Thursday, September 6, 2012

PIT VIPERS, VAMPIRE BATS AND 'BIOLOGICAL LEARNING'

In earlier posts, especially the post 'Mutations,' I put forward the notion that there are two aspects to the creation of anything that is functional; the selection or creation of the right material and the creation of the right shape. The inventor of the screwdriver must pick a material that is strong and rigid enough (clay and rubber screwdrivers would be useless), and the screwdriver must have a shape that is both narrow enough in one area to fit into the groove of the screw and of an appropriate shape in another area so that it can be turned by a human hand.  Obviously the material, the wood and the metal, of a screwdriver does not 'cause' the shape of the screwdriver; no more than the shape of the screwdriver 'causes' the wood and the metal to be there.  Both the shape and the material for the screwdriver, and for any other functional creation, were caused by the 'idea' for the screwdriver which materialized in the mind of the screwdriver inventor who 'desired' to find a way to fasten things together and whose idea included screws and a tool for tightening and loosening screws. At least with man made functional objects, things begin with a desire to accomplish a certain task and materialize, at least on a mental level, to an idea, which includes both materials and shape, and may include several components, and then this idea is manifested by actually constructing both screwdrivers and screws. In the same way, electricity, by itself, does not 'cause' there to be Chevy Volts, plastics do not 'cause' Tupperware, and rubber does not 'cause' Kobe Bryant Athletic Shoes.

As silly as all this sounds, this is precisely the thinking in modern biology.  Genes are coded for proteins; and either the genes, (which are materials composed of a string of nucleic acid molecules), or  proteins,(which are materials composed mainly of amino acids), are credited with the creation of the most complex, elaborate and amazingly sophisticated biological apparatus.  Consider the following article which I have  reproduced in part and which appeared in the August 28th, 2012 issue of the New York Times:

                 AS GENES LEARN TRICKS, ANIMAL LIFESTYLES EVOLVE 

"......For the fer-de-lance (a snake) to find its prey in the dark, it ..... relies on infrared sensors.  But that ability, which it shares with a select group of other snakes, was acquired the old-fashioned-way: It was evolved, of course.  And recent understanding of how some snakes and other animals detect infrared light is providing some striking examples of how new lifestyles can evolve when old genes learn some new tricks.
     Closely related to the rattlesnake, the fer-de-lance is also a pit viper, a member of a group of venomous snakes named for the deep sensory pits between the nostrils and eyes.  These specialized pits enable the snakes to detect infrared light in the form of heat.
     Humans and other warm-blooded animals emit heat as infrared radiation. Pit vipers are so adept at infrared sensing that some can detect potential prey a meter away. 
     To understand how snakes evolved their infrared detection systems, a group of scientists led by Prof. David Julius at the University of California, San Francisco, searched for potential infrared sensing proteins in the western diamondback rattlesnakes. They looked in particular at genes active in the nerve cells that are connected to the pits, called trigeminal neurons (the neurons that are prominent on the surface of our human faces are also trigeminal neurons).  
     They found one gene, known as TRPAI, that was 400-fold more active in rattlesnake trigeminal neurons than in other kinds of neurons.  Moreover, they found that the TRPAI gene was not highly active in the trigeminal neurons of snakes lacking pits.  These two pieces of evidence suggested that TRPAI might encode a protein involved in infrared sensing.
......The TRPAI gene encodes a type of receptor protein known as an ion channel.  In humans and other mammals, when the protein is exposed to and binds specific chemicals the channel opens, allowing ions to flow into nerve cells and setting off a sequence of events that produces a nerve impulse.
     In pit vipes, however, Dr. Julius and his collaborators discovered that the TRPAI has evolved to be especially heat-sensitive.  While the receptor is not activated in most snakes by temperatures approaching 37 degrees Celsius (98 degrees Farenheit, our normal body temperature), the western diamondback rattlesnake TRPAI receptor is stimulated around 27 degrees Celsius (80 degrees Farenheit), creating a "thermal image" of the heat source in the snake's brain that is used to aim its strike.  Pit vipers are not the only animals or even the only snakes to have evolved infrared sensing.  Pythons and boas have also evolved heat-sensing pit-organs on their faces, although of a different structure.  Dr. Julius and his team found that TRPAI was also highly expressed in the trigeminal neurons of phython and boa pit organs, about 65-fold and 170-fold higher, respectively, than in the trigeminal neurons of other snakes lacking pits.  Similarly, their TRPAI receptors were 5 to 8 degrees Celsius more heat-sensitive than typical snakes.
     In both groups of snakes, changes in the structure of the TRPAI receptor, and the evolution of very high levels of expression in their sensory pits, endowed the animals with sensitive infrared detectors.
     The large evolutionary distance between pit vipers and pythons and boas indicates that the two groups of snakes separately evolved infrared sensing.  
     But TRPAI is not the only means of infrared sensing.  Dr. Julius's laboratory recently investigated the mechanism of infrared detection in another group of animals so equipped: the infamous vampire bats.  This small group of blood-feeding bats also has sensory pits around the noses that the animals use to locate the warmest areas on the surface of their furry prey, where blood flow is the greatest.  Dr. Julius's team found that the bats had recruited a different ion channel/receptor called TRPVI to become an infrared sensor.
......Both the TRPAI and TRPVI genes are hundreds of millions of years old, having arisen deep in evolutionary history, while vampire bats, pit vipers, and pythons and boas are much younger species.  The histories of these genes and animals, and the repeated invention of infrared sensing, demonstrate how the evolution of new abilities does not necessarily require new genes, but new variations of old genes and new ways of using them."

Now there are a fair amount of biological details in this article and it all sounds very straightforward and 'scientific,' but please bear with me as I try to explain as clearly and simply as I can how so much of it is utter nonsense, precisely of the "plastics creating Tupperware" variety.

  "changes in the structure of the TRPAI receptor, and the evolution of very high levels of expression in their sensory pits, endowed the animals with sensitive infrared detectors."  The reader gets the impression from this that once the TRPAI receptor became more sensitive to heat changes, that, by itself, endowed these animals with infrared detectors.  If  TRPAI and TRPVI receptors are somewhat more sensitive to heat in pit vipers and vampire bats, this does not by any means confer infrared vision to the pit viper or the bat. Let me briefly discuss some of the apparatus involved in infrared vision in the pit viper.


First there are the pits themselves.  They are found on both sides of the face stretching from the nostril to the eye.  They are separated from the rest of the body by a membrane and an air pocket.  This separation keeps the heat generated by the snake itself from interfering with the infrared reception of the external object. Many blood vessels surround the trigeminal neurons of the pits.  These extra vessels allow the neurons to quickly cool off after they are heated up, so that the infrared image does not linger and blur.  There are also domed structures covered with pores which reflect wavelengths other than the infrared which might inadvertently heat the receptors and blur the image.


The trigeminal nerves follow different paths with different sensory pit animals, but they always wind up in the optic tectum of the brain, the same portion of the brain that receives neural stimulation from the eyes also processes these infrared cues.  It is believed that the facial pit acts similarly to a pinhole camera, where the location of the source of thermal radiation is determined by the location of the radiation on the membrane of the pit.  This alone, however, would produce at best a very weak, low resolution image.  It is also believed that some focusing and sharpening of the image occurs in the trigeminal nerve tract and it is possible that the visual and infrared stimulation are integrated to further sharpen the image.  I think that the shape of the pit may also assist in the visualization.  In the same way that we can locate the source of a sound by the slight time differential of when the sound first hits one ear and than the other (sound sources to the right would hit the right ear first); in the same way there may be a slight differential between the right sensory pit heating up and the left, informing the snake that the heat source is on the right.  Also, there may be a time differential between when the most outward neurons of the pit are fired and the neurons in the deepest part of the pit are fired. The closer the heat source was, the shorter that differential would be; so the shape of the pit may help the snake locate the position and distance of the heat source.


To review and also to way, way oversimplify: for a snake to develop an infrared vision system it would have to somehow grow sensory pits with a membrane separating the pits from the snake's body to isolate the snake's body heat from the body heat of the prey that it is visualizing; it would have to develop a complex vascular system to cool off the infrared sensing neurons once heated so that the image of its' prey doesn't linger and blur with the next image as the prey moves; it would have to develop domed structures covered with tiny pores to deflect other wavelengths of the visual spectrum that may inadvertently increase the temperature of the receptors and blur the image; it would have to develop some system of sharpening and focusing the image, either in the trigerminal nerve tract, or by developing a system of using timing differentials in the fired neurons to determine position, distance and movement; and it would have to move the trigerminal nerves located in the area of the snake's face between the nostril and the eye, nerves which in snakes without sensory pits, connect to the thalamus and conduct touch/position and pain/temperature sensations and reconnect them to the optic tectum of the brain where firing patterns are translated into visual images instead of heat and pain sensations; and also it would have to find a way for the TRPAI receptors to become more sensitive to heat so that they would open up ion channels and cause neurons to fire with smaller changes in temperature.


If you think about it further, for all this to occur, major changes in the genetic firing patterns of the snake embryo would have to happen, because the protein material for all these structures of the sensory pits and the extra blood vessels, are manufactured by the firing, transcription and translation of genes.  And this is to say nothing about changing the pathways of the trigerminal nerves and rearranging the real estate of the optic tectum of the brain, and the creation of all these new shapes: the shapes of the sensory pits, the domed structures covering the membranes, the membrane and the air duct, to name a few; all of these structures are not dictated by the genome (remember the author said that the genome had not changed); the genome is merely the list of all the recipes that can be used in the making of the materials for the construction of the body.  Just as in our own body, the same genome produces the material for our legs, eyes, stomachs, our fetal body, infant body, child body and adult body; our brains, kidneys, hearts and intestines.  In the caterpillar the same genome produces an egg, a caterpillar, a pupa and a butterfly.  New structures are determined by the re-arrangement of the firing pattern of genes in the earliest embryonic development during the time when the embryonic cells are mitotically dividing and twisting and turning and folding and unfolding in an impossibly complex way and when genes are being fired, even in the snake embryo, billions, if not trillions of times every day.  And all of this is somehow (and please don't ask biologists about this, because they don't have the faintest idea) perfectly coordinated and synchronized with a technical precision that our finest hi tech equipment cannot even approach.  And all of that, may I remind you, creates the delivery system for all the right materials to be in exactly the right place at the right time.  It does not determine, in any way, how all these materials are shaped to bring this amazingly complex assortment of proteins and sugars and fats into the shapes and shapes within shapes and shapes within shapes within shapes that make up a snake embryo.


So how is all this accomplished? Is it done by "genes learning new tricks"?  Let's get serious for a moment.  Genes do not learn new tricks.  Genes do not remember old tricks.  Genes do not perform  tricks period.  The genes, themselves, are just not tricky.  They are strands of nucleic acid molecules which sit passively in the nucleus of cells until a protein molecule binds with another nucleic acid molecule near the gene and causes the strand of molecules to separate from the other strand which it is attached to; and then it passively allows itself to be copied by mRNA polmerase and then, at the behest of another molecule, returns to its original position alongside its companion strand.  That's what genes do.  Oh, yes, they also replicate themselves which is also done passively as part of a cell's mitotic division and at the behest of protein molecules entering the nucleus from the surrounding cytoplasm of the cell.  They don't think; they don't perform tricks; they are simply recipes for proteins which the body (but not the body, by itself) uses in a multitude of ways to build all the amazing structures of living beings including people and pit vipers.


"the bats had recruited a different ion channel/receptor called TRPVI to become an infrared sensor." This is yet another mindless and perfectly scientifically acceptable way of talking about the creation of life and all its wondrous complexity.  The bats themselves did it.  Really?  Do you think it was an individual bat or did a group of them get together to decide which ion channel/receptor to recruit? And did they decide on how to change the original ion/channel receptor to become more heat sensitive?  Did the bats, themselves, make the changes in the amino acid structure of the TRPVI protein because they wanted it to be more heat sensitive?   Aren't we supposed to be more intelligent than bats?  Which ion channel receptor would you recruit if you decided you wanted infra-red night vision?  And then, once you decided which one to use, how would you go about implementing this decision?  We hear this nonsense all the time.  "It took the (fill in the species) .........million of years to learn how to (fly, have infrared vision, walk upright, etc.)  Do we learn anything about our own biology?  Yes, if we take biology classes.  But there was a whole lot of evolving of living organisms before there were biology classes, wasn't there?  And even if you take biology classes, even if you took every biology class that was ever offered, how would you begin to, in the most minute way, alter the structure or organization of your own biological functioning?  The truth is that animals know absolutely nothing about their biology, learn absolutely nothing about their biology, and  have no way of changing it if they did learn. We are the recipients, and until the advent of Victorian Darwinian thinking, the grateful recipients of a body that allows us to survive and that is our servant in that it allows us to do whatever it is that we want to do.  It is the servant of our desires, and it has a fantastically complex, transcendentally complex, gloriously complex system of biological apparatus that allows us to stay alive and continue to have desires. Notice I said desires, not needs.  Animals don't have the faintest idea what their needs are.  That is something that biologists and researchers determine.  Animals have sets of desires, so they eat what they want to eat and when they want to eat, they sleep when they want to sleep and where they want to sleep, they drink what they want to drink and when they want to drink, they stop doing something when they feel pain, they continue doing something when they feel pleasure, and they have sex, usually with a member of the opposite sex but the same species, when they are horny, and in this way (thanks to you know who) they survive and their species manages to survive.  But to say that animals "learn" to do anything that has to do with changing their biological structures is idiotic no matter how many advanced degrees the person has who is spouting this nonsense.


So did they do it "the old-fashioned-way"?  Was all this "....evolved, of course."  I tell you this whole business of saying that "it was evolved, of course", or, "it just evolved that way," is the most shallow, mind numbing, idiotic, conversation stopping, thought stopping thing that anyone can say in our society.  It is a killer of curiousity and of any deep reflection into the meaning of life or the pursuit of self-knowledge. And it finds its way into the 'thinking' or 'non-thinking' of every modern biologist.  Everything I described so far about the infrared visualization system, and I described it in it's barest essentials, is needed in order for the system to work.  If the nerves were not somehow separated from the thalamus in the brain and connected to the optic tectum, there would be no visualization.  If there were no membrane and air duct separating the sensory pits from the snakes own body heat, there would be no vision.  If there were no extra blood supply to cool off the heated neurons, there would be no vision.  If the TRPAI receptors did not fire at subtle temperature changes there would be no vision.  If there were not domed structures adhering to the pit membrane to ward off unwanted heat from other frequencies, there would be no vision.  So how in the world was this gradually 'evolved', which is a process, as I understand it, that takes at least hundreds of thousands of years of gradual changes as copying accidents in the replication of genes accumulate in the most amazing, jaw droppingly fortuitous way, to eventually produce a working infrared visualization system?  First of all, what happens to all those snakes who, for those hundreds of thousands of years do not have working visualization systems, but have partially 'evolved' systems; in other words, systems that don't work?  How does this jibe with Darwin's notion that evolution proceeds advantageous mutation by advantageous mutation.  What would be advantageous about having a trigeminal nerve that was migrating from the thalamus to the optic tectum and no longer responded to a rise in temperature either by heat or by a visualization?  What would be advantageous about a half built and non-working dome, about a half built blood supply that was en route to the sensory pit area (also under construction) but hadn't gotten there yet.  What possible advantage would any organism have supplying blood and using energy to sustain all these half built and non-functional systems?  Wouldn't these 'partially-evolved snakes with non-working infra-red sensing equipment' be naturally selected out by the more efficient snakes that weren't diverting their energy into building all this, for the moment, useless equipment? It's so ludicrous.  And, as I said earlier, genes are associated with shapes but they do not 'cause' shapes. To say that a strand of nucleotides causes any shape, besides the shape of the one protein that they produce, never mind the incredibly complex, interrelated and synchronous shapes of sensory pits, membranes, vascular systems, light reflecting domes, and re-arrangement of nerves and optic tectums, is actually more ridiculous than saying that electricity 'causes' Chevy Volts.


And, what the author said in the beginning of the Times article was that there was no change in genes; that the pit vipers had the same genes as other rattle snakes, it was just that these old genes were learning new tricks. If the only "trick it was learning" was to have a  more heat sensitive TRPAi gene, 
then that pit viper would have a stronger reaction to heat, a reaction that it clearly does not want in the hot desert climates that it finds itself in.  It is only when the trigeminal nerve gets rerouted away from the thalamus and to the optic tectum, and all the various shapes are developed that I mentioned above, that anything happens regarding heat sensitive vision. 


Since every animal that is a product of sexual reproduction receives two sets of genes, one from the father and one from the mother, and each animal is a mixture of these two sets, then, every individual within a species has somewhat different equipment than the other members of that species.  As Darwin observed, some members of a species are better able to function, live to adulthood and have progeny than others, so that, over time, some traits become more dominant and, within the same species, necks may get longer, teeth may get sharper, coloration may change, etc.  But these within species changes of traits has nothing to do with structural changes, or the development of whole new organs, the reapportionment of the real estate of the brain and the reorganization of entire  skeletal, nervous, digestive, sensory or locomotive systems.


Also, it has been noticed that copying mistakes in the replication of genes can cause a change in the quality of life of the offspring and it has been proposed that as these changes accumulate over time, whole new species develop.  There is absolutely no proof of copying mistakes causing structural improvements or any kind or structural innovation in any species..  Again, genes are the recipes for materials, not shapes.  To understand the confusion regarding these supposedly fortuitous mutations, you have to keep in mind that the body is not only a factory that produces chemicals, but the body, or the genes, or "something" actually grows the factory (the process from a fertilized egg to an adult).  Scientists study changes in the chemicals made in the adult body; enzymes, which are used by the body in digestive fluids and in the bloodstream.  These proteins are not part of the structure of the body, but do their work as individual molecules moving through the body fluids.  A mutation in a gene that manufactures one of these enzymes could cause an advantage or a disadvantage to an organism's ability to digest certain foods and to ward off or become more vulnerable to microbial invaders.  But this has nothing to do with the exponentially more complicated firing of genes used in the structure, in the building and shaping of the body.  Any mutation in those genes, which are fired in transcendentally complex sequences and which manufacture proteins that work in concert with multitudes of other protein molecules and with the brain and nervous system, would be deleterious, if not fatal, to the functioning of the whole system.



  "The large evolutionary distance between pit vipers and pythons and boas indicates that the two groups of snakes separately evolved infrared sensing."  So we are to believe that this process, this 'evolution' of infrared sensing, involving pits, membranes, relocation of nerves, extra blood supply, etc., happened not just once randomly, but twice.  In fact, as the author states, it happened thrice and not even in snakes, but in rodents, "the infamous vampire bats also have sensory pits around the noses that the animals use to locate the warmest areas on the surface of their furry prey, where blood flow is the greatest."  Maybe you see it differently, and if you do, please let me know, but does it really make any sense to think that this ridiculously freaky occurence of the right sequence of thousands upon thousands of genetic copying accidents, which do not even cause new 'shapes' anyway, occured randomly at least three separate times,winding up with all this amazingly precise, amazingly complex and amazingly synchronized equipment? Doesn't it make so much more sense to realize that infrared sensing using sensory pits, ion channel proteins and trigeminal neurons is an idea that is adapted somewhat differently in different animals, in the same way that the human idea of a wheel appears in different sizes and different materials in a variety of different machines?

When the author says it "evolved, of course," what he is really saying is that it happened randomly, accidentally, without the involvement of any intelligence.  But he is saying that by rote, because that is what he has been taught, because that is what he has come to believe, with no real  explanation of how it ever could have happened randomly, even once, no less three separate times.

Our bodies, brains and nervous systems are created from a series of ideas.  Yes, life forms within species adapted as environments changed.  This system of adaptation (the mixing of genes in sexual reproduction) and the amazingly complex and accurate system of gene swapping in microbes, are also ideas, ideas to assist in the survival of a species. The genome is the list of materials (actually the list of the recipes for the materials) that an organism has available to it, to form all the various structures it needs.  The firing pattern of the genes is the delivery system to get all those materials to the exact place and at the exact time that they need to be there.  The shaping of these materials into these biological structures is done by a communication of ideas directly from the cosmic consciousness, from divine intelligence, in the form of energy templates, or astral bodies, which the protein molecules of the growing organism fill out (I understand that this seems very far out and is explained in more detail in other posts, but the shaping of the body and all its various structures is not the only evidence of transcendent and omnipresent intelligence in the universe.  Please read more of this blog.)


In the development of different species which evolutionary geneticists diligently study and endlessly argue about, when they track the historic appearance of various genes, they are really tracking the point in time when the available genome of an existing organism did not provide all the materials necessary for the construction of the next idea; so that the existing genome had to be rearranged, a new sequence of nucleotides had to be inserted, a new system of firing this new gene, transcribing this new gene, translating this new gene, delivering this new gene where it needs to go, integrating the new material manufactured by this new recipe (gene) into not only a new structure, but into perhaps several new structures, a new system of maintaining and controlling this new structure by a new system of nerves and new connections to the brain, a new system of supplying nutrients and removing wastes from this structure, by reconfiguring and adding to the circulation system, all of that had to take place and take place in concert with one and other.  That doesn't mean that everything necessarily happened in one generation.  It may have taken several generations for this idea to be introduced in a gradual way, because no matter what changes were introduced, they had to be gradual enough to insure the survival of the organism which was the recipient of all this change.  This changed organism also needed to develop new feeding patterns, defending patterns, hunting patterns, maintain its equilibrium and locomotion, etc.  It needed to still be connected and guided by its parents or colony and not be so far along that it could not understand them or that they could not understand it.  That means that the history of the origin of species happened gradually but much more abruptly, in spurts, rather than the endless slog of random mutation by random mutation, as Darwinists contend. And that is exactly what biological history indicates:  The sudden appearance of microbes; the sudden appearance of eukaryotic cells, of multi-cellular organisms, of oxygen metabolizing organisms, of creatures with skeletons; the sudden appearance of all the basic body forms and structures that we see here today in the Cambrian explosion; all of this points to evolution as an introduction of ideas, but only when environmental conditions on this planet (temperature, atmosphere, earth's magnetic field, availability of oxygen and phosphorous, necessary food sources, etc.) were ready for the introduction of  more complex ideas.


Also, the appearance of almost identical structures in different organisms, whose genetic make-up is different, whose embryology is different, and whose entire method of biological construction is different, even though the final result is almost identical, doesn't that also give very strong evidence that these structures are ideas; ideas that were applied to different organisms with different body plans and different genomes, in the same way that wheels or levers or screws (all human ideas) appear in a wide variety of materials in a wide variety of uses throughout the world of man made machines?


To say that something "evolved, of course,"is a way of deluding yourself into thinking that you know how something happened when you don't.  It is a way of removing wonder and gratitude and replacing it with a smug feeling of satisfaction, that if I don't know how it happened then "they" (scientists) know how it happened ("they" don't know either).  I don't know how it happened, and I know I don't know how it happened, but  I appreciate the wondrousness of it; I appreciate the transcendent intelligence that had to be employed in the construction of this world, both inanimate and biological; and I appreciate your patience in reading this post.


Your comments are always welcome.


 





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