Talk:Metabolism/Draft

There seems to be agreement that this is a very nice article, and this version can be approved. I think the main purpose of approval is to let editors move on to other tasks, and doesn't preclude later enhancement of this article. Gareth Leng 06:00, 31 December 2006 (CST)

I have just removed Nancy's phrase stating that "energy from NADH is larger than from ATP", since the free energy change of reactions using an electron donor (like NADH) is dependent on the redox potential of the electron acceptor: e.g. it takes a 180 mV difference in a two-electron redox reaction to generate a 30 kJ/mol free energy difference (equivalent to the hydrolysis of an ATP molecule). I am also changing the "to approve" link, so that the approved version will not have that error.. Pedro Silva 05:45, 1 January 2007 (CST)

I have made three minor edits, added Eco Cyc ref and reset the approval URL pointer to the latest edition. It has my editorial YES APPROVE vote David Tribe 15:54, 4 January 2007 (CST) Looks good to me too. Chris Day (Talk) 15:56, 4 January 2007 (CST)

Fine for approval. Nancy Sculerati MD 16:17, 4 January 2007 (CST)

Talk history

According to Larry's intructions on the Approval page, I am sticking this tag on behalf of Nancy ... I set the time limit to December 28th so that the Christmas' holiday does not prevent any interested editors from contributing or removing the approval. Pedro Silva 05:06, 21 December 2006 (CST)

Dear Pedro, A nice start indeed, and an example to all the slower-moving biologists like myself. But i wonder what your plan is: To leave this article in outline format, or to turn it into a narrative like an old-fashioned encyclopedia article. I don't say that i know what is better for something like this.

The reason for a little more of a narrative is that some student looking for metabolism might start at, say, biology, which will have a sentence or two (or an outline link), referring to biochemistry, ditto, which will then refer to here. At some point along the chain he should encounter an elementary discussion of metabolism as a whole (however it may seem to you and to me, for which the topic is the proper subject of a year-long academic course.)

Another matter--how should we incorporate a metabolic map into Cz--I mean a full size complex poster. I can see how to put in a section, but it would be a formidable job doing the whole thing, even if looked at section by section. But it would make an ideal clickable map. I don't think there's a good example in WP. DavidGoodman 22:39, 31 October 2006 (CST)

Dear David,

I was thinking of providing a short narrative that would provide a framework to understand the basic outline of metabolism. I think that detailed descriptions should remain in the existing pathway-specific articles, in order to keep article size manageable. It would be nice to have a good metabolic chart, but too much detail would make in unreadable. I have made a such a chart (it is in my Metabolism pages, in www2.ufp.pt/~pedros/bq/integration.htm) but I find it somewhat unappealing: Art and drawing were never my stronger side ;-) Pedro Silva 06:00, 1 November 2006 (CST)

Nor mine. Perhaps there will be someone here who's good at this. As you say, It will take someone very good to get it to work well. DavidGoodman 16:38, 1 November 2006 (CST)

I just looked this over for the first time, prompted by a message from the "to approve" biology workshop page. I think that as it stands, there is nothing that precludes approval. I would like to come up with a paragraph aimed at the reader who thinks of "metabolism" in the whole organism sense, including multicellular animal, meaning us people [;-)] if I can come up with it. I think whoever knows how should put one of those time limit approval messages here in the talk page, you know - "unless removed this article will be approved on say 2 days from now". Nancy Sculerati MD

Thank you for your input, Nancy! I tweaked your addition a bit. I will be waiting for the approval by another editor to stick the "to approve" template: since I wrote most of it, my vote does not count :) Pedro Silva 06:36, 20 December 2006 (CST)

Hey Pedro. I've actually commented out the approval template because I came to approve it - but when I skimmed the article I noticed that none of the images were coming through. I don't know exactly why that is, but i did check that nothing happened in the version change - and the "to approve" link had the same problem. I'm copying this note to both your and Nancy's page, since I suspect it's more likely to be seen there. Thanks! -- Sarah Tuttle 20:15, 28 December 2006 (CST)

Pre-approval edits

Pedro, I've managed to do to you exactly what would raise my ire when it was done to me on biology. All I can say, is I came to appreciate that the nudges of others, (though not always correct), always forced the article into a more accurate and interesting state. So, please, forgive me in advance. (1) I have made some changes in the first paragraph to reflect anabolism and catabolism in whole organisms. Please make sure they are correct. (2) I made a few minor edits in history, I think bringing in health sciences and medicine for insensible losses is good, because its true and it might lead the user through hyperlinks. (3) I "added" more of a caption under your (beautiful, and I love it, but its not finished) "metabolism" cartoon because it's actually (I think) a "catabolism" cartoon and I know that it would be improved if a simple phrase about each process was added. Point out the mitiochondrium. Add in the cytochromes clearly. (4) I copied the image and re-labelled it "anabolism"- not that I actually made the image (I've got to learn how- what program do you use-adobe illustrator?), but I hoped you would- show the nucleus and the endoplasmic reticulum, simple schemas of protein synthesis etc. (5) Can you fit an image of cell division somewhere? Or of growth of a plant bud? That aspect of catabolism. Any way, I'm going to send you a message on your talk page, and ask Gareth and Chris and David to take a look, I think this is going to be a great article. Nancy Sculerati MD 09:38, 29 December 2006 (CST)

No need to apologize :-) I enjoyed your edits, and feel they did improve the text. Before I read your message, I had already improved the captions following your hints. I also made an "anabolism" picture, before seeing that you intended it to be about whole cell processes :-( There it is, anyway... But do feel free to put another image! About the program I used for those pictures: just plain old Paint. Not fancy, but that is the only one I can handle. (and at about the level of my lack of skill) Unfortunately, I do not believe I would be able to draw those things you asked ...

PS: I was not involved in the Biology article (too busy fixing metabolic articles).. But I did follow the process in the talk page ;-) Pedro Silva 10:18, 29 December 2006 (CST)

Well, I've called out the swarm of editors to buzz over metabolism. With the Chiropractic article, I learned that what looks good to a couple of us is better reviewed and polished by the swarm. I think the changes you have made are to the good. I am sure there will be a few more improvements, but we must remember that better, as well as perfect, is an enemy of the good, and so we will await the swarm and hope for a rapid approval- rather than a major demolition. As long as there are several editors involved Pedro, I think that once we have the article in an agreed state to be approved, that you should nominate it for approval. Nancy Sculerati MD 10:41, 29 December 2006 (CST)

P.S. would you mind looking at snake venom? Nancy Sculerati MD 10:41, 29 December 2006 (CST)

What has been written is excellent, and i think at the appropriate level. but 2.1 to 2.6 as listed look as if they were intended to be sections that have not yet been written; I imagine they are intended as a list of subordinate topics. I have changed format a little in a way that I hope indicates this. DavidGoodman 12:52, 29 December 2006 (CST)

I think this is a very nicely written article. I've added a short section on regulation of metabolism and done a quick copy edit.Gareth Leng 06:23, 30 December 2006 (CST)

I've also linked this to Hunger, which you might like to take a look at.Gareth Leng 06:48, 30 December 2006 (CST)

Rather late I've come to realize this is up for approval. I've added some details relating to reducing power and anabolism, and I'm happy to add my Editorial approval to the item as it now stands David Tribe 18:41, 30 December 2006 (CST)

Something to consider for the future Fred Neidhardt, Moselio Schaechtet, aJohn Ingraham use a framework for metabolism (orig created by Franklin Harold ) that may be better than that used here. Its based on blocks of 1.Fueling reactions 2 Biosynthesis 4 Macromolecule synthesis 4)assembly ( of organelles).

They also would be a superb practical diagram for this page

It worth considering for a future major rewrite but for the moment and for reasons of pragmatism, Im not pushing it for this first edition David Tribe 19:40, 30 December 2006 (CST)

image:weight lifter

Matt Innes had this great picture of a muscular weight lifter that we ended up not using in aanother article. I asked him to upload it to metabolism, and thought we could change the caption to something about anabolism. Nancy Sculerati MD 08:10, 30 December 2006 (CST) Think we'd have to be careful not to suggest that that weighlifter was using banned substances :-)Gareth Leng 05:50, 31 December 2006 (CST)

The red weightlifter is certainly a great image Good to see fellow Microbiologists are so versatile Pedro David Tribe 20:31, 3 January 2007 (CST)

Couple of quick copy edit checks?

Hey guys, the article looks great! Found two sentences that need work (see bold), whether before or after approval:

• The Golgi apparatus of cells contains the of the enzymes used for protein posttranslational modification (an anabolic process).

• Alternatively, the electron acceptor may be a molecule totally unrelated to the metabolic pathway that released the electrons now present in NADH, in which case a respiration is said to occur.

I didn't make any changes as I wasn't sure where you are in the process. Otherwise, as an author in this field, it looks great. --Matt Innis (Talk) 14:38, 2 January 2007 (CST)

Chris got 'em. --Matt Innis (Talk) 20:00, 2 January 2007 (CST)

Finished my addition/changes

OK, I just went through this article changing what I thought were misleading points (leading to misconceptions) and some factual errors. i tried to document these change in my edit summaries but will be happy to discuss the point in more detail here. From my perspective it seems OK now, although, I wonder if there is a another way to present the lists of pathways at the end? i think this latter concern is fairly trivial and will be better left for after the grand opening. Chris Day (Talk) 17:36, 2 January 2007 (CST)

So do we now have to change the version on the ToApprove template, or should everyone take one more look before we do that? Otherwise all of Chris's changes are lost again. --Matt Innis (Talk) 20:03, 2 January 2007 (CST)

They would not be lost, just transferred to the draft version. Since I corrected what I thought were a few errors I would recommend some version after my additions. Preferaably after others have proof read and approved my own changes. i see Nancy has already improved some of the bits i changed. I changed the chemotropic section quite a bit so someone needs to check that it makes sense. Chris Day (Talk) 21:22, 2 January 2007 (CST)

Hi, Chris!

I liked your work, but in the process you included an error: fermentation is NOT a special case of respiration: the redox state of the carbon atoms in the products is equal to the redox statre of those atoms in the reactants (check e.g. Brock's microbiology textbook). Therefore I think that paragraph must be changed... I also see you considered my redox potential discussion in photosynthesis as inaccurate :(. iThat discussion may be quite technical, but it IS correct (check e.g. the photosynthesis chapter in Voet & Voet's "Biochemistry" ) Pedro Silva 04:14, 3 January 2007 (CST)

Added brief mention of insulin and glucagon.Gareth Leng 06:50, 3 January 2007 (CST)

Hi Pedro, good catch on the fermentation and it seems more clear the way it it currently written (and correct ;). With regard to the redox potential it is possible i was confused with what you had written. The part of the sentence i had a problem with was the following (bold):

"in these reactions, excitation of a photosystem caused by absorption of a light photon markedly lowers its redox potential. Since electron flow tends to occur from low potential species to high potential species, the excited photosystem transfers electrons to higher potential species in an electron transport chain present in the thylakoid membrane."

First don't electrons move to the low potential? I agree that the reaction center redox potential is lowered, this is due to the loss of the electron. In fact, it is so low that it can accept electrons from water (photosystem II is the only enzyme complex that can achieve this reaction). Or am I misunderstanding your nomenclature here. That was why i cut out the whole discussion since it seems quite advanced for this type of article and the nomenclature can make the concept harder to grasp. Chris Day (Talk) 10:02, 3 January 2007 (CST)

Electrons move towards high redox potentials: the relationship between free energy and electric potential is

                            ΔG=nzFΔE

where n is the number of charged species moving, z is their charge (-1 for the electron) and F is the Faraday constant (about 96500 C/mol). Therefore a spontaneous electron transfer (ΔG<0) entails ΔE>0, i.e. electrons move towards higher redox potentials. That's also the reason why electrons move from NADH (E⁰ = -320 mV) to oxygen (E⁰ = 820 mV) and not the other way around. In photosynthesis, P680 has a potential around 900 mV, and that is why it can take electrons from water (the redox pair water/oxygen has a potential of 820 mV). After flashing light, the redox potential of P680 decreases to about -800 mV, which enables it to transfer electrons to the pheophytins, etc. all the away up (in redo potential) to photosystem P700 (redox potential around 400 mV). Flashing P700 reduces its potential to below -1 V, enabling it to transfer electrons to ferrredoxin and (ultimately) NADP⁺ (redox potential about -320 mV) Pedro Silva 10:26, 3 January 2007 (CST)

Hi Pedro, just read this. Yes, I embarrassingly got it mixed up. I must edit with a text in front of me in future. I was imagining the standard graphs of ETC's that have the potenital on the y axis. I just naively assumed the values below zero would be negative. Chris Day (Talk) 14:59, 4 January 2007 (CST)

fantastic

Hi everyone! This article is looking fantastic. I just wanted to confirm - if you want to keep the changes made, you need to update the "to approve" template link. Also, maybe list the approving editors down here that approve it (with changes). Thanks! It looks like (if there are no objections) we can get this sorted by the end of today. :> -- Sarah Tuttle 11:37, 4 January 2007 (CST)

I approve it with the new changes. The version number of the most current version is http://pilot.citizendium.org/wiki?title=Metabolism&oldid=100017814. Pedro Silva 11:53, 4 January 2007 (CST)

I just added a change. In the chemotropic section, it seems strange to not mention the ATP production aspect of oxidative phosphorylation since the whole section is written from that perspective. I tried to address that with the most recent edit. Chris Day (Talk) 15:16, 4 January 2007 (CST)

Suggestions

This looks great, but I don't think "heat" from metabolism is covered enough or mentioned early enough (warm blooded / cold blooded mentioned early enough as well?). I also think you might consider making a section on the differences of human metabolism with age and with disease. Perspiratio insensibilis is not linked and I examples of this type of energy (mass/heat) loss should be given instead of giving what it isn't. In other words, explain today's understanding of perspiratio insensibilis instead of the understanding after the initial publication(s). I also wonder if excretion should be covered more - more explanation about nitrogen and its toxic qualities and why the body wants to get rid of it and examples of how and when it gets rid of NH3(converted to urea -explain the evolutionary reason for converting nh3 to urea, uric acid, etc in different species). You may also consider adding more of how metabolism has evolved and get a biologist who specializes in this area write a section on it. When almost all of life in terms evolution species-health can be crudely (but comically) broken down to - "we eat and sleep to have enough energy to have sex" - college biology teacher first day of class - metabolism seems pretty important in terms of evolution. My read was cursory so I may have missed some minor (included) points. -Tom Kelly (Talk) 13:50, 4 January 2007 (CST)

Jan 4 Vote for Approval

I agree that this version is fine for approval. Nancy Sculerati MD 16:16, 4 January 2007 (CST)

Agree. Well done Pedro, Gareth Leng 16:37, 4 January 2007 (CST)

Hooray. All approved and put to bed. Congrats. -- Sarah Tuttle 16:46, 4 January 2007 (CST)

Good job guys! Keep 'em comin'! --Matt Innis (Talk) 07:26, 5 January 2007 (CST)

Standard Disclaimer still at top!

Unlike the other 3 articles approved till date, this one still has the standard disclaimer at the top! Supten 04:45, 10 January 2007 (CST)

A vernacular explanation

I think the first paragraph of the article could be marginally improved by the addition (not a replacement) of a simpler, jargon-free definition, if possible. This does not mean I think it isn't a great article, by the way--it's just an idea I had. Congratulations, Pedro, and the rest of you. --Larry Sanger 11:23, 12 January 2007 (CST)