Monday, January 7, 2019

Jaw to Ear Magic


Evolutionists claim the mammilian ear bones (ossicles) derived from the jaw bones of non-mammilian ancestors. This claim is demonstrably false by science because evolutionism is based upon a paradigm which is formed into an endless number of assumptions for which there either is no supporting evidence or which contradicts the physical evidence.


Three of the most serious problems for this idea that evolutionists simply ignore because they value their assumptions and philosophy of evolutionism more than they respect science.

1. Liaoconodon hui is dated to the Early Cretaceous at 120 which is 40–75 Ma (million years after) after the appearance of the first fully formed mammalian middle ear.1 This is 75 Ma younger than the first “definitive mammalian middle ear” (DMME), Hadrocodium.2

2. The 75 MY that Liaoconodon hui precedes Hadrocodium is nearly equal to an entire geologic period - the Cretaceous, which lasted supposedly 79.5 MY. It should not take 75 MY for the middle ear to evolve if a precursor middle ear and "difinitive middle ear" required vastly less time to evolve. Why an entire geologic period of time for this transition? Is it logical that any anatomical feature could take so long to evolve considering the evolutionist's timescale for the evolution of fish into land-dwelling amphibian tetrapods or other such complete transitions in anatomy?

       1. Meng, J., Wang, Y. and Li, C., Transitional mammalian middle ear from
           a new Cretaceous Jehol eutriconodont, Nature 472:181–185, 2011.
       2. Luo, Z.-X., Crompton, A.W. and Sun, A.-L., A new mammaliaform from
           the Early Jurassic and evolution of mammalian characteristics, Science
           292(5521):1535–1540, 2001.

3. The genetic pathway for the ear bones and jaw bones of the creatures involved are not the same!

The evolutionists use an opossum skull in their images trying to show the evolution of the jaws of mammals because it is believed that their bones follow the same developmental pathway as their assumed evolutionary transitional forms of the animal groups Thrinaxodon, Probainognathus, and Morganucodon. This is highly selective and unscientific, since other mammals have a different developmental pathway for the same bones!

There have been two competing theories of the development of the middle ear bones (ossicles). The oldest theory stated that all of the middle ear components developed from the first pharyngeal arch. More recent studies have concluded that the components of the middle ear, including the ossicles, develop from both the first and second pharyngeal arches! In humans, the mandible (lower jaw bone) develops from the first pharyngeal arch only. Yet the tympanic bones (ossicles) of the middle ear are developed by both the first and second pharyngeal arches. Thus, two genetic development pathways through both the first and second pharyngeal arches work together to form the ossicles, as well as other structures of the middle ear. It cannot be said therefore that the claim of the evolution theory that the middle ear bones (ossiles) evolved from the first pharyngeal arch which develops the mandible in mammals is responsible for the evolution of the human or other mammilian ossicles. If the theory were correct, since the mandible of mammals develops from the first pharyngeal arch only and has no genetic development pathway from the second pharyngeal arch, then the ossicles of the human middle ear would likewise develop from the first pharyngeal arch only, and would have no contributing development pathway from the second pharyngeal arch. But this is not the case with humans. Therefore, since both the first and second pharyngeal arches represent separate genetic development pathways which are involved in the development of the middle ear bones, we must conclude:

1. the genetic information for the development of the ossicles is located in separate gene sets in different loci of the DNA resulting in separate genetic developmental pathways, which indicates a designed information process.

2. the theory that the human middle ear developed from the mandible of an imagined ancestor is untenable, since human ossicle development is conducted from not just the first pharyngeal arch, but the second arch also. If the theory of mammilian ossicle development were true, this should not be the case.

3. modern scientific discovery has yet again discredited an evolutionary story because it has revealed that the evolutionist's assumptions are not supported by the scientific facts.

These facts present unanswerable questions for the evolutionist, which reveal the unscientific, faith-based, outrageously illogical beliefs of evolutionism:

1. How can undirected, unintelligent molecular interactions (random mutation) create complex gene sets (or any gene at all) and their co-expression to develop any structure of an organism? The process of fetal development is the most complex process that exists in the world. How can something orders of magnitude more complex than anything man (an intelligent agent) is capable of designing be produced by random, unintelligent molecular interactions which contradict the 2nd law of Thermodynamics?

2. How is it logical that undirected, unintelligent molecular interactions can result in anything which is unfathomably complex and intricate? The concept contradicts the laws of nature - 2nd Law of Thermodynamics, which verifies that matter moves towards disorder, not towards complexity - the opposite of what evolution claims has happened (and must still be happening) trillions of times?
3. How could evolution (an outrageous number of unintelligent, undirected molecular interactions) cause a second genetic developmental pathway (2nd pharyngeal arch) to become integrated with the developmental pathway of the mandible so as to produce the middle ear?

4.  What environmental pressures could possibly exist to cause jaw bones to evolve into ear bones?

5. What possible environmental pressure could cause new developmental pathways to evolve that result in a more complex hearing mechanism than already existed, and then integrate them into an ear that already exists?

6. How could Natural Selection cause bones to detach from the jaw and remain in the anatomy without removing them because they are uselessly floating in soft tissue? Natural Selection should remove useless and functionless features!

7. How could natural Selection cuase migrating and functionless bones to slowly integrate, in numerous successive steps, into the hearing system of an animal that already has functional hearing, since introducing a completely new structural design and merging it with an already functioning one should disrupt hearing until the process were complete?

How could the genetic information that determines the developmental parthway of jaw bones become swapped with the genetic information that determines the develpomental pathway for the incus and malleus of the middle ear? How could the influence of the environment cause this change in genetic development pathway by numerous successive genetic mutations? For evolution to accomplish this, each mutation would have to be selected because it caused a beneficial change to the morphology of the articular bones of the jaw through the process of evolving into the bones of the inner ear.

Amphibians and reptiles (including birds) use the quadrate and articular bones as part of the hinge joint of the jaw. In mammals, these bones are not part of the jaw hinge.

In mammals, the hinge joint of the jaw is the temporomandibular joint, where the mandibular condyle fits into the mandibular fossa (which is part of the temporal bone). See the skulls page for more detail. The quadrate and articular bones are not part of the jaw hinge.

The difference between the inner ear bones and their imagined jab bone precursors is stark, without transitional form, and of unknown mechanism. It is therefore a sheer assumption not based upon physical evidence, as admitted in the fosllowing statement:

"The sharp contrast between the precise structure of these tiny mammalian bones and their non-auditory reptilian counterparts drew the attention of Associate Professor of Animal Biology Karen Sears and postdoctoral researcher Daniel Urban, who led the study." In the developing ears of opossums, echoes of evolutionary history https://www.sciencedaily.com/releases/2017/02/170216104002.htm

University of California Berkley states they know of no mechanism for the imagned transition of jaws:

"For reasons we don't fully understand, several lineages of synapsids — including the one that would eventually give rise to the mammals — began to evolve changes in the jaw joint." - https://evolution.berkeley.edu/evolibrary/article/evograms_05

They then state,

"Originally the quadrate and articular bones formed the jaw joint, but these synapsids (e.g., Probainognathus) evolved a second pair of bones involved in the jaw articulation."

So - they are claiming these evolutionary changes to jaw bone numbers and locations has in fact taken place, but acknowledge they do not know of a mechanism for such evolution - the development of new, integrated bones in jaws and their changing integration and form over time. How is that scientific?

They then state,

"This unusual paired condition did not last long, though. Soon, the quadrate and articular lost their function in jaw articulation and even their position in the jaw as they evolved."

Their assumption is presumed because of their belief that one kind of organism existed prior to another. Sedimentology demonstrates that the difference in time between these organisms becoming buried in sediments is months at most because strata form horizontally and in numbers, not one at a time over vast ages of time.

They then state,

"So, over time, the synapsids' quadrate-articular jaw joint (which the rest of the tetrapods possess) was replaced by a dentary-squamosal joint (which all living mammals possess), while the quadrate and articular migrated, shrank, and became part of the complex of middle ear bones."

The bones which comprize the jaw or animals is determined by seperate pathways by cell specialization. The bones claimed to migrate and change in morphology are developed by the different physical arrangement of specialized cells early in the development of the animal. The process which determines how cells are organized to become physically arranged and fused together is not understood:

"The cranial sutures form as the margins of the developing bones approximate, and the mesenchymal tissue separating the bone fronts is recruited into the osteogenic fronts (Opperman, 2000). It remains unknown whether the formation and spatial arrangement of the sutures occurs as a response to the approximation of the bone fronts, if they are prepatterned in a manner similar to the joints in the developing limb, or if signals from the surrounding epithelia determine the position of the sutures." Cranial Suture Biology

Kelly A Lenton, ... Michael T. Longaker, in Current Topics in Developmental Biology, 2005  https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/squamosal-bone

The cranial sutures form as the margins of the developing bones approximate, and the mesenchymal tissue separating the bone fronts is recruited into the osteogenic fronts (Opperman, 2000). It remains unknown whether the formation and spatial arrangement of the sutures occurs as a response to the approximation of the bone fronts, if they are prepatterned in a manner similar to the joints in the developing limb, or if signals from the surrounding epithelia determine the position of the sutures.

In humans, the middle ear bones (ossicles) are derived from separate origins in the first and second arch mesenchyme. (Mesenchyme, in vertebrate embryology, is a type of connective tissue found mostly during the development of the embryo.)

The evolutionists use an opposum skull in their images trying to show the evolution of the jaws of mammals because it is believed that their bones follow the same developmental pathway as their assumed evolutionary transitional forms of the animal groups Thrinaxodon, Probainognathus, and Morganucodon. This is highly selective and unscientific, since other mammals have a differrent developmental pathway for the same bones!

Scientists admit they do not know the mechanism for these independant developmental pathways becoming changed by evolution:

"A new developmental mechanism for the separation of the mammalian middle ear ossicles from the jaw[2]"Multiple mammalian lineages independently evolved a definitive mammalian middle ear (DMME) through breakdown of Meckel's cartilage (MC). However, the cellular and molecular drivers of this evolutionary transition remain unknown for most mammal groups. Here, we identify such drivers in the living marsupial opossum Monodelphis domestica, whose MC transformation during development anatomically mirrors the evolutionary transformation observed in fossils. Specifically, we link increases in cellular apoptosis and TGF-BR2 signalling to MC breakdown in opossums. We demonstrate that a simple change in TGF-ß signalling is sufficient to inhibit MC breakdown during opossum development, indicating that changes in TGF-ß signalling might be key during mammalian evolution." - Hearing - Middle Ear Development  https://embryology.med.unsw.edu.au/embryology/index.php/Hearing_-_Middle_Ear_Development

I could ask a hundred more question no evolutionist is capable of answering, all of which reveal the unscientific, illogical, faith-based, miraculous nature of the evolution belief system.

Sorry Charlie. Go fish.

Tuesday, November 6, 2018

Atheism is Disproved by Logic


There are no questions for which either an answer does not exist in theism, or for for which an answer, if found, would not comport with theism. However, there are questions for which atheists can provide no answer because the existence of the premise cannot exist if atheism were true. The fact that such questions can be asked verifies atheism is not true. Here are a few examples.

Because atheists claim (and supposedly believe) that a human is a soulless bag of matter, none of the following questions comport to atheism, and no answer can be provided for them by any atheist.

 

Premise 1: Chemical reactions happen do not happen in the past or future. There have been chemical reactions that have occurred in the past, and others will happen in the future. However, all chemical reactions happen in the present.

Question: 1. If our thoughts are merely chemical reactions in a physical brain, how can prediction or anticipation exist?

Premise 2: Humans produce non-physical entities which have no basis in matter nor are they comprised of it. Here is a short list:

1. information
2. algorithms
3. linguistics
4. persistence of Self-Identity, personal intentions
5. philosophical reflection
6. consideration that results in a change of mind
7. un-confessed lies
8. the comprehension of the process of time
9. the recollection of past events
10. the existence of qualia (private experiences)
11. the truth that people are genuinely moral agents
12. the ability to understand and appreciate a state of affairs
13. the aptitude to evaluate and plan for future activities with inbuilt contingencies
14. the perception and appreciation of beauty
15. the aim of improving an activity one performs by concentrating
16. the continuous volition of intending and attending
17. restricted access
18. incorrigibility
19. accountability
20. admonition
21. ethical thought
22. moral thought
23. creativity
24. hatred
25. love
26. jealousy
27. determination of will
28. belief
29. disbelief
30. pretending
31. sophistry
32. apostasy
33. honor
34. inhibition
35. embarrassment
36. superstition
37. suspense
38. fear
39. anticipation
40. opinion
41. curiosity
42. inquiry
43. investigation
44. shame
45. surprise
46. prediction
47. premises


Question 2: If our thoughts are merely chemical reactions, how could they produce things which have no mass and cannot be measured, which is true of all non-physical entities?

Premise 3: Humans express free will in a number of ways. If atheism were true, then out thoughts are merely chemical reactions, including our assertions and opinions, and out thoughts would simply be chemical reactions determined by the proximity of matter to matter which has taken place because prior reactions have produced the conditions which causes other reactions to take place. Therefore, whenever an atheist states, "There is insufficient evidence for the existence of God." it is merely chemical reactions that have produced the sound waves that form the words.

If our thoughts are merely chemical reactions, how could those reactions allow for opinions, truth, facts, beliefs, reasoning, faith, hope, value, desire, trust, etc.? Is it rational to say these things arise from the interactions of mater? Can chemistry give an opinion?

Premise 4: Computers remember nothing. They store data or instructions in the form of switch positions which relate to on or off states. A computer has no memory of anything in the past. Atheists claim human brains are the computers which produce and store all human memories.

Question 4: How is it logical to say a human can have memories if our brains are merely chemical computers?

Premise 5: Atheists say our thoughts are merely physical, material chemical reactions and that physical causation explains all phenomenon.

Question 5: If physical causation explains all phenomenon, why do humans understand and continuously produce and engage with the concept of the non-physical?

Premise 6: Atheists say physical causation explains all phenomenon. However, language is dependent upon symbolism, and symbolism does not exist in material processes of chemistry and physics. For example, the letter "D" is not a sound. It represents a sound. The letters which comprise the word "dog" are not an animal. They symbolically represent an animal. The words, "The dog is very quick." is not a dog moving quickly. The words represent a dog moving quickly.

Question 6: Since language depends upon symbolism, why are humans able to use speech?

These and countless other questions one can imagine demonstrate that atheism does not comport to our reality and has no explanatory power. Because such questions demonstrate that the philosophical materialism of atheism is logically false, and therefore an atheist cannot provide logical answers to them, we know that atheism is a false belief. By the way, if atheism were true, an atheist could not believe anything.

 



Tuesday, August 21, 2018

Evolutionism and the Damage Done


Another failure of evolutionism is the scientifically invalid belief that mutation is a grand designer. 90 years of mutation experimentation has demonstrated with 100% consistent results in over 1 million studies that mutations design nothing and cannot therefore be the base mechanism for the design of anatomical features or biological function. Mutation is a destroyer of genetic information and causes biological weakness, stillbirth, death after birth, disease, and deformity, none of which support evolution but instead contradict it. Evolutionists go so far as believing that mutation generates information, linguistics, and algorithms of DNA! This of course is impossible, since these are non-physical fundamental entities (not a property of or comprised of matter) and cannot be produced by material cause, but are in fact demonstrated to arise only from intelligence, which verifies empirically that all life is a a product of intelligence. Evolutionists refuse to accept this 90 yrs of consistent experimental data because they are stuck with holding fanatically to the false belief that mutation is our designer. But that view is anti-scientific since it denies 90 yrs and a million studies which show that mutation is a destroyer, not a designer. Natural Selection does not help the matter, since it cannot see individual mutations with consistency. Entire mutants are selected by NS, not individual mutations unless they cause gross harm. The accumulation of genetic damage is compound in fact, since we know know that genetic information is overlapping and nested - highly compressed - and any given mutation likely causes damage to more than one gene at the same time, in fact, possible several!

Evolutionists hold religiously to their pseudo-scientific idea that mutation is a grand designer and pretend the consistent result of 90 yrs of study have not proven otherwise because once they accept real science, their false worldview falls like a fake house of cards. Atheists should be kept away from science like a small child should be kept away from a box of matches. They have done more damage to scientific knowledge than should be allowed. For example, their false claim about most of the human genome being garble left over by evolution was disproved and the creationist prediction that the entire genome would be discovered to be critical information for the development and regulation of a human body was proven correct. But the harmful false assumption of the evolutionist held back genetic science for 40 years, causing geneticists to study only the protein coding genes - about 1-2% of the genome. Had evolutionists not enforced their pseudo-scientific paradigm upon genetics, we would know far more about DNA today and would likely have cured some diseases or found good treatment for them. It's too bad that you cannot tell the children who died because of it that you are sorry that your discredited worldview stood in the way of them having a happy life.

The highly compressed nature of genetic information:

 "For more than 30 years, we have understood that genes may be organized within genomic DNA in complex spatial arrangements. In particular, gene-coding sequences can overlap: a given segment of genomic DNA can encode more than one gene product, with the overlapping genes often oriented on opposite strands. In some cases, the overlapping genes are organized such that one gene is entirely contained within the chromosomal region occupied by another gene. In such instances, the internal gene is referred to as a “nested” gene." - An Overerview of Nested Genes in Eukaryotic Genomes by Anuj Kumar. Eukaryotic Cell September 2009 vol. 8 no. 9 1321-1329.

"According to a painstaking new analysis of 1% of the human genome, genes can be sprawling, with far-flung protein-coding and regulatory regions that overlap with other genes." - DNA Study Forces Rethink of What It Means to Be a Gene by Elizabeth Pennisi. Science 15 June 2007, Vol. 316 no. 5831 pp. 1556-1557

"Alternative pre-mRNA splicing is a central mechanism of gene regulation in eukaryotic cells. Genetic regulation at this level is especially common in the vertebrate nervous system, where many proteins important for neural development or function are made in multiple iso-fomrs through alternate partterns of splicing. Proteins that contribute to the excitability of neural tissue often show plicing regulation that is quite complex in both the number of different mRNAs produced and their region-specific Expression." - John Stamatoyannopoulos, Scientists discover double meaning in genetic code, Science Daily December 12, 2013

The cSlo sequence in the chicken genome codes for 576 variants which have function in helping to detect numerous sound frequencies. - Splicing in the Inner Ear: a Familiar Tune, but What Are the Instruments? Douglas L Black

"UW scientists were stunned to discover that genomes use the genetic code to write two separate languages. One describes how proteins are made, and the other instructs the cell on how genes are controlled. One language is written on top of the other, which is why the second language remained hidden for so long." - Scientists discover double meaning in genetic code, Stephanie Seiler, UW Health Sciences & UW Medicine

"Reduce the Probability of Beneficial Mutation There is growing evidence that much of the DNA in higher genomes is poly-functional, with the same nucleotide contributing to more than one type of code. Such poly-functional DNA should logically be multiply-constrained in terms of the probability of sequence improvement via random mutation. We describe a model of this relationship, which relates the degree of poly-functionality and the degree of constraint on mutational improvement. We show that: a) the probability of beneficial mutation is inversely related to the degree that a sequence is already optimized for a given code; b) the probability of beneficial mutation drastically diminishes as the number of overlapping codes increases. The growing evidence for a high degree of optimization in biological systems, and the growing evidence for multiple levels of poly-functionality within DNA, both suggest that mutations that are unambiguously beneficial must be especially rare." - Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation, George Montañez, Robert J. Marks, Jorge Fernandez, and John C. Sanford, Baylor University, Cornell University

Regarding the compound damage some mutations cause, Dr. John Stamatoyannopoulos, University of Washington associate professor of genome sciences and of medicine has said,

“The fact that the genetic code can simultaneously write two kinds of information means that many DNA changes that appear to alter protein sequences may actually cause disease by disrupting gene control programs or even both mechanisms simultaneously,” said Stamatoyannopoulos." - Scientists discover double meaning in genetic code, Stephanie Seiler, UW Health Sciences & UW

Tuesday, July 24, 2018

Genetic Algorithms


Claim: DNA is a product of nature and not designed.

Response: Genetic information posesses algorithmic operations which verify the Intelligent Design of DNA.


Websters Dictionary, Definition of algorithm: a procedure for solving a mathematical problem (as of finding the greatest common divisor) in a finite number of steps that frequently involves repetition of an operation; broadly : a step-by-step procedure for solving a problem or accomplishing some end especially by a computer

Algorithms verify empirically that DNA is a product of Intelligent Design because,
1.  Procedures are actions which are specified and ordered to accomplish a goal, such as solving a problem.
a.  Specifying and ordering actions to accomplish a goal requires forward-thinking. 1 
b.  Forward-thinking is a mental activity. 1 
c.  Problem-solving involves consideration and decision making.
d.  Consideration and decision making are mental activities. 2 
2.  Therefore, it is empirical that mental activity is the cause of algorithms. 1 
3.  The molecular machinery of the cell performs algorithmic procedures prescribed by genetic information. 2  3 
4.  Therefore, mental activity has designed the algorithms in genetic information. 4  5  6 
5.  Since genetic information and algorithms are supremely complex, the mind which designed genetic information is supremely intelligent.

Example: When transcribing information from DNA into RNA, the machinery of the cell uses an algorithmic process to replace the codes for base pairs:

"One strand of the DNA double helix is used as template (the lower strand from 3' to 5' in our example above) to synthesize RNA. RNA is complementary to the template strand. So, given a template strand, the algorithm consists in changing every occurrence of: A - U, T - A, C - G, and G - C." - Transcription and Translation Algorithms, American University of Armenia June 2016, Introduction to Bioinformatics


Scientists design algorithms to represent the activity of celular machinery.

In order to better understand the procedures by which some of the molecular machines of the cell retrieve and store the information in DNA, scientists design algorithms which represent their operation. This verifies that the machinery of the cell is performing algorithmic procedures. Secular scientists are very careful not to state that the algorithms they design for this purpose are replicas of actual algorithms which are programmed into the DNA because this would be an admission that life is designed by intelligence. Though they may acknowledge that what the cell's machinery is doing is algorithmic or can be described with algorithms, they will say that the algorithms they write are mere representations of chemical activity designed by evolution. This behavior could be likened to someone saying that the automobile which is parked in front of them is not actually an automobile, but rather it is simply a collection of parts which operate like an automobile. Treating what is obvious in this manner constitutes a tautologyforced upon them by their denial of Intelligent Design and their dogmatic adherence to the evolution paradigm. Evolutionists employ this kind of tautology in other ways as well, such as saying the information encoded in DNA is not actually information in a technical sence, but that they simply use the word "information" to describe it because it is convenient to do so.


The following is a algorithm designed by a computer programmer to mimick the transcription of DNA into RNA performed by celular machinery:

// Define our inputs and output variables.
dna_strand = "ACATAGGCCTAC";
rna_strand = "";

// Define a transcribe function thats takes a dna strand as its parameter.
transcribe = function(input_dna_strand) {
    // Setup a variable to store the result of our function's algorithm
  result = "";   // Map each character(nucleotide) of our DNA strand to the corresponding
  // RNA equivalent and append it to our growing RNA strand
  input_dna_strand.map(function(nucleotide) {
     if(nucleotide == 'A') {
     result = result + 'U';
    } else if(nucleotide == 'C') {
     result = result + 'G';
    } else if(nucleotide == 'T') {
     result = result + 'A';
    } else if(nucleotide == 'G') {
      result = result + 'C';
    }
  });

  // Return the result of our function's algorithm completing.
  return result;
};

// Store the result of calling our transcribe function
rna_strand = transcribe(dna_strand);

// Print our result. 3' - "UGUAUCCGGAUG" - 5'
console.log(rna_strand)


1.  "As Berlinski (2000) has argued, genetic algorithms need something akin to a "forward looking memory" in order to succeed. Yet such foresighted selection has no analogue in nature. In biology, where differential survival depends upon maintaining function, selection cannot occur before new functional sequences arise. Natural selection lacks foresight." - Stephen C. Meyer, Intelligent Design: The Origin of Biological Information and the Higher Taxonomic Categories, Proceedings of the Biological Society of Washington, August 4, 2004m

2.  "No known hypothetical mechanism has even been suggested for the generation of nucleic acid algorithms." - Chance and necessity do not explain the origin of life, Cell Biology International, Volume 28, Issue 11, November 2004, p. 730, Jack T. Trevors and David L. Abel,

3.  "All known metabolism is cybernetic - that is, it is programmatically and algorithmically organized and controlled." - Chance and necessity do not explain the origin of life, Cell Biology International, Volume 28, Issue 11, November 2004, Pages 729-739, J.T. Trevorsa, D.L. Abel,

In fact, the algorithmic processes discovered in living systems are so excellent, that they are improving the algorithms written by computer programmers to be applied in modern technology, as stated in this paper:

4.  "Computer science and biology have enjoyed a long and fruitful relationship for decades. Biologists rely on computational methods to analyze and integrate large data sets, while several computational methods were inspired by the high-level design principles of biological systems. Recently, these two directions have been converging. In this review, we argue that thinking computationally about biological processes may lead to more accurate models, which in turn can be used to improve the design of algorithms. We discuss the similar mechanisms and requirements shared by computational and biological processes and then present several recent studies that apply this joint analysis strategy to problems related to coordination, network analysis, and tracking and vision." - Algorithms in nature: the convergence of systems biology and computational thinking, Saket Navlakha, Ziv Bar-Joseph, Molecular Systems Biology (2011)

5.  "We present evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range-indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene; we utilize this fact to build a Coding Sequence Finder algorithm, which uses statistical ideas to locate the coding regions of an unknown DNA sequence. We resolve the problem of the non-stationarity feature of the sequence of base pairs (that the relative concentration of purines and pyrimidines changes in different regions of the mosaic-like chain) by describing a new algorithm called Detrended Fluctuation Analysis (DFA)." - Statistical and linguistic features of noncoding DNA: A heterogeneous Complex system

6.  "We are applying the principles and methods of information theory and coding theory to incorporate phenomena observed on different levels of abstraction of the genomic error correction system. This method for rigorous treatment of DNA-repair enables describing its functionality quantitatively and algorithmically." - Error correction algorithms for DNA repair

Tuesday, July 10, 2018

Linguistics Properties of Genetic Information


Claim: DNA is a product of natural chemistry.

Response: DNA posesses language properties, including symbolism, which do not exist in physics or chemistry. A mind is necessary to create language and symbolism.


Premises:

Genetic information posesses the following linguistics characteristics:
1.  DNA is a "book" of encoded/written information organized into chapters (chromosomes), phrases (sequences), words (codons) and letters (nucleotides) governed by punctuation.
2.  Written language is a code system comprised of arranged symbols which represent an entity seperate from themselves. 1 
3.  The symbolism of encoded/written language is an immaterial abstract construct of mind, and is not comprised of or a property of matter.
4.  Genetic information posesses the language properties of phonetics, punctuation, syntax, grammar, and semantics. 2 

Conclusions:

Because DNA is a system of encoded/written languge,
     1. physics and chemistry cannot have created the immaterial, abstract properties of linguistics in DNA, which require an intelligence. 3 
     2. an intelligence is necessarily the cause of the genetic information which defines living systems
     3. living systems have been designed by intelligence, and the concept of the evolution of living systems is falsified by the linguistics of DNA


1.  Websters Dictionary, Definition of Language:
1       a : the words, their pronunciation, and the methods of combining them used and understood by a community  .  studied the French language
         b (1) : audible, articulate, meaningful sound as produced by the action of the vocal organs
            (2) : a systematic means of communicating ideas or feelings by the use of conventionalized signs, sounds, gestures, or marks having understood meanings   .  the language of mathematics
            (3) : the suggestion by objects, actions, or conditions of associated ideas or feelings
                        .  language in their very gesture —William Shakespeare
            (4) : the means by which animals communicate  .  the language of birds
            (5) : a formal system of signs and symbols (such as FORTRAN or a calculus in logic) including rules for the formation and transformation of admissible expressions
            (6) : MACHINE LANGUAGE 1
2       a : form or manner of verbal expression; specifically : style  .  the beauty of Shakespeare's language
          b : the vocabulary and phraseology belonging to an art or a department of knowledge  .  the language of diplomacy  .  medical language
          c : profanity
                        .  shouldn't of blamed the fellers if they'd cut loose with some language —Ring Lardner
            3 : the study of language especially as a school subject  .  earned a grade of B in language
            4 : specific words especially in a law or regulation  .  The police were diligent in enforcing the language of the law.


2.  "The genetic language is a collection of rules and regularities of genetic information coding for genetic texts. It is defined by alphabet, grammar, collection of punctuation marks and regulatory sites, semantics. There is a review of these general attributes of genetic language, including also the problems of synonymy and evolution. The main directions of theoretical investigations of genetic language and neighbouring questions are formulated: (1) cryptographic problems, (2) analysis of genetic texts, (3) theoretical-linguistic problems, (4) evolutionary linguistic questions. The problem of genetic language becomes one of the key ones of molecular genetics, molecular biology and gene engineering." - The genetic language: grammar, semantics link (1K)

3.  "Biologic systems and processes cannot be fully accounted for in terms of the principles and laws of physics and chemistry alone, but they require in addition the principles of semiotics— the science of symbols and signs, including linguistics." - Sungchul Ji’s, professor of Rutgers University, The Linguistics of DNA: Words, Sentences, Grammar, Phonetics, and Semantics link (1K)

4.  Linguistics Features of Noncoding DNA Sequences link (1K)

Wednesday, June 27, 2018

The Genetic Code



Claim: The Genetic Code is not anactual code because it is not designed.
It's simply an association of molecules preserved by Natural Selection during Abiogenesis.

Response: Codes 8  require a coder. The genetic code demonstrates Intelligent Design.
Undirected chemistry does not produce codes.


Design properties of the genetic code:
1.  it specifies. Specification 9  is not a product of happenstance associations in the environment, such as natural chemistry.
     Specification is directed by minds.
2.  it is language which instructs as to which, what, when, where, if, then, start, stop, pause, more, less. 1 , 2 
     These describe mental processes.
3.  it specifies instructions 10 , which require consideration, forward-thinking, and decision making, which are mental processes.
     Mental processes are immaterial and take place in minds, not in physical chemistry. 7 
4.  it specifies complex physical arrangements which have mechanical function - machiney  1   3   5   6 
    a.  complexity is not produced by natural chemistry. Nature experiences chemical entropy instead.
    b.  machinery is designed because it is intentional and purposed.
        Intention and purpose are products of minds. Physical materials, such as natural chemistry, neither intend or purpose 7 .
5.  it specifies the design of organisms at both the micro and macro levels:
    a.  the machines of the cell and their intended function
    b.  the anatomical features of the organism and their intended function
6.  it specifies the unfathomably complex regulation of genes, like instruments in an orchaestra, duiring fetal development to produce the anatomy of an organism. This constitutes a level of complexity and design that is truly mind-bending, and is the highest complexity that exists. It is vastly superior to man's highest technology and requires supreme intelligence. To say that a mind of supreme intelligence and technological ability is not the cause of the genetic code and information it produces is to deny the obvious and defy reason and rationale.


Instructions coded in the DNA represent instructions which,
1.  specify cell specialization (which type of cell a cell is to be)
2.  specify the arrangement of cells during fetal development for the production of the body plan and anatomy
3.  direct the machinery of the cell about how to transcribe (read) genetic information (i.e. when or where to start, stop, pause, etc.)
4.  specify the assembly of RNA molecules
5.  specify the assembly of protein molecules


RNA molecules are composed of four nucleotides: adenine (A), guanine (G), cytosine (C), and uracil (U) and represent instructions which,
1.  regulate gene expression (i.e. which gene and/or when to transcribe)
2.  specify the type and order of amino acids to be translated into a protein
3.  specify a catalyst for chemical reations


Proteins are used by cells as,
1.  building blocks for the physical features of cells and organisms
2.  components of molecular machinery
3.  catalysts in chemical reactions


1.  The Genetic Code is a language system using three consecutive nucleotides, called triplets to form "words", called codons. Each codon represents one of the 20 different amino acid molecules which are used by the machinery of the cell as instructions.

2.  "DNA consists of a code language comprising four letters which make up what are known as codons, or words, each three letters long." - The digital code of DNA

3.  "Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like the machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts." - The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists, Bruce Alberts, President, National Academy of Sciences, Professor, Department of Biochemistry and Biophysics, University of California

4.  "We have also come to realize that protein assemblies can be enormously complex. Consider for example the spliceosome. Composed of 5 small nuclear RNAs (snRNAs) and more than 50 proteins, this machine is thought to catalyze an ordered sequence of more than 10 RNA rearrangements as it removes an intron from an RNA transcript. As cogently described in this issue of Cell by Staley and Guthrie 1998, these steps involve at least eight RNA-dependent ATPase proteins and one GTPase, each of which is presumed to drive an ordered conformational change in the spliceosome and/or in its bound RNA molecule. As the example of the spliceosome should make clear, the cartoons thus far used to depict protein machines (e.g.Figure 1) vastly underestimate the sophistication of many of these remarkable devices." - The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists, Bruce Alberts, President, National Academy of Sciences, Professor, Department of Biochemistry and Biophysics, University of California

5.  "The case I want to make for you is that proteins are machines. You have 20,000 types of machines in your body, and other living organisms have other kinds of protein machines. There's tens of thousands to hundreds of thousands of different machines. And the first case I want to make for you is that these are real machines. That's not a metaphor. They use energy, they spin around, they pump, they act to cause force and motion." - - Ken Dill, Director, Laufer Center for Physical and Quantitative Biology, Professor, Physics and Chemistry, Stony Brook University, The protein folding problem: a major conundrum of science: Ken Dill at TEDxSBU

6.  "I've just shown you a few examples of tens of thousands of protein machines, but the case I want to make for you is just to convince you they are real machines, just at the super microscopic level." - Ken Dill, Director, Laufer Center for Physical and Quantitative Biology Professor, Physics and Chemistry, Stony Brook University, The protein folding problem: a major conundrum of science: Ken Dill at TEDxSBU

7.  "The assertion that neuroscience demonstrates the material nature of the mind is an ideological assertion, a misuse of neuroscience to serve a tenuous materialist agenda. In Wolfgang Pauli’s deathless phrase, the materialist explanation of the mind ”isn’t even wrong.” It’s superstitious nonsense. Materialism can’t explain the mind, because the salient characteristics of mental states — intentionality, qualia, persistence of self-identity, restricted access, incorrigibility, and free will — do not admit material explanations. A coherent and meaningful understanding of the mind requires a repudiation of this materialist superstition. Strict materialism offers some insight into behavioral correlations — behavioral arousal is associated with activation of neurons in the brainstem reticular activation system — but materialism offers nothing to explain the subjective properties of mental experience, which constitute the mind as we actually experience it. A genuine understanding of the mind must be open to immaterial causation, because there is nothing in materialist science (or materialist philosophy) that can account for subjective experience." - The Mind and Materialist Superstition, Michael Egnor, award winning neurosurgon, November 26, 2008

8.  Websters Dictionary, Definition of Code:
1     :   a systematic statement of a body of law; especially : one given statutory force
2     :   a system of principles or rules  .  moral code
3     a : a system of signals or symbols for communication
       b : a system of symbols (such as letters or numbers) used to represent assigned and often secret meanings
4     :   GENETIC CODE
5     :   instructions for a computer (as within a piece of software)  .  writing code for a new app


9.  Websters Dictionary, Definition of specification:
1     :   the act or process of specifying
2     :   a detailed precise presentation of something or of a plan or proposal for something —usually used in plural
       b : a statement of legal particulars (as of charges or of contract terms); also : a single item of such statement
       c : a written description of an invention for which a patent is sought


10. Websters Dictionary, Definition of instruction:
1     a : PRECEPT  .  prevailing cultural instructions
       b : a direction calling for compliance : ORDER —usually used in plural  .  had instructions not to admit strangers
       c : instructions plural  :  an outline or manual of technical procedure  :  directions
       b : a code that tells a computer to perform a particular operation
2        : the action, practice, or profession of teaching