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This page has been locked to prevent editing. You can view and copy the source of this page: <p class="O" align="justify" v:shape="_x0000_s1026"><span lang="EN-US"><font color="#000000" size="3" face="Arial"><font size="5">Welcome to<font size="4"> <em>[[openfree]]</em> [[Image:Openfree.gif]] </font>Biomatics home</font></font></span><span lang="EN-US"></span>&nbsp;</p> <div><span><font color="#000000"><font face="Arial Unicode MS"> <table border="1" cellspacing="1" summary="" cellpadding="1" width="100%"> <tbody> <tr> <td><font color="#000000" size="3">Biomatics is a discipline that networks [[biology]], [[philosophy]], [[mathematics]], [[informatics]], and [[mechanics]] to describe all&nbsp; biological information structures in holistic ways. It is also a short name of&nbsp;[[Systems Bioengineering]]. Unlike [http://bioplanet.com/what_is_bioinformatics.html bioinformatics] which is the science of information retrieval from textual data, biomatics involves&nbsp;engineering, cellular and molecular&nbsp;biology,&nbsp; and hardware.&nbsp;<br /> <br /> <font size="2">The major&nbsp; difference between biomatics and other biological fields such as [[bioinformatics]] is that Biomatics is associated with <strong>design and construction</strong> of biological objects and machineries under mathematical principles.</font></font></td> </tr> </tbody> </table> <br /> </font></font></span></div> <div><span><font color="#000000"><font face="Arial Unicode MS">The name [[Biomatics]] was coined in 1994 to differentiate a research field from&nbsp;Bioinformatics which is too computational and theoretical. Biomatics&nbsp; describes a field of biology that&nbsp;is not only theoretical but also&nbsp;has mechanical, designing,&nbsp;and synthetic aspects under clear top down principles. <br /> <br /> [[The future of Biomatics and Biology]]<br /> [[Biology and mathematics are perhaps the closest disciplines in science]]&nbsp; | [[Biomatics versus Omics]]<br /> <br /> <br /> <br /> <div align="left"><a herf="http://biomatics.org/index.php/Wiki-Help"></a>&nbsp;<font size="4"><font size="2"></font><a class="external text" title="http://www.google.com/search?hl=en&amp;q=site%3Abiomatics.org&amp;btnG=Search" rel="nofollow" href="http://www.google.com/search?hl=en&amp;q=site%3Abiomatics.org&amp;btnG=Search"><strong><font color="#3366bb">Sitemap</font></strong></a></font><br /> <hr /> </div> </font></font></span></div> <br /> <h2>[[Biomatics lab]]</h2> Philosophical, mechanical, mathematical&nbsp;and informational understanding of Biome. A place to theorize,propose and&nbsp;work on projects in a collaborative environment.<br /> <br /> <br /> <h2>Applications</h2> <div align="justify"> <ul style="MARGIN-RIGHT: 0px" dir="ltr"> <li>[[Smart molecules]] <ul> <li>[[Molecular Robotics]] </li> <li>[[Development of artificial organs and appendages]] </li> <li>[[Development of human machine interfaces]] </li> </ul> </li> <li>[[Medical Biomatics]] <ul> <li>[[Protein Folding]] </li> <li>Molecular Codes <ul> <li>[[The Amino Acid Code]] <ul> <li>[[The Histone Code ]] </li> <li>[[The Microtubule code]] </li> </ul> </li> <li>[[The Telomere Code]] </li> </ul> </li> <li>[[Computational Oncology]] </li> <li>[[Pharmacogenomics]]&nbsp; (Pharmacoepigenomics) </li> <li>[[Pharmacobiomatics]] </li> <li>[[DNA Microarray Analysis and Gene Expression Profiling ]] </li> <li>[[Intervention of Aging]]&nbsp; </li> <li>[[Computational Psychology and Psychiatry]] </li> </ul> </li> <li>Molecular Electronics <ul> <li>[[Bioware]] <ul> <li>[[Protein Based Computing]] </li> <li>[[Reverse BioEngineering]] </li> </ul> </li> </ul> </li> <li>[[Forensic Biomatics]] </li> <li>[[Sports Biomatics]] </li> <li>[[Discovery of Mathematical Techniques and Theory]]<font size="3" face="Times New Roman"><br /> </font>&nbsp; </li> </ul> </div> <hr /> <p>&nbsp;</p> <h2>Biological Mathematics or Principia BioMathematica</h2> <p>It is evident that some form of computation takes place in biological systems and indeed within single molecules.&nbsp; It thus follows that some form of mathematics occurs in these computations.&nbsp; Whether it be basic set theoretical concepts such as subsets, intersection, and union or more complex manipulations such as [http://www.cs.unm.edu/~brayer/vision/fourier.html Fourier transforms of visual data].&nbsp;&nbsp;&nbsp;<br /> <br /> <br /> <font size="3" face="Times New Roman"></font><font size="3" face="Times New Roman">The term &ldquo;Biomatics&rdquo; consists of a cross contraction of [[Biological Mathematics]].&nbsp; The concept that is meant to be defined is the study of mathematics as it occurs in biological systems.&nbsp; This is in contrast to the concept of mathematical biology, which is the use of mathematics to describe or model biological systems.&nbsp;&nbsp;<br /> </font><font size="3" face="Times New Roman"><br /> &nbsp;A tentative definition might be:&nbsp; The seamless development of mathematics and computation from a few clearly stated axioms and rules of inference in pure logic as embodied in an atomic/molecular medium.&nbsp;&nbsp;&nbsp;Or,&nbsp;the study of &quot;[[smart molecules]]&quot;.<br /> <br /> <br /> </font><font size="3" face="Times New Roman"></font>&nbsp;</p> <h3>Background</h3> <p><br /> [http://en.wikipedia.org/wiki/Gottfried_Leibniz Gottfried Leibniz]&nbsp;considered the following thesis in the late 17th century:&nbsp; (Some or all of) mathematics can be reduced to formal logic.&nbsp;&nbsp;</p> <p><font size="3" face="Times New Roman">It is often described as a two-part thesis.<br /> </font><font size="3" face="Times New Roman">&nbsp;&nbsp;&nbsp;&nbsp; 1. All mathematical truths can be translated into logical truths.&nbsp; <br /> &nbsp;&nbsp;&nbsp;&nbsp; 2. All mathematical proofs can be recast as logical proofs.&nbsp;&nbsp;&nbsp; <br /> In other words, that all mathematical truths and proofs can be restated in the vocabulary of logic.&nbsp;<br /> </font><font size="3" face="Times New Roman"><br /> By the late 1800s [[Karl Weierstrass, Richard Dedekind and Georg Cantor]] had all developed methods for defining the irrationals in terms of the rationals.&nbsp; [http://en.wikipedia.org/wiki/Giuseppe_Peano Giuseppe Peano] had also gone on to develop a theory of the rationals based on his now famous axioms for the natural numbers.&nbsp; Thus, by [http://en.wikipedia.org/wiki/Gottlob_Frege Gottlob Frege]'s (predicate calculus) day (1848-1925) it was generally recognized that a large portion of mathematics could be derived from a relatively small set of primitive notions</font><font size="3" face="Times New Roman">&nbsp;</font></p> <p><font size="3" face="Times New Roman">In 1910, [http://en.wikipedia.org/wiki/Bertrand_Russell Bertrand Russell] and [http://en.wikipedia.org/wiki/Alfred_North_Whitehead Alfred North Whitehead] collaborated on [http://plato.stanford.edu/entries/principia-mathematica/ Principia Mathematica], an attempt at a detailed deduction of mathematics from logic, which proved to be greatly influential yet controversial.&nbsp;&nbsp;<br /> </font><font size="3" face="Times New Roman"><br /> In Bertrand Russell's words, it is the logicist's goal &quot;to show that all pure mathematics follows from purely logical premises and uses only concepts definable in logical terms&quot;.&nbsp;<br /> </font><font size="3" face="Times New Roman"><br /> &nbsp;As a result, the question of whether mathematics can be reduced to logic, or whether it can be reduced only to [http://en.wikipedia.org/wiki/Set_theory set theory], remains open.&nbsp; However, in light of modern theories of evolution, [[fractal geometry]], physics, chemistry and computer science, some concepts are now self-evident.&nbsp; Given that biological systems perform some sort of mathematics, and acceptance of evolution, it follows that these mathematical systems have evolved and therefore must have started from some initial state.</font>&nbsp;Biomatics further raises at least the possibility that all of mathematics may be based on elemental algebraic structures as embodied in such molecules as the amino acids.</p> <h3>Intramolecular Computation</h3> <p style="MARGIN-RIGHT: 0px" dir="ltr"><br /> &nbsp;&nbsp;<font size="3" face="Times New Roman"> Consider an algebraic system embodied in a molecule consisting of N atoms.&nbsp; In the case where N = 3&nbsp; we find the [http://biomathelogical.blogspot.com/ cube group] (in terms of abstract algebra).&nbsp; (Note that N = 1 and N = 2 can represent groups as well).<br /> </font><font size="3" face="Times New Roman"><br /> [[Group theory]] (abstract algebra) is a well-developed branch of mathematics that provides many theorems and definitions.&nbsp; The key concept is that it describes, formally, a small (fundamental?) mathematical system consisting of a set and an operation on the members of that set.&nbsp; Could this then be nature&rsquo;s way of evolving a system of mathematics and computation from a set of primitive notions?&nbsp; It seems it must inevitably be so, for ultimately what separates the different species, from viruses to man, is the complexity of the molecules that carry the blueprint for the ontogeny of the species.<br /> <br /> <br /> </font><font size="3" face="Times New Roman"><br /> </font><font size="3" face="Times New Roman"></font><font size="3" face="Times New Roman">As computer scientists, we seek and think in terms of information storage and processing.&nbsp; We seek to compare and contrast biological manifestations of computer science paradigms including:<br /> <br /> [[Algorithms]] <br /> [[Data structures]]<br /> </font><font size="3" face="Times New Roman">[http://www.claymath.org/library/annual_report/Sturmfels.pdf Theorems]<br /> [[Computer Architecture]]<br /> </font><font size="3" face="Times New Roman">&nbsp;&nbsp;&nbsp;&nbsp; [[Switching elements (gates)]]<br /> </font><font size="3" face="Times New Roman">&nbsp;&nbsp;&nbsp;&nbsp; [[Circuitry]]<br /> </font><font size="3" face="Times New Roman">[[Finite State Machines]]<br /> </font><font size="3" face="Times New Roman">[[Mathematics]]<br /> &nbsp;&nbsp; &nbsp;[[Cubology]]<br /> &nbsp;&nbsp;&nbsp; [[Hexagonology]]<br /> </font><font size="3" face="Times New Roman"><br /> We apply our knowledge and linguistics to analyzing, describing, and comparing natural phenomena to artificial processing.&nbsp; For example, image processing, graphics, [[Artificial Intelligence]], are well-developed bodies of scientific endeavors, with many potential candidate concepts.</font><font size="3" face="Times New Roman"><br /> </font><br /> <font size="4"><strong>See Also</strong><br /> <br /> <strong>External Links</strong></font><br /> [http://biomathematics.org BioMathematics.org]<br /> [[Biomatics Inc. Japan]]: Bioinformatics company in Japan. It is nothing much to do with Biomatics.org<br /> [http://www.systems-biology.org/ SystemsBiology Institute]&nbsp;<br /> [http://www.biomaticsinc.com Biomatics Inc.]: Digital Imaging analysis company.<br /> [[Biomatics Germany]]: Web development for life science.&nbsp;<br /> [http://psoup.math.wisc.edu/archive/sosfaq.html Self organization FAQ]<br /> [http://www.aaai.org/aitopics/html/alife.html Creation of artificial life forms]&nbsp;<br /> [http://www.WorldWideWanderings.net Wim Hordijk's home page]</p> <p style="MARGIN-RIGHT: 0px" dir="ltr"><a href="http://homepages.force9.net/calresco/">CALResCo, home of this FAQ</a><br /> <a href="http://foto.hut.fi/~markus/selforg.html">Links to SOS online papers/sites</a><br /> <a href="http://life.csu.edu.au/vl_complex/all.html">Complex Systems virtual library</a><br /> <a href="http://lslwww.epfl.ch/~moshes/alife_links.html">Complex Adaptive Systems</a><br /> <a href="http://views.vcu.edu/complex/">VCU complexity research group</a><br /> <a href="http://www.alcyone.com/max/links/alife.html">Artificial Life links</a><br /> <a href="http://www.brint.com/">Complex Systems &amp; Chaos Theory</a><br /> <a href="http://www.cogs.susx.ac.uk/users/ezequiel/alife-page/complexity.html">SOS bib</a><br /> <a href="http://www.cpm.mmu.ac.uk/~bruce/combib/">Measures of Complexity</a><br /> <a href="http://www.cpm.mmu.ac.uk/~bruce/combib/selforganizing.html">Self-org measures</a><br /> <a href="http://www.ezone.com/sos/">SOS on the Web</a><br /> <a href="http://www.cpm.mmu.ac.uk/~bruce/evolcomp/">What is complexity ?</a><br /> <a href="http://www.krl.caltech.edu/avida/">The Avida Group</a><br /> <a href="http://www.santafe.edu/">Santa Fe Institute</a><br /> <a target="_top" href="http://www.the-scientist.com/2008/9/1/36/1/">Biology's Gift to a Complex World</a> (The Scientist, 9/2008)&nbsp;<br /> <a target="_top" href="http://www.newscientist.com/channel/tech/robots/mg17523626.000">Machine Nature</a> (New Scientist, 28/9/2002)&nbsp;<br /> <a target="_top" href="http://www.sciencemag.org/cgi/content/full/277/5334/1931">Computer Design Meets Darwin</a> (Science, 26/9/1997) </p> <hr /> &nbsp; [http://bioism.org Bioism.org] | [http://funktopia.net Funktopia] | [http://biolicense.org Biolicense]&nbsp;&nbsp;| [http://bioreligion.org Bioreligion.org] | [http://omics.org Omics.org] | [http://matics.org Matics.org] | [http://biocompany.net Biocompany.net]<hr /> <p>&nbsp;&nbsp;</p>

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