GaryGaulin
Posts: 5385
Joined: Oct. 2012
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| Quote (ChemiCat @ Feb. 05 2015,08:51) | A bit of background about why I came to this forum.
I am an ex-chemist with a grounding in organic analysis. I stumbled across the phrase "molecular intelligence" and came here to see this new research into an area of chemistry of which I hadn't heard.
Imagine my disappointment when I discovered it was just an unsubstantiated and untested assertion by a creationist trying to smuggle "the Trinity" into science. Even worse was the time I wasted trying to make sense of 40+ pages of incomprehensible drivel. It should be a criminal act to mangle the English language like that.
So, Mr Gaulin, are you going to test this assertion and publish your test results as evidence so that we can verify them? Or, as I suspect, are you just going to throw insults and ignore the need for YOU to provide said evidence?
I would like to thank sincerely the efforts, patience and stamina of both NoName and N. Wells for exposing the stupidity of this "theory". |
If you are unable to make sense of anything I said then I would only be wasting my time on someone who wants to see "drivel" from a creationist trying to smuggle "the Trinity" into science.
But for everyone else this is what the "ex-chemist" is unable to figure out:
| Quote | From:
https://sites.google.com/site.......ign.pdf
Unimolecular Intelligence
Clues to the origin of intelligent living things are found in rudimentary molecular systems such as self-replicating RNA. Since these are single macromolecules that can self-learn they are more precisely examples of “Unimolecular Intelligence”, as opposed to “Molecular Intelligence”, which may contain millions of molecules all working together as one, to self-replicate.
REQUIREMENT #1 of 4 - SOMETHING TO CONTROL
The catalytic (chemically reacts with other molecules without itself changing to a new molecular species) ability of ribonucleotide (A,G,C,U) bases combine to form useful molecular machinery. Where properly combined into strands 100 or more bases in length they become a rapidly moving molecule that can control/catalyze other molecules in their environment, and each other, including to induce each others replication. Unlike RNA that exists inside a protective cell membrane these RNA's are directly influenced by the planetary environment, which they are free to control. Modern examples include viruses that over time learned how to control the internal environment of their host to self-assemble protective shells with sensors on the outside for detecting suitable host cells to enter and control. After invading the cells other sensors detect when conditions are right to simultaneously reproduce, thereby overwhelming the immune system of their hosts, which would otherwise detect then destroy them.
REQUIREMENT #2 of 4 – SENSORY ADDRESSED MEMORY
The ribonucleotide sequences are a memory system that also acts as its body. On it are molecular sites, which interact with nearby molecules to produce repeatable movements/actions. Its shape can include hairpin bends that are sensitive to the chemical environment, which in turn changes the action responses of its code/memory to nearby molecules, and to each other. Their activity also changes their molecular environment, much the same way as living things have over time changed the atmosphere and chemistry of our planet. This suggests self-organization of a complex collective molecular self-learning system involving diverse molecular systems, which both compete with and sustain each other.
REQUIREMENT #3 of 4 - CONFIDENCE TO GAUGE FAILURE AND SUCCESS
Molecular species that can successfully coexist with others in the population and the environmental changes they cause are successful responses, which stay in the collective memory. Molecular species that fail are soon replaced by another more successful (good guess) response. The overall process must result in collective actions/reactions that efficiently use and recycle the resources available to multiple molecular species, or else there is an unsustainable chemical reaction, which ends when the reactants have consumed each other, resulting in an environmental crash.
REQUIREMENT #4 of 4 - ABILITY TO TAKE A GUESS
For such a rapidly replicating molecule RNA editing1 type mechanisms can become a significant source of guesses. Also, molecular affinity, which is in part measured by the hydropathy index, will favor assimilation of complimentary ribonucleotides. Where these are in limited abundance the next best fitting molecule may replace them, or cause other changes to its structure, which may work as well or better, for their descendants. This makes it possible for these complex molecules to automatically try something new, when necessary.
Molecular Intelligence
Molecular intelligence (a living thing, life) is emergent from naturally occurring machine-like molecules which together build and maintain cells like we together build and maintain cities. This form of intelligence is sustained by a “replication cycle” that keeps it going through time. Biologically, our thought cycles exist as a brain wave/cycle rhythm but (where physics willing) the system would still work as well by replicating itself (and stored memories) on a regular cycle, as does molecular intelligence. If our brain worked this way then it would replicate/replace itself upon every new thought we have, could this way sustain itself nearly forever. Without cellular intelligence (discussed in next section) to add moment to moment awareness molecular intelligence is at the mercy of the environment, has no way to efficiently forage for food, but they still soon enough can control the planet’s surface/atmospheric chemistry.
Chromosomal subsystems may be separately modeled. The flowchart becomes:
[ ]
Since cells of multicellular organisms can reconfigure even eliminate parts of their genome in order to “differentiate” into many cell types only our germ cells (which produce egg/sperm) would be fully representative of the memory contents of a molecular intelligence system. With all of the memory cycles before the one that made us is included, our molecular intelligence is currently estimated to be over 3.4 billion years old.
REQUIREMENT #1 of 4 - SOMETHING TO CONTROL
In some bacteria and later in time plants, molecular intelligence systems could likely control the Reverse Krebs Cycle (also known as the Reverse TriCarboxylic Acid Cycle (TCA cycle), Reverse Szent-Györgyi–Krebs Cycle or Reverse/Reductive Citric Acid Cycle). This cycle is the center of cellular metabolism, consuming carbon dioxide while providing energy and molecular intermediates that are used to build amino acids and other vital biomolecules needed to sustain its growth.
A dozen or so catalytic molecules form an assembly line that makes an increasing complex molecule from the molecule it started with. Upon completion of the cycle the molecule breaks in half resulting in an additional molecule required for biosynthesis, while the other half is what it started with, which can then go through the cycle all over again. At any stage through the assembly cycle one of the various molecules may be drawn by molecular forces into a nearby biosynthesis reaction. At least part of the Reverse Krebs Cycle can be catalyzed by volcanic clay/dust/mineral in sunlight making it possible that the cycle was once a common feature of planetary chemistry.2 3 Other clay/minerals are useful for the self-assembly of protocells.4
Animals cannot produce their own food and must instead consume plants and their liberated oxygen to run the cycle in the opposite direction to gain food and energy by disassembling what was previously assembled. There is here a balance between the producers (plants) and consumers (animals) which together maintain a relatively constant oxygen level in the atmosphere.
Additional molecular systems which exploit these metabolic cycles could emerge in environments where the cycle already exists as an uncontrolled reaction. If true then we can here predict self-assembly of a precellular starter mechanism that metabolically produces all that is needed to produce a living genome from scratch, instead of a nonliving/nonfunctional genome first needing to establish this metabolic cycle. Where the energy to power the cycle is from sunlight, the system would have already been light sensitive, the first step toward a more complex sense of vision.
Self-assembly and disassembly of cellular organelles is also easily controlled by molecular intelligence. For example, before division of complex cells the nuclear membrane must automatically self-disassemble to allow access to the chromosomes so they can be pulled by spindle fibers to opposite sides. After division of the chromosomes, internal environmental conditions change causing a nuclear membrane to automatically reassemble around each of the two sets so there are then two nuclei inside the cell. With there then being essentially two cells inside one, the outer cell membrane has two nuclei to self-assemble around which causes them to separate so each can go their separate ways.
Coacervates can resemble living cells, and can appear intelligent, but they only demonstrate uncontrolled (non-intelligent) propulsion. They are not even protointelligence (where it is then at least almost intelligent). When molecularly controlled by a “cell” these forces can power spinning flagella motors and other forms of locomotion, but coacervates meet the first requirement only. We can say that coacervates are a twitching body with no brain/intelligence to control it.
Microscopic coacervates5 can be made by adding red-cabbage pH indicator solution with egg yolk that provides membrane forming phospholipid molecules that form vesicles around other components of yolk. Indicator solution is made by slowly adding fresh leaves from a grocery store red-cabbage to around 1/3 pan (around twice the volume of whole head before pulling each leave) of boiling water that should just cover after leaves soften down and lose coloration. Use large basket strainer to remove liquid (can follow with finer mesh as from plastic fabric or stainless steel coffee maker basket), refrigerate. Remaining solids will eventually settle to bottom. For more pure supernatant you can later pour clear liquid into another container, or centrifuge.
REQUIREMENT #2 of 4 – SENSORY ADDRESSED MEMORY
In living things molecular intelligence cycles through time by continual replication of genetic Addressable Memory (chromosomes) where output actions are stored as coded genes (addressed by regulatory elements) that catalyze production of many kinds of proteins that control and maintain the cell. This memory core is always made of RNA or DNA (threadlike crystal) that can be extracted then sequenced.
In a biological memory system data elements include genes that are addressed by one or more species of sensor molecules, which the gene is sensitive to. What is sensed by sensors addresses corresponding data elements that store appropriate action to be taken in response. The Data at that address is coded on the gene that gets turned into a protein molecule able to perform some Action somewhere in the cell. The Addressing turns a gene (or any data location) on or off (or analog value of throttle).
Molecular streams and conveyors of different kinds inside the cell help transport sensor and data molecules to their proper destination. In 3D systems made of matter, many Data locations can be performing Data Actions and all at the same time yet there is plenty of space for Addressing and Data flow to the rest of the circuit.
Duplication of existing memory is how a new memory location is often added to a DNA based RAM system. Single gene duplication is not the only way to increase information in some cases (not normally humans) it is also possible to duplicate a whole chromosome or all of them in the cell one or more times (polyploidy). Duplication of one gene (data element) adds a single functional new Data location to memory, but there can be more than one gene in each duplication event. In all cases there is a more reliable way for memory to increase in size, than random single base insertions and other additions that would just keep scrambling the information already there.
When studying duplication events it becomes important to understand how genes moved to a new location in a chromosome (or to another). Where after replication the strand unwound to occupy the same chromosome territory6 it would have been duplicated to an adjacent strand that ends up in a different place after the chromosome supercoils just before separation to one of two sides of cell. The chromosome later unwinds then starts protein production again. It here important to have a 3D understanding of what the chromosome territories look like when genes are in full production inside the nucleus where there are molecular streams forming genetic circuits, which places genes that otherwise appear to be far apart in close proximity to each other. One or more genes can also be pinched out of a territory, or have other secondary function (such as recall of past experience somehow useful for producing a good-guess) even though it is not used as a protein production gene anymore. Where duplication included a change in gene coding, what produced the change becomes important. We cannot assume they are all random copy errors, where there may be a mechanism that works with experience stored in nearly all of its active and inactive genes it has in memory.
One way of specifically adding a new memory at a given address is homing endonuclease genes (HEGs) that home in on a particular portion of the DNA, inactivate a gene and insert a copy of itself in the deactivated gene. This homing/addressing occurs in the sperm cells, is passed on to successive generations.
Molecularly Addressed regulation sites turn genes on when they are needed, then metabolic pathway molecular feedback turns off before they start overproducing. Replicating additional genes would help it build up levels of mRNA (for manufacture of their respective protein product) faster, but not necessarily change the amount present in the cell because of production rate of each gene being controlled to only produce what is needed. There are then more than enough viable copies to replace ones that may go bad. Not producing anything useful could make it prone to being chemically switched off or eliminated by the epigenetic success gauging part of the mechanism not finding that useful to it anymore.
Chromosomes arrange into a network of independently addressable areas of molecular flow inside themselves called chromosome territories. There is here an organization present that allows each compartment to specialize in a certain gene driven function, a localized form of addressing where there are routes to travel to reach any given address.
REQUIREMENT #3 of 4 - CONFIDENCE TO GAUGE FAILURE AND SUCCESS
In molecular intelligence the confidence levels are gauged as in cybernetics, the interdisciplinary study of the structure of regulatory systems, which includes molecular systems that are required for basic growth and division of cells where most rudimentary confidence levels are as in homeostasis.
Where confidence in conditions being suitable for replication are great enough another replication cycle can be initiated. Or where a dry spell threatens survival, some cells can take evasive action by becoming a spore (seed) with hard watertight shell around the most vital molecular intelligence (only) part of the system. The next level cellular intelligence that once controlled flagella and other motor systems ceases to exist, until conditions improve and its cellular intelligence can again emerge from its molecular intelligence, to once more become a swimming/migrating cell.
REQUIREMENT #4 of 4 - ABILITY TO TAKE A GUESS
Complex forms of molecular intelligence have sensory receptors on their surface membrane for different morphogenetic proteins (substance that evokes differentiation). Interaction of the protein with the receptor initiates a cascade of events that eventually turns on some genes and turns off others, aiding differentiation of the cell into brain, muscle and other unique cells. Successful actions to take in response to environmental conditions are recalled from its RNA/DNA memory. New memories can be formed as in the classic example of the origin of nylonase7 whereby a successful response to environmental chemistry conditions is the result of a good guess that leads to a new action to be taken.
At the molecular intelligence level, good guesses are taken using mechanisms such as crossover exchange, chromosome fusion/fission, duplications, deletions and transpositions (jumping genes) whereby a coded region of DNA data physically moves to another location to effectively change its address location. Information shared by conjugation may possibly include good guesses which are incorporated into its genome. Somatic hypermutation occurs when immune cells are fighting a losing battle with germs. The cell then responds by searching for a solution to the problem by rapidly taking good guesses. This produces new defensive molecules which become attached to their outside, to help grab onto an invader so it can be destroyed.
Although a random guess can at times be better than no guess at all, uncontrolled random change (random mutation) in DNA coding is normally damaging. These are caused by (among other things) x-rays and gamma rays, UV light, smoke and chemical agents. Molecular intelligence systems normally use error correction mechanisms to prevent “random chance” memory changes from occurring. To qualify as a random guess the molecular intelligence system must itself produce them. An exception is where random change/mutation is the only available guess mechanism, which may have been all that existed at the dawn of life, to produce the very first living/intelligent things.
Without some form of good-guess genetic recombination the learning rate of the system would be very low. Offspring would normally be clones of their parents. Therefore a part of the cell cycle often has crossover exchange where entire regions of chromosomes are safely swapped, to produce a new individual response to the environment that should work as well or better. This is a good guess because the molecular intelligence is starting with what it has already learned then tries something new based upon that coded knowledge. This is not randomly mixing coding regions in an uncontrolled genetic scrambling which can easily be fatal.
Regardless of population size a molecular intelligence “gene pool” still relies on single individuals to come up with unique solutions to problems such as digesting nylon, antibiotic resistance and differentiation into new cell morphologies. A gene pool is the combined memory of a "collective intelligence" or more specifically "molecular collective intelligence". By using conjugation to share information, a colony of bacteria (or other cells) can be considered to be a single multicellular organism.
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The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.
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