Talk:Mathematical and theoretical biology

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Untitled

I reverted the partial AE -> BE shift in the spelling - BE was the first spelling used for any variant word [1]. In addition, this was only a partial shift, made spelling inconsistent in the article. Guettarda 13:16, 5 Apr 2005 (UTC)

Thank you for this change. Porcher 14:42, 5 Apr 2005 (UTC)

referencing

I think there's a problem with the referencing on this page. The idea of footnotes is, well, they are meant to refer to something at the foot of the page! That should give the full formal reference, and *that* may in turn link to a copy of the paper. But I don't expect to have to download some PDF to find out which paper you are referring to.

In fact, I much prefer the Harvard referencing style. If I say in the text "genes are selfish (Dawkins 1976)" then probably 70% at least of the people reading the article wouldn't need to go look & see what book I was referring to, so it saves them time. If you don't allow Harvard referencing, most people are not going to have time or bother to look up every single reference, so they loose out on some information.

See further WP:Cite --Jaibe 20:36, 29 March 2006 (UTC)[reply]

pointless comment: Harvard style referencing is awesome as it puts metadata (who and when was the data made) with the data! That paradox is so bad that some people hate it (or they hate sorting the reference list alphabetically). --Squidonius (talk) 11:22, 24 April 2008 (UTC)[reply]

Citecheck template removed

The citecheck template covers a narrow sort of problem: if an editor doubts that a citation presents information appropriately (such as giving inaccurate facts or quoting out of context). It seems that some other template would be appropriate here. See Wikipedia:Citing sources and Wikipedia:Cleanup resources. Durova 02:49, 3 September 2006 (UTC)[reply]

Woe to the future.

an increasing interest in in silico experimentation due to the complications involved in human and animal research.

That's a euphemistic way of saying "an increasing interest in not performing experiments because they're too hard. "In silico experimentation" is an oxymoron.

Also, this entire "Importance" subsection is purely speculative, subjective, unreferenced, and unjustified. It should be removed. --75.58.54.17 23:49, 26 October 2007 (UTC)[reply]

Merge of Computational biomodeling

The following discussion is closed. Please do not modify it. Subsequent comments should be made in a new section.

The result was merge into Mathematical biology, 1 disagree present. -- Squidonius (talk) 11:48, 24 April 2008 (UTC)[reply]

A merge tag was placed on this article in November. I have changed the tag there to mergeto and added the mergefrom tag here. The discussion is directed here. There is none on the other article. This merge seems sensible. Please discuss below. --Bduke (talk) 00:41, 26 December 2007 (UTC)[reply]

Agree Mainly the definitions are vague and no way established, and hence author specific and overlapping. Mathematical modelling, mathematical biology and computation biology should be one but mentioned. In my opinion there are too many separate records in bioinformatics/compbio, which is ironic that the bio topic which should know more about networks actually is an unlinked agregate of records. --Squidonius (talk) 23:16, 23 February 2008 (UTC)[reply]

Disagree:

"Computers are to biology what mathematics is to physics" Harold Morowitz

I would echo that sentiment, and add that the Computational Biology Wiki should not be merged with the Mathematical Biology Wiki. It seems unlikely to me that there will ever be a math capable of modeling life, but an approximate and pragmatic computational biology seems plausible. 209.90.238.134 (talk) 05:09, 12 March 2008 (UTC)[reply]

Being a a semantics/grey line issue on the definition of its breath, that the two may or may not be identical is "debated", but a page with only 3 lines in it is a nearly useless article. If we can establish why the two may differ, we can add a section to each pointing out this issue with a good reason and with references, if they are both the same shade of gray changing the title to "mathematical biology and computation modelling" might be wise.

In reply, in my opinion they are the same due to:

- fyi, ppl in physics do similar analyses and models.
- Nobody here is saying mathematical biology is computational biology. Instead, that it is an aspect of compuation biology, that of making models with maths on a computer and hence a synonym of computational modelling.
- Mathematical biology is making mathematical models using computers, a tool that allows complex mathematics and to run through all combinations (dynamic modelling still involves maths).
- All quantitative computational models are mathematical models.
- All "good" models are quantitive as qualitative models can be derived from quantitative and not viceversa.
- The definition of good model to approximate life is ambigous, as it does define what robustness is considered acceptable and what system is in focus. Saying a whole planet to the molecule level is not an isolated system (in this hypothetical scenario dinosaurs would be alive, say). Reguarding robustness, adding noise to the system at a point of dimuishing returns (every protein can interact with any other protein, say, is a waste of effort as only a few specific changes have an effect). so, even though currently untractable, life on an isolated system to an extremely high degree of robustness is mathematically possible (unless life is a miracle).
- Stuff like normalizing a qPCR intensity is not mathematical biology, but just algebra in biology, mathematical biology is identical to theoretical physics.

In summary, is there a computer model that is not quatitative (=mathematical)? and is mathematical biology only "theoretical" model building? I do not want to have an edit war even less over semantics, so please point out where I am mistaken, thanks #REDIRECT --Squidonius (talk) 18:14, 13 March 2008 (UTC)[reply]

DISCUSSION FROM OTHER PAGE (error in system when tag were placed) Computational biomodeling mean making biological models with a computer. Mathematical biology is more apt title and is a richer page, although it is completely orphaned I think. --Squidonius (talk) 18:56, 20 November 2007 (UTC)[reply]

There are actually a few articles that this article could be merged in (or replaced by).

Systems biology and Computational biology are two similar fields;
Molecular modelling and Protein structure prediction are covered in their own articles;
some other areas with significant overlap, such as artificial life are hyperlinked in the article.

It is not clear from this article how computational biomodeling relates to these subjects. Is it really a concept that deserves its own article? I would suggest to merge any relevant content into Mathematical biology, Computational biology or others and mark this article for deletion. Hendrik Fuß (talk) 15:52, 19 December 2007 (UTC)[reply]

Hendrik: No, a page should not be deleted after merging the text into some other article. Since that would loose the edit history and thus the attribution to the authors of this text which breaks the GFDL license. But from a more practical point: Someone might already have put links to this article from other web sites or have web browser shortcuts to this article. And the old author(s) might come looking for it. So instead this page should be redirected to the article it was merged into.

--David Göthberg (talk) 23:18, 13 April 2008 (UTC)[reply]

The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

List of Names

what's with this list?? It's completely arbitrary and incomplete... I'd suggest just getting rid of it 128.200.174.63 (talk) 22:10, 9 July 2009 (UTC)[reply]

Agree: We need to delete the list of names. There are too many famous theoretical biologists to have an exhaustive list on this main page. The current list has people of various degrees of notability, and I can not think of a clear line as to how notable one would have to be in this field to make the list. MATThematical (talk) 16:35, 27 February 2010 (UTC)[reply]

Merge with Theoretical biology?

The lead of this article says that mathematical biology is also called theoretical biology. However, there is a separate article theoretical biology.

My own original research suggests that MB and TB are nowadays essentially synonyms. It seems that MB is used almost inclusively in the US, and TB is frequently used in Europe. I guess some people think MB sounds more respectable, and others are doing qualitative theoretical work and need the more inclusive term TB. Historically, the field seems to have started with TB that cannot possibly be called MB.

I see two possibilities:

1. Merge the MB and TB articles into a single article Mathematical and theoretical biology. This longer term has significant frequency in the real world. [2] Optionally discuss the two usage of "MB" and "TB" if possible, i.e. if reliable sources discussing this can be found.

2. Keep the MB and TB articles separate. Due to massive overlap between the two topics we need a strategy to:

... avoid making one article into a content fork of the other.
... avoid confusing the readers.
... avoid disputes whether a certain researcher or subfield falls under MB or TB.

My personal favourite would be to merge the two articles for now and split them later if and when a consensus for doing so develops. Presumably such a consensus would be based on a reasonable post-split strategy.

A potential problem is that apparently mathematical biology is a subfield of computational biology, while theoretical biology is not. Hans Adler 07:38, 21 November 2009 (UTC)[reply]

I would gladly hand theoretical biology to the first topic that can demonstrate an RS claim on the name (the current article is simply unsourced and/or WP:SYNTH). Can you find even a single RS equating TB with MB (so as not to base the merger simply on OR)? On the imperfect overlap issue, would some sort of 'reverse merger' (keeping TB's name but MB's content) make more sense? Hrafn^Talk_Stalk^(P) 08:06, 21 November 2009 (UTC)[reply]
- Encyclopedias routinely discuss several different but related concepts in a single article. Even though a lot of people mistake Wikipedia for a dictionary, it is no exception. That some experts (I am clearly not one at all) think it makes sense to discuss the two together is suggested by the existence of a European Society for Mathematical and Theoretical Biology and a Mathematical and Theoretical Biology Institute. There are also joint link lists on the web. [3] [4] Even if this is only an artefact of a strong weight of interdisciplinary groups between two distinct subjects, it might still make sense to discuss them together.

I found a personal view on this area [5] that suggests to me that there are terminological problems here caused by a recent explosion of interest in mathematical and computational biology, which emerged out of theoretical biology. Perhaps this has led to a domination of mathematical biology by computational biology, which doesn't really fit under theoretical biology? In any case I guess the new landscape of fields, subfields and demarcations between them has not yet stabilised; or only so recently that it's not yet reflected in the names of institutions etc.

It would be best to have input from researchers who see themselves as mathematical, theoretical or computational biologists. Hans Adler 08:34, 21 November 2009 (UTC)[reply]

PS: Perhaps we have been talking past each other. I am talking about the strategic decision of which article titles to have. I am not trying to defend the current content of the article theoretical biology at all. In practice a merge could consist in translating and adding some of the material from the solid and uncontroversial German article de:Theoretische Biologie, finding suitable inline citations for it (the German Wikipedia insists on a more summary citation style that wouldn't be acceptable here), and adjusting some existing language at this article.

Note that what you would expect to be the companion article for mathematical biology, de:Mathematische Biologie, doesn't even exist, while de:Biomathematik uncontroversially redirects to de:Theoretische Biologie. Also note the first picture at de:Mathematische Biologie, showing the cover of Uexküll's German book on Theoretical Biology. The caption translates as follows: "1920 Early standard work of pre-mathematical theoretical biology". Hans Adler 08:47, 21 November 2009 (UTC)[reply]

Perhaps the following translation of the [Historical] Evolution section of de:Theoretische Biologie helps, even though it may well be original research by the German editors: "Theoretical biology, which has been strongly expanding in the Anglo-Saxon sphere for a while, is more recently also on the rise in Germany. This is witnessed by the establishment of several chairs in theoretical biology; a diversification of research fields can be observed. A centre of theoretical biology in Germany is located at theInstitut für Theoretische Biologie at Humboldt University Berlin. Historically, some non-mathematical parts of biology were occasionally subsumed under theoretical biology." Hans Adler 08:55, 21 November 2009 (UTC)[reply]

That is more than enough RS basis for equating the two fields. I therefore support the proposed merger. Hrafn^Talk_Stalk^(P) 09:11, 21 November 2009 (UTC)[reply]

Support merger as the two fields are not demonstrably distinct. The relationship with Computational biology will need to be addressed later. -- Scray (talk) 15:18, 21 November 2009 (UTC)[reply]
Merge. I'm no expert and haven't tried to research the matter, but based on what has been said here and a scan of both articles (and to a small extent de:Theoretische Biologie), the argument for merging these seems sound (that is, they are either the same field or at least very much overlapping). Kingdon (talk) 22:37, 22 November 2009 (UTC)[reply]

As a passer-by, I just note the existence (not mentioned above) of the two separate categories Category:Mathematical biology and Category:Theoretical biology which would also need to be thought about ... merge or make one a subcat of the other? Melcombe (talk) 14:55, 16 December 2009 (UTC)[reply]

I think they should be merged as well. Both are rather small, neither really fits into the other as a subcategory (computing related to biology isn't theoretical biology, and the early non-mathematical work on theoretical biology isn't mathematical biology), but most and most articles would fit into both. Hans Adler 16:03, 16 December 2009 (UTC)[reply]

I think Mathematical Biology should be merged into Theoretical Biology. In some fields, there exists a difference: such as Mathematical Physics and Theoretical Physics. In the case of physics, the distinction is that Mathematical Physics studies the Math that used by Physics (i.e. ODEs, PDEs, parts of topology, etc) while Theoretical Physics studies Physics for which we can not yet conduct experiments, or for which there is no predictions (or disagreeing predictions) of theory and experiment. In biology however, all 3 field: Mathematical, Computational, and Theoretical study Biology. All 3 fields try to produce theories (but do not conduct experiments) for certain parts of biology. It just happens that in Mathematical biology, the theories are mathematical, and in Computational biology the theories are computational. However, they are still theory building, and hence fall under Theoretical Biology. I do not have a good source for this, and will get back to this talk page if I find one. However, a good approach is to look at the scope of one of the leading journals of theoretical biology (Journal of Theoretical Biology) and see that it includes many of the best works in Mathematical Biology. --DFRussia (talk) 21:55, 28 February 2010 (UTC)[reply]

Look at the title of this article. The merge has been done already. What has not been merged yet is the categories. Hans Adler 22:14, 28 February 2010 (UTC)[reply]

The related Category:Mathematical biology has been nominated for deletion, merging, or renaming. You are encouraged to join the discussion on the Categories for discussion page.

The related Category:Theoretical biology has been nominated for deletion, merging, or renaming. You are encouraged to join the discussion on the Categories for discussion page.

Actually, I just noticed that the article Theoretical biology still existed. I have merged it into this one now. The merge discussion for the categories has completed today, with the result that they are also being merged. Hans Adler 00:36, 8 March 2010 (UTC)[reply]

Rereading DFRussia's comment: The problem with "Theoretical biology" as the title for the merged article is that mathematical biology also includes some parts of bioinformatics that are purely computational and not theoretical. Moreover, the title "mathematical biology" seems to be more popular recently, so I guess it wouldn't be a good idea to drop it. Hans Adler 00:40, 8 March 2010 (UTC)[reply]

Maps vs. Difference equations

In the list of deterministic equations used in mathematical biology, maps and difference equations are separated. Aren't these the same thing, at least from a mathematical biology sense. I know that maps are more general in a mathematical sense, but I don't quite see why they are separated. Perhaps write the list with "difference equations/maps", or delete maps all together. They are both continuous state space and discrete time. If they are in fact different this should be mentioned in this article. --MATThematical (talk) 16:50, 27 February 2010 (UTC)[reply]

Evolution = population genetics ???

The article currently says Evolutionary biology has been the subject of extensive mathematical theorizing. The overall name for this field is population genetics. I would say that although there is a big overlap, much of evolutionary biology is not population genetics, e.g. paleontological investigations. --Ettrig (talk) 14:53, 1 December 2011 (UTC)[reply]

But paleontological investigations do not involve mathematical and theoretical biology. There are sophisticated measurement techniques, but those are not considered mathematical biology when they take place in other fields. Joannamasel (talk) 16:02, 1 December 2011 (UTC)[reply]

Introduction

In the beginning, the article states

It includes at least four major subfields: biological mathematical modeling, relational biology/complex systems biology (CSB), bioinformatics and computational biomodeling/biocomputing.

As someone who has a degree in mathematical biology, I have the feeling that this is misleading. In my opinion,

mathematical modeling in biology is the traditional core field of mathematical biology;
bioinformatics is not part of mathematical biology as it is more closely related to computer science / statistics than mathematics;
systems biology is an area of research the draws from several fields, including mathematical biology, bioinformatics, biology and physics;
computational biomodeling: I don't know this topic too well.

I would recommend to change this part of the article. Any other opinions?--109.45.105.190 (talk) 05:33, 17 June 2014 (UTC)[reply]

I agree, and am deleting the sentence. Joannamasel (talk) 16:52, 4 July 2014 (UTC)[reply]

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Proposed merge with Relational Physiology

This appears to be one person's neologism and/or pet theory. The term "relational physiology" does get a couple of hits on Scholar, but they are not related to it. This theory and its author get exactly one hit on Scholar; it has no cites. Justlettersandnumbers (talk) 12:10, 19 January 2016 (UTC)[reply]

14:34, 19 January 2016 (UTC)

This is a fair criticism. The following sentence and ref might be merged into the said Mathematical and theoretical biology page (under the section relational biology), and omit the Relational Physiology page altogether or redirect from there:

In was suggested that in the physiological context a relational approach entails focusing on the functional organization of living systems that are embedded in a responsive and adaptive environment, analyzing processes rather than objects, implementing natural input statistics and closed-loop experimental designs.^[1]

--ZoB1958 (talk) 14:38, 19 January 2016 (UTC)[reply]

References

^ Marom, Shimon (2015). Science, Psychoanalysis, and the Brain: Space for Dialogue. (Chapter 5: Reflections on Relational Physiology). Cambridge University Press. pp. 90–168. ISBN 978-1-10710118-0.

Done as suggested above.

--ZoB1958 (talk) 17:00, 19 January 2016 (UTC)[reply]

ZoB1958, I've undone your addition to the article, as the only citation was to the author of the theory; I believe that it should not be re-added until and unless there is some take-up of the concept by other academics, so that the content can be cited to independent reliable sources, in accordance with our policy on verifiability. Justlettersandnumbers (talk) 20:10, 19 January 2016 (UTC)[reply]

For those interested in phylogenetics, and clade presentations

Could you have a look at this effort, here, to use clade diagrams to summarize pharma business acquisitions. My take at present is that the images created are devoid of standard quantitative meaning—nothing is captured by vertical and horizontal line lengths, as far as I can tell—and so they are a misapplication of this maths/graphic presentation method. Moreover, I argue that they are misleading (presenting a time axis, but not making spacing of events proportionate to the historical time differences), much harder to maintain (consider adding entries to a std Table versus this graphic), more likely to diminish article quality (in their ambiguity of content, again, over a std Table with clear headings), and therefore practically amenable to decay as a result. I would add to this, in this esteemed math-bio context, that they would make those who trained us, and other purists in methodology and meaning (and Edward Tufte more generally), turn in their graves/beds. After having a look at the User page and at a couple of pages linked on that sandbox page, leave your opinion here, regarding the overall effort? Thanks for your opinion. Cheers. Le Prof Leprof 7272 (talk) 01:37, 23 March 2016 (UTC)[reply]

Sorry about the inappropriate posting above. I have opened a discussion in the appropriate forum, here: Wikipedia_talk:WikiProject_Companies#Diagrams, for anyone who is interested Jytdog (talk) 03:26, 23 March 2016 (UTC)[reply]

Jytdog moved the question to a new forum, the one where it is least likely to be viewed with rigour, see last comment and link. I reply there. I stand by the fact that maths theor biol is an appropriate venue to call for experts, and that it was appropriate to call out to you you at this location, to ask your input. All coming from this area, I would appreciate if you state for the record, if you have any real knowledge on this matter (have ever actually done a cladogram-type computations/presentations). Transparency, please. Le Prof Leprof 7272 (talk) 15:45, 23 April 2016 (UTC)[reply]

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[SfD-1] Marom, Shimon (2015). Science, Psychoanalysis, and the Brain: Space for Dialogue. (Chapter 5: Reflections on Relational Physiology). Cambridge University Press. pp. 90–168. ISBN 978-1-10710118-0.

[1]