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Jonathan Bartlett

Jonathan Bartlett
The Blyth Institute · Theoretical Biology

M.T.S.

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37
Publications
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31
Citations

Publications

Publications (37)
Chapter
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
The concept of irreducible complexity is a great intuitive concept which has historically lacked a well-defined theoretical basis. This paper will show how computational theory gives an adequate account for what irreducible complexity is, what irreducible complexity’s possible biological implications are, and how irreducible complexity can be usefu...
Article
Full-text available
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 mischaracteri...
Preprint
Full-text available
First year calculus is often taught in a way that is very burdensome to the student. Students have to memorize a diversity of processes for essentially performing the same task. However, many calculus processes can be simplified and streamlined so that fewer concepts can provide more flexibility and capability for first-year students.
Chapter
Full-text available
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 Abra-ham Robin...
Chapter
Nearly every programming language has some features to track memory allocations. Some, like the C programming language, are primitive. In Chapter 14, we learned how to implement basic procedures for allocating and deallocating memory for a program and managing the amount of memory we requested from the kernel.
Chapter
I’m going to now share with you the shocking truth about computers—computers are really, really stupid. Many people get enamored with these devices and start to believe things about computers that just aren’t true. They may see some amazing graphics, some fantastic data manipulation, and some outstanding artificial intelligence and assume that ther...
Chapter
Now that we know some data access techniques, we can now learn about how to store records (also known as structs or structures). A record is just a well-defined segment of data. Remember, everything in the computer is just numbers. Therefore, if we want to store multiple things about an entity, we need to know where these bits of data are. Because...
Chapter
So far, we have not gone into detail about what the memory layout of a Linux process looks like, primarily because we hadn’t covered enough material to make sense of it. In this chapter, we will look at how Linux processes work with memory and how to make your process request more memory from the operating system.
Chapter
The command line is one of the most useful tools for a programmer in the long run, but it is one that is tucked and hidden away from ordinary users. With the command line, instead of pointing and clicking to tell the computer what to do, you type commands that the computer reads and then runs. For the most part, each command is actually its own tin...
Chapter
While this isn’t a book on optimizing assembly language, I did feel I should include a few basic optimization ideas, if only so that you will understand what other people are talking about when they talk about optimization. The code in this book is not intended to be optimal; it is intended to be explanatory. Therefore, in most cases, I opted to us...
Chapter
So far, we have been learning the basics of assembly language itself—how to move, store, add, subtract, compare, branch, etc. Now that we have the basics under our belt, it is time to learn how to interface with the rest of the computer through your operating system.
Article
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Cauchy products are used to take the products of convergent series. Here, we show the limits of this approach in divergent series. Alternative approaches and formulas for divergent series are suggested, as well as their benefits and drawbacks.
Article
Wielu ludzi nie docenia wpływu wywieranego przez zasady unifikujące na badania biologiczne. Zasady te mają dostarczać upraszczających założeń w przypadku złożonych problemów, dzięki czemu można te problemy skutecznie rozwiązywać przy użyciu dostępnych narzędzi. Błędne założenia upraszczające mogą jednak prowadzić do nieprawidłowego opisu problemów,...
Article
W niektórych dziedzinach istnieją już alternatywy dla naturalizmu metodologicznego. Jednakże niewiele osób spoza danej dziedziny zna te alternatywy lub wie, jak są wykorzystywane. Niekiedy nawet sami przedstawiciele tych dziedzin stosują te nienaturalistyczne metodologie, nie wiedząc, że nie są one spójne z naturalizmem metodologicznym. W artykule...
Article
Podstawą naturalizmu metodologicznego, służącego wzmocnieniu ekskluzjonistycznego poglądu na badania naukowe, są trzy problematyczne nurty filozofii: filozofia mechanistyczna, pozytywistyczna epistemologia i doktryna niepojmowalności Boga. Każda z tych filozofii posiada wewnętrzne wady, przez które stanowiska te nie są w stanie objąć pełnego zakres...
Chapter
In Chapter 17, we learned how to use RC (resistor-capacitor) circuits to create timers. In this chapter, we are going to use our concept of timing circuits to move from one-time timer circuits to oscillating circuits.
Chapter
In Chapter 14, we learned how to do basic digital input and output with an Arduino using its I/O pins. In this chapter, we will cover how to do analog input and output as well.
Chapter
A DC motor is a device that converts DC electrical power into mechanical power. It operates by rotating a shaft using electromagnetism. DC motors are fairly simple to use, though they require slightly different reasoning from the way we have been examining circuits so far.
Article
Full-text available
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 di erentiating b...
Article
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 t...
Chapter
While most of this book has focused on hosting your application on Linode, since so much of the cloud hosting is based on AWS, I think it is worthwhile to look at some of the hosting options on AWS.
Chapter
Some things simply cannot be cached. Ad hoc reports, up-to-the-second changes, and sites where access patterns are spread across a large number of unrelated pages are all difficult to optimize using caching. For workloads like this, you can deploy a bigger database server, but eventually even those run into limits.
Article
Full-text available
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.
Article
Full-text available
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.
Article
Full-text available
This letter discusses the claim suggested by mathematical vlogger Numberphile as to whether the sequence 1 + 2 + 3 + ... is equal to -1/12.
Preprint
Full-text available
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 t...
Chapter
Full-text available
Some fields already incorporate alternatives to methodological naturalism. However, few people outside the field are familiar with these alternatives or how they are used. Sometimes these non-naturalistic methodologies are being used without the participants' cognizance that the methodology is not methodologically naturalistic. Here, we show a smat...
Chapter
Full-text available
Methodological naturalism, when used to enforce an exclusive view of scientific investigation, is based on three problematic streams of philosophy: mechanical philosophy, positivistic epistemology, and divine incomprehensibility. Each of these philosophies has inherent flaws that prevent them from being usable across the entirety of causal relation...
Chapter
Full-text available
Our notions of causation in science are often unintentionally constrained by the mathematics we use. Typically, scientific investigations use algebraic or calculus-based mathematics to model causes and effects. This predictive pattern is what most people use to classify events as materialistic, leaving events that are not so classified as non-mater...
Article
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This review presents an overview and critique of the epistemology put forth by Alvin Plantinga in defense of the warrant for Christian belief.
Book
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Programming from the Ground Up uses Linux assembly language to teach new programmers the most important concepts in programming. It takes you a step at a time through these concepts: * How the processor views memory * How the processor operates * How programs interact with the operating system * How computers represent data internally * How to do l...
Article
Full-text available
V(D)J (Variable, Diversity, and Joining segments) recombination allows the genome to encode millions of immunoglobulin proteins using a small number of germ-line DNA segments. Immune cells can rearrange these segments into millions of sequences, which are then used as templates for proteins. As opposed to alternative splicing, the DNA physically re...

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