Featured Papers by Jonathan Bartlett
Organon F, 2023
Teleological causes have been generally disfavored in biological explanations because they have b... more Teleological causes have been generally disfavored in biological explanations because they have been thought to lack rigor or act as stand-ins for non-teleological processes which are simply not yet understood sufficiently. Teleological explanations in biology have been limited to only teleonomic causes, which are teleological causes that are due to codes or similarly reified mechanisms. However, advances in the conceptualization of teleological and teleonomic causation have allowed for more quantitative analyses of both. Additionally, although teleonomy has been historically excluded from potential causes of evolution, new research has shown that teleonomy actually plays a significant role in evolution. Combining these advances with advances in computability theory and information theory have allowed for a more rigorous and quantitative analysis of the capabil- ities and limitations of teleonomy in evolution.
Mutations are often described as being “random with respect to fitness.” Here we show that the ex... more Mutations are often described as being “random with respect to fitness.” Here we show that the experiments used to establish randomness with respect to fitness are only capable of showing that mutations are random with respect to current external selection. Current debates about whether or not mutations are directed may be at least partially resolved by making use of this distinction. Additionally, this distinction has important mathematical, experimental, and inferential implications.
Communications of the Blyth Institute, 2019
Generalized Information (GI) is a measurement of the degree to which a program can be said to gen... more Generalized Information (GI) is a measurement of the degree to which a program can be said to generalize a dataset. It is calculated by creating a program to model the data set, measuring the Active Information in the model, and subtracting out the size of the model. Active Information allows GI to be usable with both exact and inexact models.
BIO-Complexity, 2020
In computer search optimization theory, active information is a measurement of a search algorithm... more In computer search optimization theory, active information is a measurement of a search algorithm's internal information as it relates to its problem space. While it has been previously applied to evolutionary search algorithms on computers, it has not been applied yet to biological systems. Active information can be very useful in differentiating between mutational adaptations which are based on internally-coded information and those which are the results of happenstance. However, biological systems present many practical problems regarding measuring active information which are not present in digital systems. This paper describes active information, how it can be used in biology, and how some of these problems can be overcome in specific cases.
BIO-Complexity, 2017
Many people underestimate the effect that unifying principles have on the study of biology. Unify... more Many people underestimate the effect that unifying principles have on the study of biology. Unifying principles are used to provide simplifying assumptions to complex problems, which allow them to be effectively tackled by the tools at hand. However, erroneous unifying principles will generate simplifying assumptions that lead towards mischaracterizations of problems which inevitably lead to invalid conclusions. The unifying principles of the current Modern Synthesis of evolution are presently being challenged by the Extended Evolutionary Synthesis. However, the Extended Evolutionary Synthesis has so far failed to provide unifying principles of its own, which has caused many to question whether or not the Extended Evolutionary Synthesis is indeed a unique synthesis of evolutionary biology. Here, the concept of evolutionary teleonomy (Ernst Mayr's concept of teleonomy applied to evolutionary processes themselves) is identified as a unifying principle of the Extended Evolutionary Synthesis. Additionally, specific examples are provided where modern research has been led astray by the unifying principles of the Modern Synthesis which would have been corrected by applying the Extended Evolutionary Synthesis with the unifying principle of evolutionary teleonomy.
Engineering and the Ultimate: An Interdisciplinary Investigation of Order and Design in Nature and Craft, 2014
At the core of engineering is human problem-solving. Creating a cognitive model of the task of pr... more At the core of engineering is human problem-solving. Creating a cognitive model of the task of problem-solving is helpful for planning and organizing engineering tasks. One possibility rarely considered in modeling cognitive processes is the use of Turing Oracles. Copeland (1998) put forth the possibility that the mind could be viewed as an oracle machine, but he never applied that idea practically. Oracles enable the modeling of processes in the mind which are not computationally based. Using oracles resolves many of the surprising results of computational problem-solving which arise as a result of the Tractable Cognition Thesis and similar mechanistic models of the mind. However, as research into the use of Turing Oracles in problem-solving is new, there are many methodological issues.
Communications of the Blyth Institute, 2020
Treating divergent series properly has been an ongoing issue in mathematics. However, many of the... more Treating divergent series properly has been an ongoing issue in mathematics. However, many of the problems in divergent series stem from the fact that divergent series were discovered prior to having a number system which could handle them. The infinities that resulted from divergent series led to contradictions within the real number system, but these contradictions are largely alleviated with the hyperreal number system. Hyperreal numbers provide a framework for dealing with divergent series in a more comprehensive and tractable way.
Dynamics of Continuous, Discrete and Impulsive Systems, Series A: Mathematical Analysis, 2019
Treating differentials as independent algebraic units have a long history of use and abuse. It is... more Treating differentials as independent algebraic units have a long history of use and abuse. It is generally considered problematic to treat the derivative as a fraction of differentials rather than as a holistic unit acting as a limit, though for practical reasons it is often done for the first derivative. However, using a revised notation for the second and higher derivatives will allow for the ability to treat differentials as independent units for a much larger number of cases.
Papers by Jonathan Bartlett
Behavioral and Brain Sciences, 2024
The analysis of proxy failure given by John et al. provides a good starting point for interdiscip... more The analysis of proxy failure given by John et al. provides a good starting point for interdisciplinary discussions. Here, the discussion of teleonomy is extended and updated to include more recent discourse on the topic.
Operator Theory - Recent Advances, New Perspectives and Applications, 2022
Differential operators usually result in derivatives expressed as a ratio of differentials. For a... more Differential operators usually result in derivatives expressed as a ratio of differentials. For all but the simplest derivatives, these ratios are typically not algebraically manipulable, but must be held together as a unit in order to prevent contradictions. However, this is primarily a notational and conceptual problem. The work of Abraham Robinson has shown that there is nothing contradictory about the concept of an infinitesimal differential operating in isolation. In order to make this system extend to all of calculus, however, some tweaks to standard calculus notation are required. Understanding differentials in this way actually provides a more straightforward understanding of all of calculus for students, and minimizes the number of specialized theorems students need to remember, since all terms can be freely manipulated algebraically.
Engineering and the Ultimate: An Interdisciplinary Investigation of Order and Design in Nature and Craft, 2014
At the core of engineering is human problem-solving. Creating a cognitive model of the task of pr... more At the core of engineering is human problem-solving. Creating a cognitive model of the task of problem-solving is helpful for planning and organizing engineering tasks. One possibility rarely considered in modeling cognitive processes is the use of Turing Oracles. Copeland (1998) put forth the possibility that the mind could be viewed as an oracle machine, but he never applied that idea practically. Oracles enable the modeling of processes in the mind which are not computationally based. Using oracles resolves many of the surprising results of computational problem-solving which arise as a result of the Tractable Cognition Thesis and similar mechanistic models of the mind. However, as research into the use of Turing Oracles in problem-solving is new, there are many methodological issues.
Communications of the Blyth Institute
Generalized Information (GI) is a measurement of the degree to which a program can be said to gen... more Generalized Information (GI) is a measurement of the degree to which a program can be said to generalize a dataset. It is calculated by creating a program to model the data set, measuring the Active Information in the model, and subtracting out the size of the model. Active Information allows GI to be usable with both exact and inexact models.
Communications of the Blyth Institute, 2021
Cauchy products are used to take the products of convergent series. Here, we show the limitations... more Cauchy products are used to take the products of convergent series. Here, we show the limitations of this approach in divergent series. Alternative approaches and formulas for divergent series are suggested, as well as their benefits and drawbacks.
Communications of the Blyth Institute, 2021
This is a short note about a more student-friendly proof of the derivative of sin(x). It relies ... more This is a short note about a more student-friendly proof of the derivative of sin(x). It relies more on geometric notions rather than trig identities, and does not require explicit use of the limit sin(x)/x (though that limit could be understood implicitly from the other considerations).
Communications of the Blyth Institute, 2020
Previous work suggests that there is an ordering to the dis-coverability of axioms, a "size" of s... more Previous work suggests that there is an ordering to the dis-coverability of axioms, a "size" of sorts. However, there is not presently a method of measuring the size of an axiom. This paper suggests two possible methods for measuing axiom size. The goal is not to produce a definitive measurement technique, but to begin the exploration of different possible size measurements for axioms.
Communications of the Blyth Institute, 2020
This letter is a follow up of a recently published paper by the author, responding to various fee... more This letter is a follow up of a recently published paper by the author, responding to various feedback he has received.
Communications of the Blyth Institute, 2020
This letter provides a proof that Active Information and Generalized Information are both Specifi... more This letter provides a proof that Active Information and Generalized Information are both Specified Complexity models, and therefore the mathematics of Specified Complexity can be used to analyze them both.
Communications of the Blyth Institute, 2019
Partial differentials are often thought of as non-algebraic units - that is, they cannot be indiv... more Partial differentials are often thought of as non-algebraic units - that is, they cannot be individually manipulated, cancelled, etc. Here we show that this is an artifact of notational problems. However, the optimal notation for partial differentials is actually a deep problem. Here, two potential alternative notations are discussed.
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Featured Papers by Jonathan Bartlett
Papers by Jonathan Bartlett
The book takes a unique approach, getting you immersed in each subject with tutorials, then building up your technical knowledge, and finally backing up and thinking about more big-picture issues. Part one introduces Docker, building and working with Docker images, and covering best practices for Docker Containers. Part two covers the practicalities of "cloud native” and managing a Kubernetes application, including a full working example. The last part covers the design of cloud and microservice architectures, including the use of enterprise message queues, multi-site configurations and the common values that such architectures follow.
This approach accelerates learning and keeps you moving forward without leaving you behind. The appendices also contain a wealth of worthwhile reference material for routine cloud application management.
Programming for Absolute Beginners offers practice problems, activities, and a host of resources to get new programmers started, plus a large glossary of terms introduced in the book and that a new programmer might encounter when learning on their own. No special software is required; this book will help you regardless of what your computer setup is, and source code will be freely available via GitHub.
Electronics for Beginners walks the fine line of focusing on projects-based learning, while still keeping electronics front and center. You'll learn the mathematics of circuits in an uncomplicated fashion and see how schematics map on to actual breadboards. Written for the absolute beginner, this book steers clear of being too math heavy, giving readers the key information they need to get started on their electronics journey.
Clear diagrams, step-by-step configuration information, and complete code listings tell you everything you need to get off the ground and start developing your cloud application today. This book introduces several cloud architectures and technologies that will help you accelerate your application in the cloud. Chapters cover load-balanced clusters, database replication, caching configuration, content delivery networks, infinite-scale file storage, and cloud system administration.
Cloud computing has dramatically changed the landscape of web hosting. Instead of spending weeks negotiating contracts for servers, new servers can be deployed with the push of a button, and your application can be resized almost instantly to meet today's needs. No matter what size of web application you are developing, you can benefit from modern cloud servers, and this is the guide to tell you how.
Metaprogramming is a computer programming technique where a specialized programming language is defined in which programs written in this language are translated into an already-existing language, where the specialized language only contains constructs that apply to specific sets of tasks. This allows the programmer to operate directly on specifications, while the complexities of integrating those specifications together are in the metaprogramming system. The metaprogramming system is tasked with keeping the metaprogramming rearrangements meaningful and consistent (Bartlett 2005).
Similarly, genetic codes for V(D)J segments do not have to rely on specific knowledge of the interactions, just of the basic specifications. The metaprogramming system is responsible for integrating the specifications in a way that functions properly. This allows for complex integrations using simple components. In mice, for instance, arginine is essential at the V/J intersection, but not all combinations of V/J segments would generate an arginine based on the segment sequences alone. However, the recombination mechanism can generate the needed arginine if neither the V nor J codes for it (Sanz and Capra 1987). Thus, the metaprogramming system is "smart" in that the interactions between components are taken care of by the metaprogramming system.
Recently, the addition of N and P (non-templated and palindromic) elements and nucleotide deletions at the junction of segments has been detected, and is non-random (Gauss and Lieber 1996). According to the metaprogramming model it is predicted that the constraints they follow use a similar pattern of "smart" joining, with the changes occurring for structural or other functional considerations. This allows hypermutation of segment regions without adversely affecting the final immunoglobulin's integrity.
A new type of metaprogramming, termed "enterprise metaprogramming", allows a single metaprogram to serve for multiple related metaprogramming systems. For example, a single metaprogram describing data entities may be read by separate metaprogramming systems to generate a database design, a C++ class specification, and a data-entry tool, each integrating with the other (Bartlett 2006).
This author recommends that biologists watch for such multi-system metaprograms in the genome, characterized by a DNA template sequence which would be recombined in multiple ways for multiple, interacting subsystems; such that the organism's metaprogramming system would cause a change at one locus to affect multiple systems, perhaps in different but related tissues. The metaprogram would act as a multisystem specification, and each differentiated tissue would act on that specification in unique ways, resulting in uniquely recombined DNA that worked together system-wide.
Partial Bibliography:
Bartlett, J.L. 2005. The Art of Metaprogramming, Part 1: Introduction to Metaprogramming. IBM DeveloperWorks. Available online only: http://www.ibm.com/developerworks/linux/library/l-metaprog1.html
Bartlett, J.L. 2006. The Art of Metaprogramming, Part 3: Enterprise Metaprogramming. IBM DeveloperWorks. Available online only: http://www.ibm.com/developerworks/linux/library/l-metaprog3/
Gauss, G.H. and Lieber, M.R. 1996. Mechanistic Constraints on Diversity in Human V(D)J Recombination. Molecular and Cell Biology 16(1):258-269.
Market, E. and F.N. Papvasiliou. 2003. V(D)J Recombination and the Evolution of the Adaptive Immune System. PLoS Biology 1(1):24-27.
Sanz, I. and J.D. Capra. 1987. V(k) and J(k) Gene Segment of A/J Ars-A Antibodies: Somatic Recombination Generates the Essential Arginine at the Junction of the Variable and Joining Regions. PNAS 84(4):1085-1089.
Active Information is a metric originally developed for computer search procedures which measures the amount of information that a search procedure contributes to finding an appropriate target. A random search with uniform probability has no Active Information, a search which consistently leads away from its target has negative Active Information, and a search which consistently leads towards its target has positive Active Information. Active Information is measured by comparing the probabilities of a search hitting its target with the probability of a random search hitting the same targets. The difference in probability is expressed in bits, computed by log2(1/p).
Historically, Active Information has only been applied to computer-based evolutionary algorithms. However, it can also be applied to biological systems. Applying Active Information to the Somatic Hypermutation (SMH) process for refining binding sites during an immune response makes an excellent test case for using this concept biologically. Because SMH primarily works by restricting the physical range of base pairs which it mutates, it simplifies the Active Information calculations. One can simply subtract log2(SMH mutation space) from log2(whole genome search space) and estimate that the SMH process contributes approximately 22 bits of Active Information to the search. Additional factors can complicate this estimate, such as taking into account the number of mutations required for hitting the target.
This is a surprise to some, because the SMH process uses a sort of “shotgun” approach to generating novelty. But the point of active information is that, even though it is a shotgun approach, the changes are limited only to one gene, rather than spread out across the whole genome. The active information is the amount of restriction that the process applies which contributes to the likelihood of finding a target. Searches that are more highly focused than SMH would have more active information, and those that are less focused would have less.
The same idea can be applied to other mutational processes, such as the SOS response system in bacteria. However, because in many of these systems the mutations are spaced throughout the genome, it is more difficult to calculate the Active Information involved.
Mutational processes which have zero or negative Active Information are probably not part of an organism’s design, while processes having large positive amounts of Active Information probably are. In addition, comparing the amounts of Active Information in different types of mutational processes may help lead to a general theory of functional adaptation in creation biology.
Bibliography
• Bartlett, J. L. 2009. Towards a Creationary Classification of Mutations. Answers Research Journal 2:169-174.
• Dembski, W. A. and R. J. Marks. 2009. Conservation of Information in Search: Measuring the Cost of Success. IEEE Transactions on Systems, Man and Cybernetics A, Systems & Humans 5(5):1051-1061.
• Papavasiliou, F. N. and D. G. Schatz. 2002. Somatic Hypermutation of Immunoglobulin Genes: Merging Mechanisms for Genetic Diversity. Cell 109(2, Supplement 1) 1:S35-S44.
• Wood, T. C. and M. J. Murray. 2003. Understanding the Pattern of Life: Origins and Organization of the Species. Broadman and Holman, Nashville.