New Studies Reveal Higher Levels of Genetic Complexity

Nucleosome With Dna Model Recent studies have described even more layers of codes and ways the genetic system is ordered in each cell. Two completely new superimposed codes have been described that greatly complicate genetic regulation—messenger RNA folding, and multi use codons called “duons.” In addition, this week the large international FANTOM project published 16 studies that demonstrate vast new complexity in the way DNA regions are triggered. In fact, more and more new studies reveal higher levels of genetic complexity.

Human perceptions alter networks of genes in cells throughout the brain, immune system and other organs, even though humans are six orders of magnitude larger than DNA genetic networks. While thought and perception immediately alter large brain circuits with many different neuroplasticity mechanisms at once, they do this by triggering gene networks deep inside all the cells in the circuit.

Smallbot   Histone_methyltransferases_and_demethylases_function_antagonistically_to_control_gene_expression_patWhen stimulating the use of DNA to manufacture new proteins, the protective protein spools, called histones, must unravel the DNA strands that are wrapped around the four large complex molecules. Markings on the histones by acetyl molecules form a code that determines whether a section of DNA will open or not. There are many other regulatory factors, including small and large RNA molecules that, also, influence whether DNA unravels from the histone.

When the DNA is unravelled and open, markings of methyl molecules attached to the DNA determine whether the specific DNA can be used.

The extremely detailed regulation of the use of each piece of DNA is through many large and small molecules that trigger, enhance, and stop transcription of DNA code to RNA—called transcription factors. Large proteins called promoters, repressors, and enhancers bind to the DNA, as well as millions of small and large RNA from non-coding regions.    

PD   Beatiful  DNA RNA  1024px-How_proteins_are_made_NSFThe next layer of complexity occurs in the messenger RNA, which, by itself, edits the code taken from the DNA. This editing, called alternative RNA splicing, can make up to 500 different proteins from the same pieces of DNA (see post). The RNA cuts out sections and sews others together. Recently, it has been demonstrated that the pieces that are sewn together by the messenger RNA may come from multiple different areas that used to be called individual genes. 

From the messengerRNA, the protein is built into a row of amino acids that forms the protein. The three dimensional folding of this row of amino acids is so complex, that currently, all the supercomputers in the world would take Jesse V.  Protein folding    lossless-page1-800px-ACBP_MSM_from_Folding@home2,000 years to calculate the folding of one average sized protein (approximately 400 amino acids). Especially neurons have many much larger proteins, each in an exact shape. (see post Protein Shape is Function). We simply cannot know how these many amino acids, each with a complex 3D shape, will fold when put in a row. 

But, somehow, the cell knows what the shape will be and edits the code to form very specific structures. With the help of special chaperone molecules, in a millisecond, the protein folds into primary, secondary, tertiary and then quaternary shapes. The entire functions of the large protein machines are based on shape and the instant folding. (see post on Protein Folding)

This post will attempt to summarize what the new studies tell us about this vast complexity. 

DNA History: Genome Study

In 2003, after ten years and great expense, the Human Genome study found only 24 thousand genes in 1.5% of the DNA. This shocked the scientific community because of the small number of so-called genes; previously the dogma was one Illustration showing the formation of an animal cell from dna angene makes one protein. That would mean we could only have 24 thousand proteins. But, we already knew there are many thousands of different proteins, different in each cell type and each brain region.

The Genome Project showed that 98.5% of the DNA was not making proteins. Also, the scientific community believed that by mapping the “genes” mutations would be identified for many diseases. Ten years after the genome project, almost no disease mutations were found in the genes. Very recently, it has been shown that most mutations that could cause disease must be in the regulatory (“junk”) DNA or the protein transcription factors that regulate the start and stopping of DNA usage.

DNA History: ENCODE in 2012

In 2012, ENCODE, Encylcopedia of DNA Elements, published many papers at once after ten years of work in 160 laboratories around the world. ENCODE found a fantastic amount of active DNA making RNA of various kinds—in at least 20% of the DNA and perhaps 50%. Twenty percent of DNA being active means that the regulatory regions of DNA are at least thirty times larger than all the “genes.”  (see posts Encode 1 Mind and Molecular Genetics, Encode 2 New Genetic Landscape, and Encode 3 Encode and Evolution).

(Another fifty percent of the DNA is found to be in the form of jumping genes – virus like pieces of DNA that sew themselves in and out of the genome and copy themselves. These are strands of DNA that can possibly code for whole arms of proteins and are probably, along with viruses, the real drivers of evolution—see post “jumping genes” where the battle to control jumping genes in each cell is described)

Dna MoleculeENCODE showed that much of the previously called “junk” DNA was, in fact, active regulatory DNA making large and small RNAs that perform a fantastic amount of tasks. It found millions of factors that influence DNA. There has been rancorous debates since ENCODE by those who still want to maintain that most of the regulatory DNA is junk—these are often scientists who are committed to a theory that all of this is random.

ENCODE found 4 million different switches that were active, often operating in multiple places at once; 18,000 places where active RNA is made; and 8 million different particles interacting to regulate these RNAs. Basically, ENCODE found that far from being junk, at least 20% of the DNA is made into important small and large RNA particles that have a use. Since then, many studies have begun to show the importance of these large and small non coding RNA.

DNA History: New RNA Code Discovered in 2013

During the same period, the importance of alternative messenger RNA splicing was described. It was found that the messenger RNA edits and alternatively splices together pieces of DNA from multiple places, including multiple “genes”, and forms as many as Fdardel RNA folding  307px-PseudoknotFold500 proteins from one piece of DNA previously called a “gene’.

In 2013, a new RNA code was found superimposed on the other code. This new code consists of a 3D structure of the RNA. Until now, messenger RNA was considered to be a linear molecule representing the letters to make a protein. But, now it is shown that most often RNA will form hairpin loops where regions of RNA have complementary sections of RNA code. This loop folding forms a secondary structure that appears to have significance in translation of RNA code into proteins. The studies showed that even closely related individuals could have different folding structures. 1900 different mutations were identified that affect these RNA structures. The other finding is that when messengerRNA meets the ribosome to present the code that will form the protein, cellular proteins must actively unfold the mRNA.

DNA History: “Duons” Described in 2013

In 2013, a very surprising discovery found that sections of DNA have a dual purpose, comprising two completely different codes at once. These regions were called “duons.”

Vector - DNA and RNAThe genetic code consists of four letters, three of which are used for each word—words are called codons. Each codon corresponds to one of the twenty-two amino acids, or a stop signal. With four letters and three combined to form codons, there are 64 possible codons. A different number of codons correspond to each amino acid. Some of the amino acids correspond to 6 different codons, and others only one. It turns out that choosing different codons, even for the same amino acid, can have unusual effects.

Until very recently, it was assumed that transcription factors bind only in the regulatory regions of DNA next to the “gene”. Transcription factors include the up-regulation of the gene activity—called activators or promoters; enhancement or co-activation of the other factors—called enhancers or co-repressors; and down-regulation—called repressors.

The big new discovery is that transcription factors bind inside at least 13% of “genes” themselves, not just the regulatory regions nearby. This was truly shocking since the DNA in the gene, then, must code for two meanings at once for two entirely different purposes.  

The first purpose is to transcribe DNA code to RNA code to make proteins. The second purpose is to bind regulatory factors, as the regulatory regions do to trigger other genes. Duons were found to affect the exact choice of the codon and had an influence the alternative RNA splicing in the messenger RNA at the next step. But, its full function must be worked out.

DNA History: Bacterial DNAs Influence Described 2013

cells colorsEach human being has 100 trillion bacteria and 1000 trillion viruses in their gut representing another 3 million active genes producing active products many of which influence human function. The totality of these active genes has been called the hologenome and is, in fact, the real genome of the human being—each microbe with its own unique genetic mechanism. Recently, it was found that the activity of these microbes is as significant as the metabolism of our liver. (See post on hologenome and intestine epithelial cell)

DNA History: FANTOM Finds Promoter and Enhancer Complexity in 2014

The new study from FANTOM, in sixteen papers last week, finds greatly increased complexity with promoters and enhancers. FANTOM—Functional Annotation of the Mammalian Genomedescribes in great detail thousands of enhancers and promoters that start the use of a piece of DNA. The increased complexity comes from FANTOMs observation that promoters work in many different places for each gene and in different places for each type of human cell. Also, for even more complexity, multiple promoters combine into larger machines, some touching the DNA and some only combining with the other promoters. Multiple structures exist for each gene in different places.

B0004319 Human chromosomes, histones and kinetochoresFANTOM’s two studies looked at 800 different types of human cells. The first study creates an atlas of places where transcription starts and stops for each cell type. The second study described enhancers (proteins that increase the manufacture of particular genes).

These studies looked a many specific cells in different tissues and found 185,000 promoters and 44,000 enhancers. The ENCODE studies used only a small number of cell types. FANTOM used a wide range of human cells. ENCODE studied much wider phenomenon, but FANTOM explored many of the human cells for the promoter and enhancer regions in much greater detail. They were able to find the beginning of mRNA and then identified regions near, where the upstream promoters lie.

Bryhall    Genetic_breakdownA very significant FANTOM finding is that there are multiple different places where transcription starts for each “gene”, again undermining the notion of the simple “gene.” It, also, found that all the different cell types start transcription using the DNA at different sites. Along with alternative RNA splicing, the entire concept of “gene” has to be reconsidered.

To find enhancers, they used similar techniques, but the enhancer situation is more complex because some enhancers are transcribed in two directions at once—from the center out in both directions and from both DNA strands. FANTOM noted that the bidirectional types of enhancers are the active important versions. Limitations of the study noted that there are probably a much larger number than was found by these techniques.

Also, most cell types have different varieties of these proteins to express the differences in the types of functions, such as a neurons versus a heart or kidney cells.

FANTOM: Specific Human Tissues

Four hundred different human cells were shown to have different regulatory proteins and different active and inactive genes. Each type also responds differently to the environment with different gene changes and interacts with other cell types. Most genes have more than one start site. The regulation of each is complex and varied.

They also looked at 250 types of cancer cells, whose patterns were noted to be extremely variable.

FANTOM compared findings of the mouse and human, to show evolutionary changes. The conserved areas were similar in both. Only 20% of the genes appear to make cellular scaffolding structures that are common to all cells. These genes appeared to be similar in mouse and human. The most similar were in fibroblasts, chondrocytes in bone, and Endocrine Systemadipocytes.

FANTOM found 80% of the genes are used for the specific functions of the types of cells from different human organs. These genes were very different in humans than mice. In human cells there are a large amount of very different enhancers and promoters and combinations of them. The human that were unique included T cells, macrophages, dendritic cells, blood cells and endothelial cells. This is in line with the very different and rapidly evolved human immune system. A previous post described the remarkably complex and intelligent intestinal endothelial cell, which is very different in humans.

Another conclusion was that since only 128 factors could be studied at once, FANTOMs findings are just the tip of the iceberg of complexity at this level.

Genetic Complexity In Many Studies

While ENCODE and FANTOM are large studies consisting of hundreds of research sites working together around the world, many other isolated Insulin molecular pathwayfindings, also, continue to show the vast complexity of the genetic machinery.

Recently, it was shown that exercise effects 10,000 genes and that insulin effects 7 thousand genes in the cell.

Recently, neurexin proteins—critical proteins that hold synapses together—were found to have 2500 variations or more.

Postsynaptic densities in synapses involve a thousand interlocking proteins and these are different in most regions of the brain involving vast genetic changes.

When Thought is Added to the Equation

BrainPerhaps most unusual are the findings of how mental events trigger vast genetic changes.

Human thought instantly alters large circuits of neurons (see post of neuroplasticity). This occurs through a wide variety of different neuroplasticity mechanisms by triggering specific gene networks and the creation of different complex machinery protein in each different brain region.

Perceptions of loneliness are very significant triggers of gene networks in immune cells causing more inflammation—130 anti inflammatory genes have been shown to lack function and 80 pro inflammatory genes were very active.

Meditation or perception of helping the community, also, triggers hundreds of complex genetic changes that stop inflammation and viruses (see post on Meditation and the Brain).

Therefore, social situations, perceptions and thoughts trigger networks of genes deep inside the cells of the immune system, hormonal systems, body organs and brain. Remarkably, the cell knows exactly the shape of the proteins needed for each of the different neuroplasticity mechanisms that occur simultaneously. Recent posts have described many of these neuroplastic mechanisms that occur simultaneously in large brain circuits, each requiring different complex gene networks. These include:

  • Manufacture and placement of more AMPA glutamate receptors
  • Calcium surge causing lasting increase in signal called LTP and “memory proteins”.
  • Dendrites change structure—size of the head of the dendrite
  • Post-synaptic density alters 1000 interlocking large proteins in each brain region
  • Change of synapse binding molecules—neurexin, neuroligin
  • Pre synaptic neurons substitute neurotransmitters & postsynaptic change receptors Signaling cascades from membrane to nucleus altered
  • Changes in axon ion channels alters electrical signal
  • Balance of inhibition and stimulation changes
  • New micro RNA’s alter process
  • Interneurons are altered
  • Mitochondria in the dendrite alters the strength of the signal
  • Proteins altered in extracellular matrix
  • Myosin motors and actin structures altered
  • Alterations of climbing fibers in cerebellum
  • NMDA glutamate receptors substitute their subunits
  • Transport motors are substituted
  • Exosomes send information from astrocytes to neurons including pieces of DNA

New Studies Reveal Higher Levels of Genetic Complexity

It is not known how many overlapping codes there are.

shutterstock_182654546 DNAThere are multiple factors that determine the opening of the histones. Multiple factors determine which pieces of DNA will be used. A fantastic array of promoters and enhancers and large and small RNAs interact in multiple ways to regulate what pieces of DNA are used. Thousands of different multiple large protein promoters operate in multiple start sites and with multiple proteins either binding to the DNA, or forming large structures by attaching to the other promoters. In some DNA there are two superimposed codes at once. Also, somehow, many different mechanisms are used to repair DNA errors (see post).

Eight million factors affect the RNA particles that are made from at least 20% of all DNA (maybe up to 50%). Messenger RNA somehow determines multiple different edits from the same pieces of DNA. Pieces are taken from multiple places, strands are cut out and others sewn together without clear direction. New 3D folding of the RNA also forms a new code.

All of these processes create a code of amino acids that the cell knows will form a very specific very complex protein shape. Proteins only work through exact shapes. Although it would take current supercomputers 2000 years to figure out the folding of one 400 amino acid length protein, proteins are actually folded in primary, secondary, tertiary and quarternary structures in a millisecond, with the help of complex proteins called chaperones. Manufactured proteins then affect all the different neuroplastic mechanisms in a large circuit at once. These proteins, also, affect immune cells throughout the body. 

Where is the regulation and control for all of this?

How can anyone say that these overlapping codes involving hundreds of thousands of interacting factors is in any way random?

With mental events triggering these gene networks deep inside of cells, how can anyone say that mind does not influence these genetic processes? 

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  • Rob Cristoph

    Truly fascinating! “How can anyone say that these overlapping codes involving hundreds of thousands of interacting factors is in any way random?” – I wonder if an analysis of the time required to randomly or otherwise evolve such level upon level of complexity would exceed the lifetime of this universe? Like any complex machine, take a 747 for example, it makes sense that the complexity is not in the design of the individual nuts, bolts and panels, but in the way that this fixed number of parts are connected together, and more so, in the control of the machine held as programming information. Great article, and I really think that we are so fortunate to have such incredible people capable of reaching such heights of investigation in such a complex field!

    • Faraz-Qammer Yusufzai-Khan

      Who said they were random ? are the millions of computer code lines in Microsoft Windows , random ? … complexity is not equivalent to cognition/self-awareness. .. The Windows operating system has been honed … : by beta-testing and updates of errors and bugs ..using huge resources.

      • Rob Cristoph

        Those that support mutation as a basis for evolution.

        • Faraz-Qammer Yusufzai-Khan

          The Question at the end was -“”How
          can anyone say that these overlapping codes involving hundreds of thousands of interacting factors is in any way random? “” ………………………….Dear RC .. I do not think that those supporting mutation as a basis of evolution think that the *codes* are random “” ?? .. pedant that I am I would say that accuracy of science goes hand in hand with accuracy of English .. The overlapping codes (ie. their sequence and interactions) * have * been honed by the reproductive efficiency of the organism they blueprint. They are not random . I have always deprecated concepts of new-age theology and higher mind , if you care to read my comments on discus … for example -below.

          • Rob Cristoph

            ” honed by the reproductive efficiency of the organism they blueprint”… that just does not fly, because reproductive efficiency, i.e., the ability to improve the design of complex systems requires a complex system to start with, and that brings us to the chicken and egg conundrum again. Life as we know it cannot exist without a cell, and a cell cannot exist without the cellular machinery, such as the ribosome, which has not evolved to any extent during the history of life. “RNA world”, rubbish I say, because that route takes us to molecules that can self-assemble because of the nature of the physics of this universe, which just moves the issue to the “programming” of the atom, and I do think that atoms also have their own “dna”. Can you explain to me my dear Faraz how it is that the hox gene body plan evolved, and why all life is based on it? No, no one can. I am not a creationist, but that and any other type of view does not negate the possibility that there is something beyond this universe that is intelligently evolving life. I can´t see any plausible explanation for the level of modular, object-oriented design that scientists are uncovering in living creatures cells as every day passes. On top of this we have the current popular theories of multiple universes, supported by Hawkings etc., and that these universes might have atoms which follow other rules… so to say. Mega complex evolution through “reproductive efficiency” just does not do it for me!

          • Faraz-Qammer Yusufzai-Khan

            “”because reproductive efficiency, i.e., the ability to improve the design
            of complex systems requires a complex system to start with,”” .. I take it that came from your head and not literature .. Reproductive efficiency .. Seems to me , some recent Articles ,Q-A’s and Comments , are rife with semantic wooliness . Its Simple maths ..Its Darwinism ..( lecture 101 !) ;the better design reproduces itself better..( but the variations are random )…lets go back to basics ok : Carl Woese published an illuminating article which I quote here “a cell resembling a primitive bacterium happened to find itself one jump
            ahead of its neighbors in >>>reproductive efficiency<<<. That cell separated and refused to share its DNA with other cells…. Its offspring became the first
            species. With its superior efficiency, it continued to prosper and to
            evolve separately. Some millions of years later, another cell separated
            itself from the community and became another species. And so it went on,
            until all life was divided into species.". [[http://www.technologyreview.com/article/403777/the-darwinian-interlude/]] …. there is a second part of my reply below.

          • Rob Cristoph

            I´ve read that article “Hence its earliest origins *likely* lie in the RNA world”… its all very speculative and without any clear hard fact. It says the ribosome dates to the lasy universal common ancestor of all life, 3.8 billion years ago. Why does it say that? Doooh, because it had to have a ribosome, and a fully functional one at that! So life goes from ZERO to LUCA in a bang, a bang, not the Cambrian bang… which was another sudden explosion of life… when the environment was right for it… So here´s something a little more concrete : “Given that many other nucleotides are possible besides adenine (A), thymine (T, DNA only), guanine (G), cytosine (C), and uracil (U, RNA only), it is extremely unlikely that organisms descendent from separate abiogenesis events (that is to say separate incidents where organic molecules initially came together to form cell-like structures) would be able to complete a horizontal gene transfer without garbling each other’s genes, converting them into noncoding segments. Also, many more amino acids are chemically possible than the twenty found in modern protein molecules.”

          • Rob Cristoph

            One set of DNA letters amongst many options, one body plan amongst many, no life based on any other arrangement although very possible, no fossil evidence of other configurations during billions of years… no early primitive ribosome structures (minor very minor variations, but nothing significantly different ever), and just a theory amongst many that maybe an RNA world magically fell together to one day spontaneously create one of the most perfect and complex macro molecules in life! Sure, its all an accident, a freak of nature, in a multiverse full of freaky universes with their own freaky laws… but at least you for one Faraz, have it clear! 😉

          • Guest

            YOU SAY “~ earliest origins *likely* lie in the RNA world”…~very speculative~without hard fact.”
            <<>>>
            ====
            YOU SAY “speculative “ ;<>
            ==
            YOU SAY :”It says the ribosome dates to LUCA, 3.8 billion years ago.~~ it had fullyfunct ribosome,~!~from ZERO to LUCA in a bang, ~”
            <>>>
            ==
            YOU SAY :” it is extremely unlikely that organisms descend from separate biogenesis events ~”
            <
            >

            <>

          • Rob Cristoph

            Well, my view is that you either have a working ribosome, or you don´t. Call it simplistic, but then again as an engineer… Anyway, your view is that all these atoms group up and form handy molecules that then form up again nicely to make functional device that operate with deep knowledge of physics at the quantum level, like the LH molecule… so perfect that it is… Your view is that all this randomness, due no doubt to the physical “nature” of the universe cause ribosomes to self-assemble, right? 🙂 However, the current expert theory is that there are multiple universes with multiple physical rule sets. This tends towards the idea that atoms, space-time itself, created or projected by whatever mechanisms it takes, are programmable, that atoms and the fabric of each universe, like dna, can be programmed differently. That takes me to the conclusion that this universe, with its constants that are so perfect and unchangeable without causing a failed universe, and the life in it, all of which follow one single rule-set, have a rather deliberate intention. But these are just my thoughts, my ideas, and I don´t care if they are wrong at all. I estimate that in about 10-15 years scientists will have uncovered uncomfortable truths that the public will need to be prepared to accept. Lets continue this conversation in 2030, that is, if we are here. 🙂

          • #YOU SAY “~ earliest origins *likely* lie in the RNA world”…~very speculative without hard fact.”LITERATURE SAYS : RNA acts as both storage of genetic information, and can fold into proteins/enzymes ‘Ribozyme’ (Ribosome’s utilize rRNA, for instance). DNA doesn’t : RNA is likely
            to be the first form of genetic Evolution Natural Selection.
            #=YOU SAY“speculative “ LITERATURE SAYS ;
            “www.paleosoc.org/Oldest_Fossil.pdf Cyanobacteria, have been traced to about
            3.5 BYA ref 2012 science daily.(sciencedaily.com/releases/2011/08/110821205241.htm): and *Apex fossils very confident dateD 3.4 BYA. RECENTLY.
            #YOU SAY :”It says the ribosome dates to LUCA, 3.8 BYA.~ it had fullyfunct ribosome,~!~from ZERO to LUCA in a bang, ~” I SAY : digressN again ,myself nor literature claim LUCA had no precursors : LITERATURE SAYS : The Minimal
            Genome Project concluded only 256 genes required..No DNA machinery needed: *Apex
            fossils too complicated to be proto-life , life originates earlier : the window is conjectured , by some,to be small (until about 3.9BYA the Earth hit by, ostensibly sterilizing ,meteorites) – Tho’,now it’s known bacteria can survive and grow in the frozen upper stratosphere…also ,be
            viable in space debris.
            #YOU SAY :” it is extremely unlikely that organisms descend from separate biogenesis events.
            ~” I SAY : please don’t digress again .No one is claiming separate events .notpertinent :LITERATURE SAYS: ~ even if that RNA is no longer universal, mitochondria were once full-bacteria ;partnershiping our single-celled ancestors.~ furthermore it is unclear if LUCA
            was a ‘species’ or a proto-nucleus-life-form
            involving horizontal transfer. Evidence of RNA relics within the **nucleus **-suggests its more ancient than previously supposed. So jury is out
            wrt reconstructn LUCA , maybe horizontal transfer makes this too difficult .
            #IMHO: alluding to paranormal scenario’s is vacuous ( and troubling) .

          • Faraz-Qammer Yusufzai-Khan

            # Evolutionary algorithms are now used to solve multi-dimensional
            problems more efficiently than software produced by human designers,#,
            #Genetic algorithms especially
            suited to solving complex optimization problems… also suggested for
            solving problems in creative design, ;combining components in a
            novel, creative way.#, .. #The automatic evolution of computer programs. by evolutionary iteration. —– It is an interesting fact that these self generated programs contain loops of code..much like in DNA in nature ” Can you “see ” now ?

          • Rob Cristoph

            I can understand what you´re saying, but those “evolutionary algorithms” you mention were designed by our best scientists, they didn´t self-evolve, and they are pathetically simple compared to the algorithms driving “life”. I would say that something has to kick the process off. The chances of such complex self-adaptive systems, capable of forward-evolving other complex systems, self-evolving is, IMHO, 1 to the infinity! If evolution were truly independent and random, we would surely see variations on the theme, not just the same cellular machinery, and hox gene controlled body plans in all life!

          • Faraz-Qammer Yusufzai-Khan

            Q-“If evolution were random, we would surely see
            variations on the theme, not just the same cellular machinery, and hox
            gene controlled body plans in all life!”-
            A-Evolution is* not random *- Its the mutation that is random.. Evolution is *selected* for success on planet Earth ( look out of the window- you will see it ) ” .. I have to stop here ..because someone has their undergear in a twist .

          • Faraz-Qammer Yusufzai-Khan

            “evolutionary algorithms ” — develop by *random* variation.. How do you know they are “pathetically simple”..because even the programmers cant work out how the self-assembled program works.!… I throw my hands up… everyone opinion is equal.(.some more equal than others ..lol )…Would that you provide data in support of your opinions..I have provided you with real data supporting evolution through selection of random variants …. (we are not digressing to the origin of life .. there is a lot of digression in this website , irksome .)

            Goodnight. Live long and may you and your offspring prosper through Darwinian selection.

          • Rob Cristoph

            Given the current understanding of the complexity of genetic coding, anything us humans can do, including coding leveraged through our interpretations of adaptive programming, is bound to be much simpler just by the fact that our scientists are just beginning to implement such coding techniques and mother nature has been at it for billions of years. Look at our computers, they have no real intelligence at all, certainly nothing more than mimicry. HAL of Space Odyssey 2010 is a far away dream as much now as it was in the 70´s. No one can explain how the ribosome evolved, no one, why do you think you know different? “mind in nature”? you may as well call it God for the lack of explanation that any scientist can give it today! The answers simply are not there, and claiming Darwin, who knew nothing of genetics was correct, is just unfeasible.

          • Faraz-Qammer Yusufzai-Khan

            May I remind you of : Fractal theory and Chaos theory.. Eigen-vectors .all mainstream (! so its not me knowing better -its in the literature ).. Previously a statement of yours said ” how could such intelligent design occur over billions of years “…now you say ” mother nature has been at it for billions of years. ” .. I humbly suggest I see a contradiction in your views… may I humbly ask where your views are reflected in peer reviewed literature ? Please provide a ref.

          • Rob Cristoph

            I hope my above post explains, which references current respected research on ribosome evolution.

            … let me add here one snippet that goes towards my point by a respected researcher:-
            “This is a very engaging and provocative article by one of the most innovative and productive researchers in the field of protein evolution,” said University of California at San Diego research professor Russell Doolittle, who was not involved in the study. Doolittle remains puzzled, however, by “the notion that some early proteins were made before the evolution of the ribosome as a protein-manufacturing system.” He wondered how — if proteins were more ancient than the ribosomal machinery that today produces most of them -“the amino acid sequences of those early proteins were ‘remembered’ and incorporated into the new system.”

          • Faraz-Qammer Yusufzai-Khan

            No one can explain ribosomes – There is plenty in peer reviwed literature – your just plain wrong. –“The modern ribosome is very dynamic- archaic ribosomes used a template – that would subsequently become the mRNA, thereby allowing the
            evolution of the code and making an RNA genome useful. Finally, a highly
            speculative timeline of major events in ribosome history is presented
            and possible future directions discussed.” Zhang et al 2009 .

          • Rob Cristoph

            Look at recent research, and let us consider key* Word usage: “According to a new analysis, even before the ribosome’s many working parts were recruited* for protein synthesis, proteins also were on the scene and interacting with RNA. This finding challenges a long-held hypothesis about the early evolution of life.”

            “This strongly suggests, first, that proteins were around before ribosomal RNAs were recruited* to help build them, and second, that the ribosomal RNAs were engaged in some other task before they picked-up* the role of aiding in protein synthesis, he said.”

            “recruited” – by what process?
            “picked-up” – by what process?

            How can so many scientific papers use such terms to wash over the fact that they still have no idea of the driver of these major evolutionary steps.
            We’re not, after all, just talking about accidental chemistry, instead major design steps, massively complex steps that require an “understanding” of the overall system design even more complex by magnitudes than the complex machine being designed, i.e. the ribosome.
            Does anyone follow that?

            Source: http://www.sciencedaily.com/releases/2012/03/120312192839.htm

          • Rob Cristoph

            Let me add here one snippet from this research that goes towards my point, made by a respected researcher:-

            “This is a very engaging and provocative article by one of the most innovative and productive researchers in the field of protein evolution,” said University of California at San Diego research professor Russell Doolittle, who was not involved in the study. Doolittle remains puzzled, however, by “the notion that some early proteins were made before the evolution of the ribosome as a protein-manufacturing system.” He wondered how — if proteins were more ancient than the ribosomal machinery that today produces most of them -“the amino acid sequences of those early proteins were ‘remembered’ and incorporated into the new system.”

          • Rob Cristoph

            … back to the chicken and the egg thing, again! 😉

          • Faraz-Qammer Yusufzai-Khan
          • John

            I spent almost a year of my life with several scientists trying to determine where in a system we had 4 elements to examine, why we were getting variations of end product. Just 4 elements. You would think that would be easy. NOT. Then working with G.E. high level scientists had a similar problem with a product that worked well and all of a sudden stopped working. Took several scientists to determine the cause that involved one component, massive testing, etc. to get to the bottom of that SYSTEM problem. Now imagine the complexity of just one cell and apply that complexity to a system! Wow. Random chance? NOT.

          • Rob Cristoph

            Exactly!

          • Rob Cristoph

            Self-evolving algorithms can be understood, they often just take the drudge out of developing suitable search techniques. So give me an example of one that cannot be understood if you like. “I have provided you with real data supporting evolution through selection of random variants” – > randon variants is not a driver of design/evolution. Any complex process rapidly reaches a point at which the number of random “variants” as you say goes exponential, i.e. infinite, meaning they fail to evolve.

          • John

            Agree. To say “time” is all you need to create a life scenario but ignoring the life span of any organism is ridiculous. Each change heading in a direction has to function for that lifespan and then be passed on. How does simultaneous functions required to create a living entity allow that to happen from generation to generation and also reproduce with no mutations? How much time would it take for a 747 to come from a junk yard of parts? If one part is missing, why don’t we see that entity that didn’t make it? How would it reproduce?

          • John

            So you are applying a binary code ( “0” and “1” ) to a quaternary code of 4? And saying they are the same? The mathematical absurdity of that is staggering.

          • Rob Cristoph

            Being primarily a software engineer/system designer, no, I don’t see. Loops in code have no relationship to the physical structure of the DNA helix as far as I can understand. As to the hype about evolutionary algorithms, its largely hype pushed on the public to make good reading. Extracting patterns or data from large or complex datasets has benefited from using some processes similar to those used in evolution, but then we all know that behind everything is pure math, so that’s to be expected. My “Smart” phone still isn’t smart, and if we had evolving software then by now phones would be smart. What we have is some useful algorithms, tiny bits out of Smart life-based systems, but no idea at all how to créate the intelligence of even an amoeba let alone an ant.

          • John

            Any system that requires complex actions from several parts SIMULTANEOUSLY can only happen if all the parts are assembled prior to starting the system. Your heart. It takes 10 separate events to assure it will beat and continue to work with each of those parts essential for its operation. 5 are mechanical and 5 are chemical requiring separate systems to have that happen. That machine works 24/7 for 100 years without maintenance. You cannot have one of those events missing and still be alive. Take that concept and apply it to the complexity of a cell requiring simultaneous events for it to survive. Now apply the fact that it REPRODUCES! Wow.

          • Rob Cristoph

            Wow is the word! Each months it get more wow too, the complexity seems almost endless, even overlaid coding in DNA which was only recently discovered. I wonder what our views will be 10-years from today!

          • John

            I tend to agree with you.

          • Rob Cristoph

            ” honed by the reproductive efficiency of the organism they blueprint” -> I can’t find any evidence to suggest that reproduction drives evolution, are there any texts published on this theory? What I have read is that selective reproduction results in as much as a 5% contribution to design change, Do you consider that reproduction somehow generated the unique hox body plan design that all living creature are based upon? How did that evolve when there was no precursor?

        • John

          With the complexity of any system, each component is dependent upon other factors and components. Every computer cannot operate without an operating system to direct and control how all the parts work together. To consider “time” as the determining factor in organization of parts is to ignore simultaneous actions required for any system to work properly. I believe time is the factor that acts like a buffer to any thought process supporting evolution that supports increased intelligence of an organism. All we see is extinction with no proof of improved organisms that re-define DNA improved complexity.

          The reason time travel is not possible, other than that observed in micro molecular structures where AMD -> ADT -> ATP then backward can be observed. To reset all the complex actions in a backward movement of time simply is impossible and now especially knowing the complexity of DNA as described herein. To think by adding time to a random chance equation will allow this kind of complexity to improve is absurd. This is especially true when you realize there has to be a continuum of events in nature and that does not happen in the real world. Change is the only thing we know is true. The more complex a system is, the more simultaneous events dictate the outcome. Because we now know that the idea of consciousness affects the way genes express, we need to factor in that to have language at the level humans have, there needs to be consciousness to allow that to happen. Going from grunts to words can only be documented by the written word or pictures and that is only happened for a few thousand years. Interesting.

          • Rob Cristoph

            I consider personally, that it would seem reasonable, given the available information, to start to wonder how such incredibly interwoven complexity could arrise when we know that single mutations are more often fatal. An example is the human visual system, only a few minor code changes resulted in color vision, however, and this is a big however, the eye seemed to have already become significantly prepared for color vision such that these final minor changes were little more than a switch to turn color vision on.
            However, if there is a “higher intelligence” behind evolution, then that intelligence has coded all life here for continual conflict, making any intelligent life suffer considerably in order to achieve any semblance of peace; and why would a good universal god want that? I think there is no clear answer at this point.

          • John R

            Personally, I believe it makes perfect sense. When you realize that God put it all together and then made the rules. If you will notice, it is when we deviate from those rules we get punished. Just look around at how we have created incredible amounts of toxins and the more we learn, the more complex it gets and the more we realize that everything is interwoven and dependent upon the whole system. Our technology in many ways is just a mutation of that system and we are paying for convenience, what we think is clever, and a whole host of medical disasters are increasing the more we apply what we believe to be good technology.

          • Rob Cristoph

            Yes John, but we have very clear evidence that God/Nature has developed a system that is dynamic and tolerant to damage, scientists have uncovered that it is a system that uses a statistical approach to almost everything. This God isn’t personal, punishment? No, look at the fate of millions of innocent new born babies in Africa. That is not punishment but a simple statistic in this great system, in fact they need to die if the genetics of their parents isn’t good enough such that they are unable to survive. This God is not kind, not in our view of personal kindness, it can not be the God from the bible, it is a hard God.
            This God also has finite resources, life is imperfect, designs improve over time, mistakes are made and corrected, there is experimentation. At best we are part of a universal life creation process, at worst, as the ancient Greeks thought, we are a soap opera for some very human gods. 😉

          • Thingumbob

            Recent research on the life cycle of proteins has some remarkable implications that reinforce the power of the epistemological method of Nicholas of Cusa and his heir, Gottfried Leibniz. This brings the issue of the human species’ potential for immortality out of the realm of mere assertion.

            Biological substance at the simplest level of proteins itself exhibits a highly controlled life and death cycle that is necessary for elementary organisms to survive. Thus the very necessity of the individual organism in a subsuming life and death cycle for its larger species nature to survive. This sort of movement from lower to higher life forms is not merely a sort of abstract classification that the purveyors of “information theory” mischaracterize as “Platonic” abstraction. Rather it is a physical certainty.

            Further, it is undeniable that the uniquely distinguishing mark of humanity that sets it apart from all other known life forms is our ability to conquer and surpass the limits of the merely biological. All other species come and go, completely unable to determine their survival by changing the functioning of their fixed nature. (Only hysterical ideologues that truly hate humanity can deny this.)

            The conception of this grand and universal hierarchical composition must become the foundation of all that deserves the name of science and art.

            http://thingumbobesquire.blogspot.com/2015/10/the-aging-of-proteins-and-subsumed.html

          • Rob Cristoph

            You have a very high opinion of the human species. I think it is a little early to say that we are the only species that can avoid extinction given that we’ve been around less time than even the dinosaurs. 99% of the human race has zero idea how their mobile phones work, let alone even a rudimentary understanding of genetic processes. The 0.1% that do have an idea are still unable to even understand protein folding, or model atoms more complex than the single electron hydrogen. We do not understand so very much, and our societies are still highly unstable, lead by tribal-politics that leads us into pointless wars, or wars in which we steal the resources of others, that I very much doubt that we are much more evolved than many other mammals. Yes we can make better tools than any other species, but whether we survive is very much in the hands of fate/nature/g/God.

          • Thingumbob

            Cusa’s idea was called learned ignorance because of the fact that in our mortal nature we can only ever become less ignorant gradually. But that does not take away from the marvelous things we potentially can accomplish.

          • Rob Cristoph

            True.

  • Jeff Graubart

    One wonders if those who deny mind in nature simply lack one. Superb essay!

  • Faraz-Qammer Yusufzai-Khan

    New
    “Studies Reveal Higher Levels of Genetic Complexity – “.. “those who deny mind in nature simply lack one.” As humans we use words and logic to communicate … I would say that the former and later phrases are non sequitur … (maybe a mis-post )?

    • Rob Cristoph

      Humans are sane?! Have you not seen the state of the human world? Human politics is still tribal, 99.9% of humans have absolutely no idea how even their phones work, and not a single scientist knows how magnetic waves actually work, or why, although they do know how to use them. Chemists can’t explain the exceptions to the octet rule, and physicists are still using a 1-electron formula from 1928. We have an awfully long way to go before we are sane or smart, and the sooner we all realise it the better… well, IMHO but what do I know! 😉

  • Thingumbob

    “How can anyone say that these overlapping codes involving hundreds of thousands of interacting factors is in any way random?” Precisely correct.
    However, one needs to differentiate mere perception from higher order uniquely human thought of the type that revolutionizes technological practice. That is an order of complexity that is nowhere to be modeled by any possible binary sort of code. Why? Because such type of thinking is necessarily not fixed but uniquely coheres in a fugal manner with the ongoing development of the universal potential.

    • Rob Cristoph

      We may use a simple binary base for programming, but that is rapidly extrapolated in C++ to a high-level object-based programming structure, clearly the genetic coding is a magnitude of orders more complex, but theoretically C++ could emulate any process that was understood, although it might not be the best vehicle for what looks like a form of multidimensional programing that in the case of “life” may be simply beyond any one person’s ability to understand. In human experience, the best software is produced when one architect can visualise and improve the entire process. When complex tasks get divided into person-manageable chunks the focus is usually lost, hence some 70+% of software projects fail. Can we get human teams to act as “one mind”? To an extent the answer is yes, but when complexity reaches a very high level, coupled with simply vast amounts of processes running simultaneously, human teams become unable to cope. It took Microsoft 20-years and hundreds of millions of dollars to make Windows stable, and that was just an operating system! 😉