restriction enzymes, or whatever else available to the cell at the moment, are available? And might this also yield immediate loss of function in the cell, rather than gain of function later down the line? Thank you again! 62.211.109.15 (talk) 20:09, 20 November 2017 (UTC)[reply]

In this case, no. The new copy of the 2933 bp segment comes immediately after the original. So the genome, where it originally read,"citG-citT-rna-rnk" now reads,"citG-citT-rna-partial rnk-partial citG-citT-rna-rnk". Generally, that's the case with DNA duplications - the copies end up right next to each other. With spontaneous duplications, there aren't the sorts of "adhesive" sequences you mention, generally. However, the occurrence of duplications is facilitated by stretches of identical sequence, so it isn't uncommon to find duplications that are flanked by copies of repetitive elements like insertion sequences. That doesn't seem to be the case with the cit duplication in the LTEE. There aren't repetitive sequences that would have facilitated the cit duplication's occurrence, but I'm not sure if they've worked out the mechanism of how the duplication originally occurred. You ask about the possibility of a loss of function due to a duplication. That is certainly possible. Imagine if a duplication was of a segment within a gene for a given function, for instance. There's a good chance that such a duplication would end up disrupting the protein sequence of the encoded protein, causing loss of function. The same is the case if there is replicative transposition of an insertion sequence, in which there ends up being a copy in the original location, and then another in a new location. The new copy could certainly disrupt a gene's function. So duplications are like other mutations in that all sorts of effects, phenotypic and otherwise, can arise from them. I hope that helps!Zaalis (talk) 20:58, 20 November 2017 (UTC)[reply]
I admit that I wrote the question with transposons in mind - as they were explained to me, the point of reinsertion can be quite far from their original location. And (again, old memories) transposons get reinserted without respecting the function of their target, so the target's loss of function is not impossible.
Well, I've learned something new - I don't think I ever came across to the concept of head-to-tail duplication in E. coli, which makes loss of function unlikely. It's been way too long I've dealt with biology with any regularity and much has happened since then. But I do like on occasion to delve a bit deeper on topics that strike me as interesting. So thank you for your explanations! 62.211.109.15 (talk) 21:37, 20 November 2017 (UTC)[reply]
You are welcome! Happy to be of help! You are correct about transposons - and insertion sequences, which are essentially simplified transposons. They often have target sequences, but of only a few letters, so a genome will have enormous numbers of them that the elements can jump into. And, no, they don't respect the function of whatever they jump into. That said, there is propensity for transposable elements to jump into intergenic regions. This likely reflects selection for transposases that preferentially mediate transposition into places that are less likely to kill the host. I'm not sure entirely how that works, though. That said, transposable elements can also cause gain-of-function mutations, as they sometimes can activate expression of silent genes. Nifty stuff, indeed! Zaalis (talk) 21:46, 20 November 2017 (UTC)[reply]

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