Researcher: Mathematics sheds light on “unfathomably complex” cellular thinking

_{Denyse O'Leary

May 5, 2018

Cell biology, Evolution, Intelligent Design, Plants}

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Queensland University of Technology (QUT) researcher Dr Robyn Araujo has developed new mathematics to solve a longstanding mystery of how the incredibly complex biological networks within cells can adapt and reset themselves after exposure to a new stimulus.

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“Proteins form unfathomably complex networks of chemical reactions that allow cells to communicate and to ‘think’ — essentially giving the cell a ‘cognitive’ ability, or a ‘brain’,” she said. “It has been a longstanding mystery in science how this cellular ‘brain’ works.

“We could never hope to measure the full complexity of cellular networks — the networks are simply too large and interconnected and their component proteins are too variable.

“But mathematics provides a tool that allows us to explore how these networks might be constructed in order to perform as they do.

“My research is giving us a new way to look at unravelling network complexity in nature.”

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“I studied all the possible ways a network can be constructed and found that to be capable of this perfect adaptation in a robust way, a network has to satisfy an extremely rigid set of mathematical principles. There are a surprisingly limited number of ways a network could be constructed to perform perfect adaptation.

“Essentially we are now discovering the needles in the haystack in terms of the network constructions that can actually exist in nature. Paper. (open access) – Robyn P. Araujo, Lance A. Liotta. The topological requirements for robust perfect adaptation in networks of any size. Nature Communications, 2018; 9 (1) DOI: 10.1038/s41467-018-04151-6 More.

Amazing how the plants, using these “unfathomably complex” networks (how long would that take to evolve, relying only on Darwinian evolution?) found their way to the right mathematical configuration. This sounds far more like structuralism (an underlying pattern, based on physics and chemistry, controls evolution) than Darwinism.

See also: A pattern of laws of tooth development identified

Comments

Well, so far so good. RPA is a robust biological feature. Interesting algebraic/topological approach to modeling cellular function. It seems the evolution speak is lip service paid at beginning and end. SOP. The paper approaches function rather than structure, so the "modularity" they speak of isn't in actual biological components, but in the function mappings in their model. So it doesn't make biological physical structure/components arbitrarily and readily scalable for free so much as refer to the scalability of the design principles applied. Answering early because I expect this post to whiz by, but I'm still digging through this.LocalMinimum_{May 7, 2018
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OLV @ 2: Hmmm, sounds incredibly wrong. "RPA", as given here, sounds like a magical convergence of engineering paradigms. Guess I have to read the paper and figure it out.LocalMinimum_{May 7, 2018
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Life must have evolved, otherwise there is a God we have to obey. If rapid change is now part of evolution, i.e. punctuated evolution, then complexity must have evolved. There are lots of random chemical reactions. And besides, you can't explain why a perfectly good and loving god would create the suffering we see in the world.Peter_{May 7, 2018
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BA77: At about the 41:00 minute mark of the following video, Dr. Wells, using a branch of mathematics called category theory, demonstrates that, during embryological development, information must somehow be added to the developing embryo, ‘from the outside’, by some ‘non-material’ method.
Psalm 139:13 New International Version (NIV) For you created my inmost being; you knit me together in my mother’s womb.Latemarch_{May 6, 2018
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of semi-related note: At about the 41:00 minute mark of the following video, Dr. Wells, using a branch of mathematics called category theory, demonstrates that, during embryological development, information must somehow be added to the developing embryo, ‘from the outside’, by some ‘non-material’ method.
Design Beyond DNA: A Conversation with Dr. Jonathan Wells – video (41:00 minute mark) – January 2017 https://youtu.be/ASAaANVBoiE?t=2484
The following article further solidifies Dr. Wells claim:
Intelligent Design and the Advancement of Science - Brian Miller - December 11, 2017 Excerpt: DNA was expected to be the primary source of causality behind the operation and development of life. Such beliefs have previously raised concerns from leading scientists and mathematicians. For instance, physicist Walter Elsasser argued that the unfathomable complexity of the chemical and physically processes in life was “transcomputational” — beyond the realm of any theoretical means of computation. Moreover, the development of the embryo is not solely directed by DNA. Instead, it requires new “biotonic” principles. As a result, life cannot be reduced to chemistry and physics. An unbridgeable gap separates life from non-life. Similarly, mathematician René Thom argued that the 3D patterns of tissues in an organism’s development from egg to birth and their continuous transformation cannot be understood in terms of isolating the individual proteins generated by DNA and other molecules produced in cells. The problem is that the individual “parts” composing tissues and organs only take on the right form and function in the environment of those tissues and organs. More recent work by Denis Noble further has elucidated how every level of the biological hierarchy affects every other level, from DNA to tissues to the entire organism. Based partly on these insights, Thom concluded in his book Structural Stability and Morphogenesis that the process of development should be thought of as being controlled by an “algebraic structure outside space-time itself” (p. 119). Likewise, Robert Rosen argued that life can only be understood as a mathematical abstraction consisting of functional relationships, irreducible to mechanistic processes. He observed that life is fundamentally different from simple physics and chemistry. It embodies the Aristotelian category of final causation, which is closely related to the idea of purpose. The conclusions of these scholars challenge materialistic philosophy at its core. https://evolutionnews.org/2017/12/intelligent-design-and-the-advancement-of-science/
Moreover, this, what can be termed, positional information, that is coming into the developing embryo,,
Positional Information - Lewis Wolpert - 15 SEP 2016 Excerpt: Some of the best evidence for positional information comes from regeneration experiments, and the patterning of the vertebrate limb. Central problems are how positional information is set up, how it is recorded and then how it is interpreted by the cells. A number of models have been proposed for the setting up of positional gradients, and most are based on diffusion of a morphogen and its interactions with extracellular molecules; however, diffusion may not be reliable mechanism. There are also mechanisms based on timing. There is no good evidence for the quantitative aspects of any of the proposed gradients and details of how they are set up. http://onlinelibrary.wiley.com/doi/10.1002/9780470015902.a0020914.pub2/abstract
,,, which is not reducible to DNA sequences and which specifies the three-dimensional arrangement of the molecular components of the cell, is found to be enormous. Much greater than the sequential information, as great as that sequential information is, that is encoded on DNA.
How many different cells are there in complex organisms? Excerpt: The nematode worm Caenorhabditis elegans, the cellular ontogeny of which has been precisely mapped, has 1,179 and 1,090 distinct somatic cells (including those that undergo programmed cell death) in the male and female, respectively, each with a defined history and fate. Therefore, if we take the developmental trajectories and cell position into account, C. elegans has 10^3 different cell identities, even if many of these cells are functionally similar. By this reasoning, although the number of different cell types in mammals is often considered to lie in the order of hundreds, it is actually in the order of 10^12 if their positional identity and specific ontogeny are considered. Humans have an estimated 10^14 cells, mostly positioned in precise ways and with precise organization, shape and function, in skeletal architecture, musculature and organ type, many of which (such as the nose) show inherited idiosyncrasies. Even if the actual number of cells with distinct identities is discounted by a factor of 100 (on the basis that 99% of the cells are simply clonal expansions of a particular cell type in a particular location or under particular conditions (for example, fat, muscle or immune cells)), there are still 10^12 positionally different cell types. http://ai.stanford.edu/~serafim/CS374_2006/papers/Mattick_NRG2004.pdf
In the following video, it is noted that the information to build a human infant, atom by atom, would take up the equivalent of enough thumb drives to fill the Titanic, multiplied by 2,000.
In a TED Talk, (the Question You May Not Ask,,, Where did the information come from?) - November 29, 2017 Excerpt: Sabatini is charming.,,, he deploys some memorable images. He points out that the information to build a human infant, atom by atom, would take up the equivalent of enough thumb drives to fill the Titanic, multiplied by 2,000. Later he wheels out the entire genome, in printed form, of a human being,,,,: [F]or the first time in history, this is the genome of a specific human, printed page-by-page, letter-by-letter: 262,000 pages of information, 450 kilograms.,,, https://evolutionnews.org/2017/11/in-a-ted-talk-heres-the-question-you-may-not-ask/
The following video states that "There are 10^28 atoms in the human body.,, The amount of data contained in the whole human,, is 3.02 x 10^32 gigabytes of information. Using a high bandwidth transfer, that data would take about 4.5 x 10^18 years to teleport 1 time. That is 350,000 times the age of the universe."
Will Teleportation Ever Be Possible? - video - 2013 https://youtu.be/yfePpMTbFYY?t=76 Quote from video: "There are 10^28 atoms in the human body.,, The amount of data contained in the whole human,, is 3.02 x 10^32 gigabytes of information. Using a high bandwidth transfer that data would take about 4.5 x 10^18 years to teleport 1 time. That is 350,000 times the age of the universe." If we forget about recognizing atoms and measuring their velocities and just scale that to a resolution of one-atomic length in each direction that's about 10^32 bits (a one followed by thirty two zeros). This is so much information that even with the best optical fibers conceivable it would take over one hundred million centuries to transmit all that information!,,, (A fun talk on teleportation - Professor Samuel Braunstein)
To provide further evidence for information coming into the developing embryo ‘from the outside’, it is also important to note that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,,,
Looking beyond space and time to cope with quantum theory – 29 October 2012 Excerpt: “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,” http://www.quantumlah.org/highlight/121029_hidden_influences.php
And these quantum correlations which somehow arise from outside spacetime, are now found in molecular biology on a massive scale. In every DNA and Protein molecule,,,
Darwinian Materialism vs Quantum Biology - video https://www.youtube.com/watch?v=LHdD2Am1g5Y
The implication of finding 'non-local', beyond space and time, and ‘conserved’, quantum information in molecular biology on such a massive scale, is fairly, and pleasantly, obvious. That pleasant implication, or course, being the fact that we now have direct physical evidence strongly indicating that we do indeed have an eternal soul that is capable of living beyond the death of our material bodies. As Stuart Hameroff notes in this following video, “the quantum information,, isn’t destroyed. It can’t be destroyed.,,, it's possible that this quantum information can exist outside the body. Perhaps indefinitely as a soul.”
“Let’s say the heart stops beating. The blood stops flowing. The microtubules lose their quantum state. But the quantum information, which is in the microtubules, isn’t destroyed. It can’t be destroyed. It just distributes and dissipates to the universe at large. If a patient is resuscitated, revived, this quantum information can go back into the microtubules and the patient says, “I had a near death experience. I saw a white light. I saw a tunnel. I saw my dead relatives.,,” Now if they’re not revived and the patient dies, then it's possible that this quantum information can exist outside the body. Perhaps indefinitely as a soul.” - Stuart Hameroff - Quantum Entangled Consciousness - Life After Death - video (5:00 minute mark) https://youtu.be/jjpEc98o_Oo?t=300
Verses:
James 2:26 As the body without the spirit is dead, so faith without deeds is dead. Matthew 16:26 For what is a man profited, if he shall gain the whole world and lose his own soul? Or what shall a man give in exchange for his soul?
bornagain77_{May 5, 2018
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Abstract
Robustness, and the ability to function and thrive amid changing and unfavorable environments, is a fundamental requirement for living systems. Until now it has been an open question how large and complex biological networks can exhibit robust behaviors, such as perfect adaptation to a variable stimulus, since complexity is generally associated with fragility. Here we report that all networks that exhibit robust perfect adaptation (RPA) to a persistent change in stimulus are decomposable into well-defined modules, of which there exist two distinct classes. These two modular classes represent a topological basis for all RPA-capable networks, and generate the full set of topological realizations of the internal model principle for RPA in complex, self-organizing, evolvable bionetworks. This unexpected result supports the notion that evolutionary processes are empowered by simple and scalable modular design principles that promote robust performance no matter how large or complex the underlying networks become.
"simple and scalable modular design principles that promote robust performance no matter how large or complex the underlying networks become" "design principles"?OLV_{May 5, 2018
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Very interesting post. Thanks.OLV_{May 5, 2018
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