User talk:Biologos

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Welcome to Wikipedia! If you have any questions feel free to ask me or an admin! SupaSoldier 19:15, 12 January 2007 (UTC)

Links

http://en.wikipedia.org/wiki/Wikipedia:Science_collaboration_of_the_week http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Beer/WikiProject_Beer_collaboration

Anthocyanin

Category:Anthocyanins is a sub-category to Category:pH indicators. Hence, the article should not be in Category:pH indicators. Nirmos (talk) 06:25, 30 July 2010 (UTC) True. Sorry.--Biologos (talk) 16:03, 30 July 2010 (UTC)

Human papillomavirus edit

Please have a look at this.Richiez (talk) 13:49, 27 September 2010 (UTC)

Rollback

I have granted rollback rights to your account. After a review of some of your contributions, I believe you can be trusted to use rollback for its intended usage of reverting vandalism, and that you will not abuse it by reverting good-faith edits or to revert-war. For information on rollback, see Wikipedia:New admin school/Rollback and Wikipedia:Rollback feature. If you do not want rollback, just let me know and I will remove it. Good luck and thanks. —Tom Morris (talk) 14:09, 16 February 2012 (UTC)

Article Feedback deployment

Hey Biologos; I'm dropping you this note because you've used the article feedback tool in the last month or so. On Thursday and Friday the tool will be down for a major deployment; it should be up by Saturday, failing anything going wrong, and by Monday if something does :). Thanks, Okeyes (WMF) (talk) 23:44, 13 March 2013 (UTC)

Your interest in 454 Life Sciences

Hi Biologos, do you plan on making the article notable now? If not, you should make your opinion known at at WP:Afd, IMO.--GrapedApe (talk) 11:32, 20 March 2013 (UTC)

Hi, thanks for the note. I will try with what we have right now. By the way, there's even more to delete: Have you seen Roche Applied Science and Roche Diagnostics? ;o) --Biologos (talk) 16:13, 20 March 2013 (UTC)

AFT5 re-enabled

Hey Biologos :). Just a note that the Article Feedback Tool, Version 5 has now been re-enabled. Let us know on the talkpage if you spot any bugs. Thanks! Okeyes (WMF) (talk) 00:44, 24 April 2013 (UTC)

Thalidomide

Biologos,

With regard to your edit to Thalidomide,

WP:MEDMOS says:

https://en.wikipedia.org/wiki/Wikipedia:MEDMOS#Drugs.2C_medications_and_devices Try to avoid cloning drug formularies such as the BNF and online resources like RxList and Drugs.com. Extract the pertinent information rather than just dumping low-level facts in a big list. For example, a long list of side effects is largely useless without some idea of which are common or serious. It can be illuminating to compare the drug with others in its class, or with older and newer drugs.

My reading of that is that Wikipedia should only list significant side effects that are pertinent because they are common or serious. For example, with doxorubicin the dose-limiting adverse effect is cardiomypathy. That's pertinent, because it shapes the appropriate use and limitations of the drug. For example, with thalidomide, painful neuropathy is pertinent because it's a dose-limiting adverse effect. Dry skin isn't a dose-limiting adverse effect. Stevens-Johnson syndrome is pertinent, even if it's rare, because it's life threatening. Pruritis isn't life-threatening.

Copying a big list side effects from the FDA labeling is dumping low-level facts.

For example, here's a selective list of adverse effects: http://dailymed.nlm.nih.gov/dailymed/lookup.cfm?setid=2eda833b-1357-4ed4-a093-194524fcb061#nlm34084-4

Wikipedia is written for the average person, not the expert, and Wikipedia is not an instruction manual for the practice of medicine. There's no purpose to listing rare and very rare non-serious side effects. It obscures the significant adverse effects. You have a long list of rare and minor side effects, with Stevens-Johnson syndrome buried towards the end.

I can't even verify where you got the "Rare" and "Very rare" adverse effects. In the sources you linked to, they just give the number of cases in the treatment and control group -- but they don't give the statistical significance. As I recall from similar calculations, they would need several thousand randomized subjects to identify an adverse effect with an incidence of 1/1,000 at p≤.05. Those adverse effects aren't statistically significant.

I would limit the adverse effects to the nih.gov list above. That was written by a scientist who understands the significance of adverse effects. Those long lists of adverse effects in the treatment group are just copied mindlessly from the clinical reports.

Nobody should be using Wikipedia to find out whether they or their patients are getting rare side effects from thalidomide. That's the practice of medicine which Wikipedia doesn't do. They should go to the package insert and to medical professionals. We're educating people. We filter what's important. Common and serious adverse effects are important. --Nbauman (talk) 20:37, 15 April 2014 (UTC)

Hi Nbauman, thank you for your message. I will write more later. Maybe we can work something out that doesn't delete all content and gives even more value than the present version.--Biologos (talk) 16:05, 16 April 2014 (UTC)

Here we go, with quotes from your message in italics:

WP:MEDMOS says: 'Try to avoid cloning drug formularies such as the BNF and online resources like RxList and Drugs.com. Extract the pertinent information rather than just dumping low-level facts in a big list. For example, a long list of side effects is largely useless without some idea of which are common or serious. It can be illuminating to compare the drug with others in its class, or with older and newer drugs.' My reading of that is that Wikipedia should only list significant side effects that are pertinent because they are common or serious.

That’s not how I understand that passage. To me this says that when listing lots of information (like side effects) it makes sense to give an indication of which of those pieces of information are particularly important. It does not say that we should keep certain information from the reader.

Wikipedia is written for the average person, not the expert, and Wikipedia is not an instruction manual for the practice of medicine. There's no purpose to listing rare and very rare non-serious side effects. It obscures the significant adverse effects.

Wikipedia is not an instruction manual for the practice of medicine or anything else, but - importantly - Wikipedia is also not giving medical advice. It serves information purposes, so it should be our aim to give as much information as possible that might be useful for any particular audience. Wikipedia is an encyclopedia, it is directed at readers seeking information, not specifically at patients. Of course, the better this information is organized, the better the readability for the individual reader.

I can't even verify where you got the "Rare" and "Very rare" adverse effects. In the sources you linked to, they just give the number of cases in the treatment and control group -- but they don't give the statistical significance.

First, I did not link the sources, I just reverted your deletion because I was not convinced by your explanation. Second, the source for the Rare and Very rare effects seems to be reference no. 10, a Product Information from Celgene, Australia.

I would limit the adverse effects to the nih.gov list above. That was written by a scientist who understands the significance of adverse effects. Those long lists of adverse effects in the treatment group are just copied mindlessly from the clinical reports.

This list is not written by someone at the NIH, but actually also a Product Information from Celgene. The side effects listed at the start of the passage are the ones mentioned also elsewhere in the Product Information, mostly in the Warnings section. This is not necessarily identical with the most serious/important side effects! One indication for the most serious side effects is what side effects are listed first in the Patient Information Leaflet (PIL). At least the European regulations require the most serious side effects to be „listed prominently first“ in the PIL, e.g. here for Thalidomide: http://www.ema.europa.eu/docs/en_GB/document_library/EPAR_-_Product_Information/human/000823/WC500037050.pdf p. 34.

Nobody should be using Wikipedia to find out whether they or their patients are getting rare side effects from thalidomide. That's the practice of medicine which Wikipedia doesn't do. They should go to the package insert and to medical professionals. We're educating people. We filter what's important.

I don’t agree. Let’s try to judge what’s important and organize/write the content according to this. Let’s not try to do the jobs of medical professionals who decide what information the patients need and what information they do not need/should not receive.

So in conclusion I suggest to leave the adverse effects listing as it is now, but a section could be added listing the most serious side effects, for instance as mentioned in the PIL I linked to. Cheers, --Biologos (talk) 09:21, 17 April 2014 (UTC)

Let me approach it this way.

You added "Confusion" to Thalidomide as a very rare side effect that may affect ≤1/10,000 people. What is your WP:MEDMOS reliable source for that addition? Are you using secondary sources or primary sources?

What is the confidence interval and P value of that ≤1/10,000 number? --Nbauman (talk) 23:27, 21 April 2014 (UTC)

Please remember that I did not add any adverse effects; I reverted your deletion of adverse effects, because your explanation was not convincing. The "Adverse Effects" section is sourced with four references, currently # 7-10. "Confusion" is mentioned as a very rare side effect in reference #10 (Australian Product Information (PI), I already mentioned it above: https://www.ebs.tga.gov.au/ebs/picmi/picmirepository.nsf/pdf?OpenAgent&id=CP-2010-PI-03581-3 ). Product Information texts are secondary sources using information from primary sources (clinical trials, PSURs etc.). Frequency information of adverse effects is always estimated using the best data sources available, it is not required and/or customary to state confidence intervals and p values. A totally unrelated reason for not using p values and such here is that this is not the place for Original Research. Cheers,--Biologos (talk) 09:10, 22 April 2014 (UTC)

Is that Thalomid product information text a secondary source? From what published primary sources did it get its information on confusion? --Nbauman (talk) 19:38, 22 April 2014 (UTC)

Are you saying that Product Information texts (which have to be reviewed and approved by the regulatory authorities of the respective country) are not reliable sources as per WP:SOURCE and should not be used for articles on drugs?--Biologos (talk) 16:08, 23 April 2014 (UTC)

Yes. I am saying that they are not reliable sources as per WP:SOURCE. They are primary sources and not secondary sources. If you read further down on WP:SOURCE, you will see, "Base articles largely on reliable secondary sources." Product Information texts are primary sources. The rare adverse events you restored are tallies of adverse event reports, with no analysis or assessments. They're not even tested for statistical significance.

Primary sources like regulatory drug labels may be used for some purposes, if we have a consensus. But we don't have a consensus to use the detailed lists of adverse effects. --Nbauman (talk) 17:45, 23 April 2014 (UTC)

We should copy this to the Discussion page of the article and continue there and/or see what others think. This might also give a better idea of whether there is a consensus. Do you agree? Regarding the use of regulatory drug labels as reliable sources in general - we cannot be the first ones discussing this. How has this been dealt with before? --Biologos (talk) 08:41, 25 April 2014 (UTC)

I had to leave this interesting conversation because of the demands of work. But you are right, this should be discussed in the MEDMOS talk pages, I think. Meanwhile, here's an editorial from The BMJ that authoritatively makes the point I was trying to make:

http://www.bmj.com/content/349/bmj.g5153 Too much information
BMJ 2014; 349 doi: http://dx.doi.org/10.1136/bmj.g5153
Published 13 August 2014
Fiona Godlee, editor in chief, The BMJ

they list 20 symptoms most commonly reported in the previous seven days, such as back pain, fatigue, and headache. Nine of these are listed in more than half of the drug information documents they reviewed, and eight are listed as an adverse reaction to more than 90% of the drugs they looked at.

The authors fear that so many possible harms will deter patients from starting or continuing treatments, or might raise negative expectations and increase rates of reporting of adverse events (the nocebo effect). At the very least, they say, organisations providing information should document the levels of evidence that link the adverse effect with the drug, and where possible provide numerical estimates of risk. They also say that greater reliance should be placed on randomised rather than observational data, except where adverse events are serious or rare. This apparently uncontroversial suggestion will, I have no doubt, raise hackles among those who question the ability of randomised trials to properly report adverse events.

More controversially still, they suggest that clinicians should “contextualise” the information they provide to patients, toning down discussion of common non-specific symptoms to reduce the nocebo effect.

--Nbauman (talk) 05:37, 24 August 2014 (UTC)

Nbauman, thank you for this. I also have not done anything in Wikipedia in the last few months because of work and just different priorities. I will try to keep an eye on this, though, and will not forget what you wrote. Cheers,--Biologos (talk) 16:18, 5 September 2014 (UTC)

cell disruption

Hello. It may interest you that someone called tenofalltrades seems determined to completely delete the "cell disruption" page, to which you previously contributed (you asked me for better refs). Over a 11 minute period in March they deleted ~22,500 words (virtually the entire page), and made no attempt to rebuild the page. Of course, the page was imperfect but I think it was still a useful compendium of information. Now it's pretty much gone.

I've tried to communicate with this person, and then reversed their changes, an effort that has now itself been reversed. I don't have the wiki experience (or the time) to deal with this anymore. So I'm writing to you and several other contributors in case others feel like preserving the page. Thanks a lot — Preceding unsigned comment added by Liamloftus (talk • contribs) 14:54, 24 September 2014 (UTC)

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Mitochondrial fusion

I might not be clear from the diff, but the citation wasn't deleted, it appears twice, so it's been consolidated to only appear one in the reference section. Before the chunk of text that was removed, you can see that <ref name=":0"> is now <ref name=":0"/> (note the / at the end of the ref tag). Headbomb {talk / contribs / physics / books} 13:36, 4 July 2016 (UTC)

Thanks and sorry.--Biologos (talk) 13:46, 4 July 2016 (UTC)

"Powerhouse of the Cell" Origins

I believe you were the first person to attribute the saying "powerhouse of the cell" to Phillip Siekevitz on the Mitochondrion page. I've been looking into the origins of the phrase, and it far predates this. Did you have a source for this somewhere else online or did you realise this yourself? Thanks, (sorry for bad formatting this is my first post) -- Wooly Cow (talk) 02:39, 15 January 2024 (UTC)

Hi, thank you for your message. I do not contribute regularly any more, sorry for my late reply. This was a long time ago. I am pretty sure that I would not have added this if I hadn't found it in some secondary source. But unfortunately I seem to have backed this statement only with Siekevitz' original article from 1957. But finding only one earlier source for this would of course falsify the statement and necessitate its removal. Biologos (talk) 08:27, 7 June 2024 (UTC)

I found my edit from 2011: [1]

This shows that I was not the first to mention Siekevitz. I did correct the spelling from 'Seikevitz' to 'Siekevitz' and added his 1957 paper. In my editing comment I mentioned an article on ask.com that the previous article lede was based on apparently, but I cannot find this article now. Maybe the paper was referenced in this ask.com article in 2011. Biologos (talk) 08:35, 7 June 2024 (UTC)

Wow thank you so much for your response! I'm sorry to have bothered you now that you're not active anymore, so it means a lot that you took the time to get back to me. Yes, I left that original comment before I had dug through all the history correctly, and now I can see that it had been on Wikipedia dating back to 10/11/11 a little before you had been involved with it, and was on some strange Indian university entrance exam tutoring websites before then.

In terms of earlier examples, there are many. The saying itself is a derivative of something Albert Claude said on the 15th of January 1948 in a lecture, which is corroborated by his Nobel Prize speech. However, he simply called them the "power plants of the cell", which isn't a verbatim match.

To get it verbatim, you can jump forward a few months to this example in 1948, or this one in 1955, or even this literal encyclopedia entry earlier from 1957.

Siekevitz was nowhere near the first person to say this. Even in his 1957 quote he references that other people have said this too. It is very interesting that because of a few edits of a humble Wikipedia page a decade ago, a benign statement managed to mutate into a false origin story with no acknowledgement of what actually happened. There are scientific papers, hospitals and medical bodies that reference this whole Siekevitz fun-fact as gospel. It's sadly evident none of them have even read the paper they all cite.

I don't have enough Wikipedia credit or whatever to edit the page, so if you'd like to try, go for it. Or, I can give you some more info if you think that is necessary (I looked into this for an ungodly amount of time so I would like something to come from it).

ps I also looked for that ask.com website and I couldn't find it either, hopefully it is archived somewhere. Wooly Cow (talk) 08:56, 7 June 2024 (UTC)

I love it! I used to get lost in research like this, too. I will try to add a quick fix now by changing "coined" to "popularized", adding Claude's lecture as a reference for the edit. And will get back here later. Biologos (talk) 09:05, 7 June 2024 (UTC)

Haha its funny you mention 'popularise' as he didn't really do that either...For example, if you look at the citations he received on that paper, of which there are 170, less than half a dozen of them were within 5 years of publication. Over 150 of them (90%) were made after 2010 once his name hit the Wiki. At the time, the paper 'Powerhouse of the Cell' didn't really make a splash, it was just another piece of snow in the growing avalanche that was the saying's prevalence. Even looking at ngrams you can see there was already growing momentum with the phrase. I did a bunch of ngram comparisons to try and isolate the source of the growth, but I couldn't, as it seemed to just be bubbling out of the entire Rockerfeller Institute community all at once.

This isn't to discredit Siekevitz or anything, he's a remarkably influential cytologist with other very popular works (some published in that same year amassing 1000's of legitimate citations) and he even wrote the first textbook that contained the phrase in 1963 called 'Cell Structure and Function'. So, he should be given the honour of introducing it to academia and to the students of the world, and for being a damn good cytologist. He knew he didn't create the saying, after all the full quote is "they have been called the power-houses of the cell". The rest though, that's history (or in this case, 8th grade bio)

Thanks for the quick edit, and have a lovely day Biologos! Wooly Cow (talk) 11:15, 7 June 2024 (UTC)

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