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Molecular and Cellular Biology Wikiproject Newsletter

Plugging away alone :)

Thanks for the kind words! I hope you can find a use for some of the stuff ive done!

Your input is requested

Your input would be appreciated at this Request for Comments. Kelly Martin (talk) 18:29, 6 December 2006 (UTC)

Vertical box on introduction to evolution

I think it does not look too bad. I like it more than horizontal box. What do you think?--Filll 04:38, 8 December 2006 (UTC)

I agree it looks a lot better. It probably still needs tweeking and a better title than overview, but its a step in the right direction. David D. (Talk) 04:50, 8 December 2006 (UTC)

Doing something about the ridiculous date autoformatting/linking mess

Dear David—you may be interested in putting your name to, or at least commenting on this new push to get the developers to create a parallel syntax that separates autoformatting and linking functions. IMV, it would go a long way towards fixing the untidy blueing of trivial chronological items, and would probably calm the nastiness between the anti- and pro-linking factions in the project. The proposal is to retain the existing function, to reduce the risk of objection from pro-linkers. Tony 05:07, 10 December 2006 (UTC)

Sandbox template

I like your glucose metabolism sandbox.. I think I'll try and steal it over at the metabolic pathways wikiproject. Robotsintrouble 15:49, 14 December 2006 (UTC)

Go right ahead and make it your own. I never really got it into a form i liked enough to start slapping it on articles. David D. (Talk) 18:35, 14 December 2006 (UTC)

I agree that the metabolism articles are quite ragtag. The individual articles don't seem to lack for information, but the overall structure and organization is quite poor... lots of repetitive information and inconsistent presentation, making it very difficult for readers to find the information they want. The pre-existing Template:Metabolism you pointed me to is in need of a complete overhaul, something I currently lack the wiki coding skills to improve. As an example, check the lipid metabolism entries in the template: They all redirect to Lipid metabolism, a detailed but confusing article about the whole process. I think the current Template:Metabolism is quite limiting in the study of Biochemistry, which is how I've become involved in this area. Why? Well, primarily because Template:Metabolism is organized by classes of compounds (lipids, proteins, carbohydrates) instead of by metabolic processes as the Italian template. Breaking down metabolism into coherent chunks is unnecessarily difficult when you classify metabolism by compounds; this creates a huge amount of ambiguity, overlap, and confusion because the processes acting on carbohydrates, lipids, and proteins are intimately interconnected. For example, 'lipid catabolism' (AKA fatty acid B-oxidation) provides energy for 'carbohydrate synthesis', but it doesn't contribute any carbon to the glucose produced in this way. So would this important process go under lipid catabolism or carbohydrate synthesis? Where do we put ketone bodies under this paradigm?

I'm unsure where to begin with this. In addition to the necessary navigation templates, I think we need to provide more context on how the different parts of metabolism are interconnected, at least in mammals. I think the first step is improving the major component articles of the metabolism content, but where should all this be integrated? In the main metabolism article, or in a new Human metabolism article, or interspersed through the major subsidiary articles?

Your help manipulating the templates would be greatly appreciated, I think that's the first step. After that, I'm not sure where to go.Robotsintrouble 03:34, 15 December 2006 (UTC)

Furthermore, is it necessary to have both of the templates below in the wiki? Frankly I prefer your Italy-derived template to both of them, although it could be improved by integrating some of the style of the following templates. Also, maybe we should merge Metabolism and Cell metabolism, either would make a great entry page to metabolism and give us a space to provide an overview of the process. Robotsintrouble 03:52, 15 December 2006 (UTC)

v t e Metabolism, catabolism, anabolism
General	Metabolic pathway Metabolic network Primary nutritional groups
Energy metabolism	Aerobic respiration Glycolysis → Pyruvate decarboxylation → Citric acid cycle → Oxidative phosphorylation (electron transport chain + ATP synthase) Anaerobic respiration Electron acceptors other than oxygen Fermentation Glycolysis → Substrate-level phosphorylation ABE Ethanol Lactic acid
Specific paths	Protein metabolism Protein synthesis Catabolism (protein→peptide→amino acid) Amino acid Amino acid synthesis Amino acid degradation (amino acid→pyruvate, acetyl CoA, or TCA intermediate) Urea cycle Nucleotide metabolism Purine metabolism Nucleotide salvage Pyrimidine metabolism Purine nucleotide cycle Carbohydrate metabolism (carbohydrate catabolism and anabolism) Human Glycolysis ⇄ Gluconeogenesis Glycogenolysis ⇄ Glycogenesis Pentose phosphate pathway Fructolysis Polyol pathway Galactolysis Leloir pathway Glycosylation N-linked O-linked Nonhuman Photosynthesis Anoxygenic photosynthesis Chemosynthesis Carbon fixation DeLey-Doudoroff pathway Entner-Doudoroff pathway Xylose metabolism Radiotrophism Lipid metabolism (lipolysis, lipogenesis) Fatty acid metabolism Fatty acid degradation (Beta oxidation) Fatty acid synthesis Other Steroid metabolism Sphingolipid metabolism Eicosanoid metabolism Ketosis Reverse cholesterol transport Other Metal metabolism Iron metabolism Ethanol metabolism Phospagen system (ATP-PCr)

v t e Metabolism, catabolism, anabolism
General	Metabolic pathway Metabolic network Primary nutritional groups
Energy metabolism	Aerobic respiration Glycolysis → Pyruvate decarboxylation → Citric acid cycle → Oxidative phosphorylation (electron transport chain + ATP synthase) Anaerobic respiration Electron acceptors other than oxygen Fermentation Glycolysis → Substrate-level phosphorylation ABE Ethanol Lactic acid
Specific paths	Protein metabolism Protein synthesis Catabolism (protein→peptide→amino acid) Amino acid Amino acid synthesis Amino acid degradation (amino acid→pyruvate, acetyl CoA, or TCA intermediate) Urea cycle Nucleotide metabolism Purine metabolism Nucleotide salvage Pyrimidine metabolism Purine nucleotide cycle Carbohydrate metabolism (carbohydrate catabolism and anabolism) Human Glycolysis ⇄ Gluconeogenesis Glycogenolysis ⇄ Glycogenesis Pentose phosphate pathway Fructolysis Polyol pathway Galactolysis Leloir pathway Glycosylation N-linked O-linked Nonhuman Photosynthesis Anoxygenic photosynthesis Chemosynthesis Carbon fixation DeLey-Doudoroff pathway Entner-Doudoroff pathway Xylose metabolism Radiotrophism Lipid metabolism (lipolysis, lipogenesis) Fatty acid metabolism Fatty acid degradation (Beta oxidation) Fatty acid synthesis Other Steroid metabolism Sphingolipid metabolism Eicosanoid metabolism Ketosis Reverse cholesterol transport Other Metal metabolism Iron metabolism Ethanol metabolism Phospagen system (ATP-PCr)

Misconceptions at Introduction to evolution

You are absolutely correct. I struggled with this when I was writing the original draft. Maybe this section should be called "Misconceptions answered"? or "Answers to misconceptions"? or something like that?--Filll 16:14, 14 December 2006 (UTC)

I like the title common misconceptions since it draws you to the section. Using 'answered' or 'answers to' makes it sound a little too defensive. Actually by their nature misconceptions are not in the form of questions so they can not be answered, as such. I am fine with the first line as written, (I wrote it of course ;) ) but i would avoid the word 'answer' if you intend to massage it a bit. David D. (Talk) 18:39, 14 December 2006 (UTC)

Thanks re Talk:Stephen Barrett

I appreciate your talking some time to join in the discussion and give some perspective. --Ronz 20:23, 14 December 2006 (UTC)

No problem, i was watching from the sidelines and it just kept getting worse and worse. It does not have to be that way. David D. (Talk) 20:38, 14 December 2006 (UTC)

Other suggestions? I watched from the sidelines for a long time, then when I read the NCAHF article at the end of August, I started working on it, hoping to avoid any other Barrett-related articles. Now I feel overwhelmed. --Ronz 21:06, 14 December 2006 (UTC)

All I can suggest is patience and use the talk page. Getting into a revert war is pointless. David D. (Talk) 21:13, 14 December 2006 (UTC)

Thanks for jumping in on Levine2112's talk page. We'll see what happens. Meanwhile, I'm not only feeling overwhelmed, but harrassed. It already looks like he's making an effort to be more civil, so maybe it was just a bad time for him. --Ronz 19:16, 18 December 2006 (UTC)

Then again, maybe not. I don't want to give him a test4, but he's definitely not allowing my comments to stay on his talk page. Suggestions?

Your comments can stay. I welcome them with open arms. However, your warnings are unwarranted on my talk page and your persistence to re-introduce them is equivalent to vandalism. I have not operated in bad faith nor have I made any personal attacks on you. Perhaps you are confusing the edits withe editor. Now then, you make a good point about consensus. Let's see where that takes us. Levine2112 19:28, 18 December 2006 (UTC)

Ouch!

I have hit a road block or two when trying to improve the lead section on evolution and in the "fact and theory" sections of the evolution and the Creation-evolution controversy articles. I have compiled a comparison between the different proposed sections of text at Talk:FactandTheoryComparison and at Talk:Evolution/LeadComparison and there is a discussion of this at Talk:Evolution. I would appreciate it if you took a peek and let me know what you think. Thanks !!--Filll 19:15, 15 December 2006 (UTC)

Biological laws

I am positive I have heard that phrase before. If you do a google search, it is clear that are over 26,000 hits, so some people use the phrase. If you look at the talk page for scientific law I have put some sites I found about biological scientific laws. There are probably more. --Filll 20:13, 15 December 2006 (UTC)

This might be due to ignorance? This is Ernst Mayr's view on the subject: "In evolutionary biology, however theories are largely based on concepts such as competition, female choice, selection, succession and dominance. These biological concepts, and the theories based on them, cannot be reduced to the laws and theories of the physical sciences. " David D. (Talk) 20:20, 15 December 2006 (UTC)

It might be that natural selection is not really a scientific law, and some people just call it a scientific law. Or it might be that there are enough exceptions to the principle of natural selection that it is not useful as a scientific law. Or it might be some linguistic difficulties as to what constitutes a law and what does not. Physical laws get violated all the time, actually. Consider zero-point energy, the nature of the vacuum, Heisenberg Uncertainty Principle etc. That is, if you have empty space, particles and energy spontaneous materialize and disappear in that empty space. This violates conservation of energy and thermodynamic laws etc, at least as classically understood. The Law of Universal Gravitation is violated of course. Even Einstein's theory of gravity (which I do not think is really called a law) looks like it is violated now. Lots of other laws in physics are violated all the time. No one worries about it. In fact, it is exciting to find a violation. A scientific law is just sort of a basic simple principle that is well established you can use to make predictions, solve problems, etc. So it might be a linguistic problem. Even things like determinism or assumptions about reality turn out to be violated. Think about Schrodinger's Cat; alive and dead at the same time. Think about EPR paradoxes. Think about "spooky action at a distance"; BCS theory that explains superconductivity relies on these weird quantum state. It makes no sense. But it appears to be true. Think about Bose Einstein condensates. Think about black holes where all the laws of physics that we know break down, or at least sort of. --Filll 20:33, 15 December 2006 (UTC)

I understand that laws can be broken but there is definitely a cultural difference between the way they are used between physicists and biologists. Part of this might be that biological systems are not as easy to present as an equation. Those ammenable to such treatment do seem to become laws. David D. (Talk) 20:42, 15 December 2006 (UTC)

It is true that most physical laws are associated with equations, although not always. It is also true that biology is not as well developed as physics because it is more complicated, so it has not become as quantitative yet as physics. As we slowly are able to measure more and more things, biology will become increasingly quantitative I suspect. And probably more quantitative laws will start to emerge. Another part of the problem is that the people doing biology, by and large, are not quantitative people at all. The same thing happened in astronomy when quantitative people invaded, and in geology when quantitative people invaded. The traditional scientists were a bit nonplussed when the new fangled quantitative scientists started to invade. Plate tectonics, for example, is purely the result of quantitative types invading geology. It is now happening in biology as well. Every major university will have a department of molecular biology and a department of biology, for this very reason. Quantitative viewpoints are different, and cause a certain amount of tension in the nonquantitative realms. Also, nonquantitative people are less tuned to look for quantitative laws or rules than quantitative people. So there can be quantitative laws all over the place, just waiting to be discovered. But since there are so few people with those skills, interests and background looking, they do not get found.--Filll 21:00, 15 December 2006 (UTC)

So based on this, aside from a paragraph or two in scientific law with some references, there is no need for a separate article on biological scientific laws. I think that we should at least have a pointer to some of the literature, and the references that claim there are no biological laws, and those that do. It should be no surprise that Schrodinger and other physicists who wrote about biology have a lot of musing in their writing about biological laws. I suspect it might just be a century or two too early to have much yet. But I am fairly confident that more is going to emerge. I suspect that biology will be by far the most exciting field of science, bar none, eventually.--Filll 21:17, 15 December 2006 (UTC)

It makes me laugh (in a good way) to see you call molecular biology quantitative. So how would you define a gene without getting your head bitten off? The biggest impedance in biology towards Laws is that the exceptions are the rule. David D. (Talk) 21:21, 15 December 2006 (UTC)

You have to realize this is very very early days. It is like physics in the year 1200 or something. But it is the start. Just wait for a century or two.--Filll 21:33, 15 December 2006 (UTC)

First, I have to find the fountain of youth. Or buy a red sports car? David D. (Talk) 21:38, 15 December 2006 (UTC)

Thank you.

Thanks, David; your words are appreciated. Have you seen my latest post on the RD Talk page? Look out some of the pages I have indicated-the attack was vicious. I now have a feeling that I am being 'stalked', if that is the right word. Hope that does not sound too paranoid! I will hang on, though, thanks to people like you. Clio the Muse 23:36, 15 December 2006 (UTC)

Solar powered sea slugs

Yes, they're very interesting little beasts, and the research that has been done on them really is top-notch. I learned quite a bit just researching the stub I put down! --Slashme 08:45, 18 December 2006 (UTC)

Re: RNA replication

Hey thanks for liking the work. I must admit that I am(or at least was) unaware of non-viral RNA-dependant-RNA replication. I mostly followed the wikipedia article itself for the diagram. A quick google search actually reveals lots of RNAi related RNA-dep-RNA replication in so many organisms, wow. I'll update the figure. While I'm talking to you, would you consider none-ribosomal peptides as a case of protein-to-protein information flow? I was mostly thinking about the polypeptide antibiotic, but I bet there are other cases (I'm asking because no one replies to the talk page) Thanks! Adenosine | Talk 19:26, 18 December 2006 (UTC)

I just don't know enough about how these long peptides are synthesised. Do you have a reference to get me started? (sorry for the lazyness, research wise ;) It sounds to me that it does not count. But I am open to changing my opinion. I think if all the peptides are aligned in an active site to get them into the correct order it may count. David D. (Talk) 19:36, 18 December 2006 (UTC)

Hey no worries. I think the wikipedia article on Nonribosomal peptides is really good on the subject. I myself think this comes down to symantics, are these things really proteins or just big molecules, etc..? I'd love to make them count as a for of information flow because it would really added some symmetry to the diagrams. Here's some reviews on the subject Adenosine | Talk 04:45, 19 December 2006 (UTC)

Your comment on LC's talk page

I know it's difficult when LC exhibits such poor judgement, but try to limit your comments to his actions rather than him. I don't think either saying he's a thug or acting like a thug is entirely appropriate. I also don't think it's a big deal, but I think the best way for him to learn is by example, and so we have to be scrupulously careful when talking to him to avoid diversions. -- SCZenz 03:09, 27 December 2006 (UTC)

I think I chose my words poorly. I have clarified my comment. David D. (Talk) 03:10, 27 December 2006 (UTC)

Please dont pronounce on my judgement here. SCZ. I dont rate your much either.--Light current 10:01, 27 December 2006 (UTC)

FA nomination for Immune system

Hi David. The FA process for our article on DNA is going quite smoothly. However, Immune system has also been nominated and this article requires quite a lot of work. As one of the more experienced MCB editors, if you have any time over the next couple of days could you have a shot at improving this? Any help would be appreciated, especially copy-editing and clarifying! Thanks. TimVickers 05:06, 2 January 2007 (UTC)

Ilena

Nice proposal. Since the guidance she needs has fallen away, she's quickly reverting to "angry mode". --Ronz 21:09, 3 January 2007 (UTC)

Sorry David. Please tell me how Barrett should be allowed to restate his case and claim libel, even after the Supreme Court of California has ruled on it against him. I also do not understand how those with one link away from every website of Barrett's empire, can post his links all over Misplaced Pages, but I am not allowed any links to my legal non profit foundation. I disagree that I bring nothing of value to the discussions of Barrett. For example, in June I tried to post that his NCAHF had been suspended for several years, but was blocked and it reverted as it his operation was legal. Now, after much ado, the article is less POV and more balanced. Also, there was a clear error in regards to Barrett Vs Rosenthal regarding Barrett's appeals that I corrected yesterday. No one else would have known this and this unfactual / unverified point would have been left on. I am further confused as to why there are Wiki articles filled with Barrett's viewpoint as a critic, even after courts have ruled him to be "biased and unworthy of credibility." I could name 20 articles that sound more like Quackwatch (which in itself is an attack site against those he deems worthy of defamation) than anything encyclopedic. I am a serious health advocate and activist with a support group of several thousand of women, run a legal non profit foundation, and have been a target of Barrett's for years. I am not the only activist who has been successful in defending myself against his meritless SLAPP suits. However, I am outnumbered here, as those in his operation, seem to have a full time job defending his articles. Thank you. 21:31, 3 January 2007 (UTC)

Which links and who are you talking about? And with resepct to your own web site, others may choose to add the site. However, it is inappropriate for you to add the site. David D. (Talk) 21:22, 3 January 2007 (UTC)

Thank you. fyslee is the Ringmaster for all of Barrett / QW / NCAHF sites, as well as Barrett's personal assistant listmaster for the healthfraud list for several years (until about 2 weeks ago). He has put hundreds (may be an underestimate) of Barrett's related links throughout wikipedia ... which all link to his own "quack files." Here is one of his Wiki pages which itemizes this. Thank you. Ilena 22:13, 3 January 2007 (UTC)