Wikipedia:Peer review/Metabolism/archive1

Metabolism
Recently expanded into what I hope is a comprehensive and broad review of the chemical basis of life. Expert and non-expert comments and criticisms would be very welcome. TimVickers 03:52, 21 March 2007 (UTC)

NOTE - Now nominated as a FAC. Nomination page is Featured article candidates/Metabolism. Thanks for all the feedback! TimVickers 19:11, 25 March 2007 (UTC)

Zephyris

 * Excellent depth and breadth of content! All content seems accurate and well referenced. Good NPOV (ie. not concentrated on human metabolism!) with good coverage of the very important, but overlooked, bacterial metabolism. There are a coupe of minor issues I have, which will be changed when I get the time :) :
 * The table in Metabolism - it makes no mention of polypeptides and presents disaccharides as a polymer.
 * Fixed.
 * Metabolism is a bit ugly - with my physics background I hope to be able to clarify and clear this up.
 * Sure, I was trying to write it for an non-expert reader with a biological slant, perhaps it is too simplified?
 * The problems a combination of slightly too simplified and some unusual terminology, chaos in place of disorder for example. - Zephyris Talk 15:29, 22 March 2007 (UTC)
 * Metabolism could use a basic example - insulin regulation of glycolysis/gluconeogenesis in liver/muscle cells?
 * Good point. I'll work on that this evening. TimVickers 16:24, 21 March 2007 (UTC)
 * New paragraph and diagram on insulin added. TimVickers 16:37, 25 March 2007 (UTC)
 * Very nice :) - Zephyris Talk 18:48, 25 March 2007 (UTC)
 * I might attack Image:Metabolic pathways small.png to make it link to the processes it presents...
 * All in all brilliant, thanks to the massive improvement by TimVickers. - Zephyris Talk 16:11, 21 March 2007 (UTC)

Fvasconcellos
Looks great—well-written, well-referenced and quite comprehensive. A few comments:
 * Under "Key biochemicals":
 * "...polymers such as DNA proteins." DNA and proteins? Am I reading this wrong? :)
 * Typo!


 * In the "Coenzymes and cofactors" subsection, I feel a bit more space could be devoted to cofactors: explaining more explicitly what they are and perhaps giving a few examples?
 * These have been re-divided into "coenzymes" and "Minerals and cofactors"


 * Image:Hemoglobin.jpg would be better as a high-resolution PNG. I realize this image is used on several pages, so perhaps making a better version would be a good idea—it could then be used throughout WP;
 * "In "Minerals": "...nerve and muscle function as these cells..." This sounds a bit off to me.
 * Reworded.


 * Under "Anabolism":
 * In the "Proteins" subsection: "Amino acids are made into proteins by being joined together in a chain by peptide bonds between their amino and carboxylate groups."—comprehensible, but a bit of a run-on sentence.
 * Simplified.


 * Finally, under "History", should "ferments" really link to vitalism?
 * No, removed. Thanks for the comments. TimVickers 18:38, 21 March 2007 (UTC)

I can't find anything seriously amiss with this article, but then again this is the non-expert review :) I personally think it's excellent, if a bit long (at 70 kB)—I'd look forward to comments from other reviewers. I presume you're aiming for FA? Fvasconcellos 17:21, 21 March 2007 (UTC)
 * As an aside, Image:A thaliana metabolic network.png—awesome.
 * Eventually, but it will need polished first. TimVickers 00:59, 22 March 2007 (UTC)
 * I'm planning to do a remake of the haemaglobin pictures, highlighting the haem groups and their binding to the protein backbone. - Zephyris Talk 15:27, 22 March 2007 (UTC)
 * Thanks for the new picture! TimVickers 18:44, 25 March 2007 (UTC)

BirgitteSB

 * Overall another quality article. My largest problem here is that the article does not always to follow it's own structure.  While it is largely structured to deal with catabolism and anabolism separately, the text seems flow more topically with processes being discussed if they follow the more specific topic no matter which heading it happens to fall under.  This makes me wonder if the article would be more natural if was structured differently.  Maybe have two small section on the general concept of catabolism and anabolism and then proceed topically.  Carbohydrates are built by anabolism how by who and used in catabolism how by who.  Proteins are built by anabolism how by who and used in catabolism how by who. Lipids, minerals, etc.  Otherwise keep the current structure but clean it up so you are strictly dealing with catabolism under the catabolism heading etc.
 * "Lipids" Many other lipids are made in cells, notably steroids such as cholesterol Is part of this paragraph missing? I don't see any earlier mention of lipids being made elsewhere. I now understand you were trying to say "Many other lipids (not mentioned previously) are made in cells (as well)".  I suppose this could be worded more clearly.
 * Reworded for clarity.


 * "Coenzymes" These coenzymes are therefore continuously recycled. I find this sentence confusing in the current context. I went on reading about ATP with idea it was that is was not actually consumed but left over to be re-used.  After re-reading and thinking about it I now understand what you are trying to say, but it could be clearer.
 * Reworded for clarity.


 * "Catabolism" I am confused as to what actually constitutes catabolism in phototrophs (At this point), especially since the opening sentence reads: Catabolism is the set of metabolic processes that release energy by breaking down and oxidising food molecules.  This opening paragraph needs to be inclusive of all five subsections following not just the first (animal centric) three.
 * Reworded to be broader.


 * "Digestion"  Animals secrete these enzymes into their guts, while in microbes, digestive enzymes are secreted into the cell's surroundings. I find this a slightly misleading as it is suggesting these to methods are in opposition, but technically they are very similar. The gut is simply a specialized part of of an organism's surroundings, it is not technically part of the organism.
 * Well, these are in opposition, as microbes don't have guts. It doesn't actually say anything about any mechanistic differences, only the obvious anatomical one.
 * I suppose I am reading this more like "Animal secrete these ezymes [internally] while in microbes, digestive enzymes are secreted [externally]" with many readers possibly misled on the fact that in this context internal to organisms = external to cells.  But this is very slight so don't worry about it.-- Birgitte SB  13:56, 23 March 2007 (UTC)
 * I thought of something here. What do you think of: "Microbes simply secrete digestive enzymes into the cell's surroundings, while animals only secrete these enzymes from specialized cells in their guts"-- Birgitte SB  17:55, 23 March 2007 (UTC)
 * Thanks! Reworded as per suggestion. TimVickers 17:07, 25 March 2007 (UTC)


 * "Carbon fixation" Now you have basically labelled photosynthesis (as a lay reader might understand it) as catabolism (In plants, photosystem II uses light energy to remove electrons from water, releasing oxygen as a waste product) and anabolism (Photosynthesis is the synthesis of glucose from sunlight, carbon dioxide (CO2) and water, with oxygen produced as a waste product) within four paragraphs.  Somehow you must differentiate these processes to the lay reader.
 * This is a tricky one, any suggestions?
 * Rearrange the article to handle light energy topically? This is the real problem with the article: to seperate catabolism and anabolism you must assume the reader has some understanding of things like photosynthesis as a whole.  Because when you try to explain photosynthesis you end folowing the energy from one process to another.  So I really think the only solutions are to A) not explain photosynthesis as a whole B) Rearrange the article to follow various processes through their cycles (Photosynthesis as whole, Protiens manufactured and digested, Fat tissue stored and then used, etc.)-- Birgitte SB  17:44, 23 March 2007 (UTC)
 * That class-by-class approach as it's own problems, since it will then be hard to make broad generalisations about the features shared between different parts of metabolism and instead turn the article into a laundry list of metabolic pathways. The two possible approaches each have their own advantages and disadvantages. I've tried adding a new lead to the sunlight capture section to differentiate the two processes for the lay reader. TimVickers 18:11, 23 March 2007 (UTC)


 * "Carbohydrates and glycans" Although the fat in adipose tissue is a major store of energy, the fatty acids in these stores cannot be converted to glucose through gluconeogenesis as vertebrates cannot convert acetyl-CoA into pyruvate. This qualification confuses me. Do only vertebrates have adipose tissue or can fatty acids actually be converted to glucose through gluconeogenesis in some metabolisms?  Also is after long-term starvation, humans need to produce ketone bodies  really limited to humans?  On a separate note wouldn't conversion of fatty tissue to glucose really be catabolism anyways?
 * Reword, broaden, the classification could be argued either way, since the breakdown to acetyl-CoA is catabolic but gluconeogenisis is certainly anabolic.


 * "Xenobiotics and redox metabolism" Do xenobiotic-metabolizing enzymes act significantly differently outside of humans?  If not it might be best to first explain the general three-step process and then mention which enzymes are particularly used by humans.  More information on different methods of dealing with this issue would be nice.
 * Added material on microbial xenobiotic metabolism and biodegradation.


 * "Thermodynamics of living organisms" I wonder if this whole section is really most appropriate in this particular article.  It certainly breaks the flow of the article for me.
 * I think I need it, since this is an area of research and relates to the discussion of energy flows in all the above sections. Originally, I had this at the beginning. Maybe it could be merged with another section?


 * "Evolution" When talking of the loss of metabolic pathways it might be good to reiterate the previously mentioned example of essential amino acids.
 * "History" This section needs the most work. It seems to lack focus overall .  What is important to understand about the history of this topic?-- Birgitte SB  19:42, 22 March 2007 (UTC)
 * I was just thinking a way to improve the history section might be to change to simply a Historiography section. Then you do not have to worry about how to relate events but only papers.-- Birgitte SB  13:56, 23 March 2007 (UTC)
 * The problem I faced with this is that it is so broad! It will have to be a history of the first few hundred years of biochemistry in a few paragraphs. Daunting, to say the least! TimVickers 16:00, 23 March 2007 (UTC)

Zephyris II

 * Would it be worth having a section on the significant differences in metabolism between organisms? A table of comparison of different metabolic pathways/major metabolic products or modified versions of Image:Metabolic pathways small.png may be suitable.
 * Further to the above, indication of the different metabolic processes tissue to tissue would be usefull (though maby more appropriate in human metabolism or metabolome.
 * Metabolism could use a clear definition of metabolome.- Zephyris Talk 08:56, 23 March 2007 (UTC)

These are both excellent ideas, but would indeed fit best in a Human metabolism article. In this article I've tried to make a broad generalisation of metabolism in all organisms and point up the differences as I go along. To be comprehensive a table we would need bacteria, archaea, protists, animals and a plant.
 * added to Anabolism section. TimVickers 18:39, 25 March 2007 (UTC)


 * Coolios (m:sp: abscent ---> absent) - Zephyris Talk 18:49, 25 March 2007 (UTC)