SCROOGE McDUCK, FOLDING NUCLEOTIDES AND 'JUNK DNA'

Here is a quote from a post that I wrote more than five years ago,

"At the moment, the great majority of the three billion nucleotides that make up the DNA in each and every one of the one hundred trillion cells of your body, is considered to be 'junk' DNA, because scientists have not, as yet, found a use for it.  It is considered to probably be a vestige of centuries and centuries of evolutionary mistakes.  Knowing that God is neither wasteful nor frivolous, and that there were really no evolutionary mistakes, (we humans, just celebrating our perhaps one hundred thousandth birthday on this planet, have the audacity to consider the dinosaur, who thrived here for one hundred sixty million years, to be an evolutionary mistake); that, in some way, the quality of our existence today, is built on the knowledge gained, the materials created and the progeny produced by all that preceded us; I suggest that there is a yet to be discovered purpose to each and every one of those three billion nucleotides and to the manner in which they are folded into the nucleus of each of our one hundred trillion cells."

What follows is an article from the New York Times that I came upon last week:

Bits of Mystery DNA, Far From ‘Junk,’ Play Crucial Role

By Gina Kolata

Published: September 5, 2012

Among the many mysteries of human biology is why complex diseases like diabetes, high blood pressure and psychiatric disorders are so difficult to predict and, often, to treat. An equally perplexing puzzle is why one individual gets a disease like cancer or depression, while an identical twin remains perfectly healthy.Now scientists have discovered a vital clue to unraveling these riddles. The human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as “junk” but that turn out to play critical roles in controlling how cells, organs and other tissues behave. The discovery, considered a major medical and scientific breakthrough, has enormous implications for human health because many complex diseases appear to be caused by tiny changes in hundreds of gene switches.

The findings, which are the fruit of an immense federal project involving 440 scientists from 32 laboratories around the world, will have immediate applications for understanding how alterations in the non-gene parts of DNA contribute to human diseases, which may in turn lead to new drugs. They can also help explain how the environment can affect disease risk. In the case of identical twins, small changes in environmental exposure can slightly alter gene switches, with the result that one twin gets a disease and the other does not.

As scientists delved into the “junk” — parts of the DNA that are not actual genes containing instructions for proteins — they discovered a complex system that controls genes. At least 80 percent of this DNA is active and needed. The result of the work is an annotated road map of much of this DNA, noting what it is doing and how. It includes the system of switches that, acting like dimmer switches for lights, control which genes are used in a cell and when they are used, and determine, for instance, whether a cell becomes a liver cell or a neuron.

“It’s Google Maps,” said Eric Lander, president of the Broad Institute, a joint research endeavor of Harvard and the Massachusetts Institute of Technology. In contrast, the project’s predecessor, the Human Genome Project, which determined the entire sequence of human DNA, “was like getting a picture of Earth from space,” he said. “It doesn’t tell you where the roads are, it doesn’t tell you what traffic is like at what time of the day, it doesn’t tell you where the good restaurants are, or the hospitals or the cities or the rivers.”

The new result “is a stunning resource,” said Dr. Lander, who was not involved in the research that produced it but was a leader in the Human Genome Project. “My head explodes at the amount of data.”

The discoveries were published on Wednesday in six papers in the journal Nature and in 24 papers in Genome Research and Genome Biology. In addition, The Journal of Biological Chemistry is publishing six review articles, and Science is publishing yet another article.

Human DNA is “a lot more active than we expected, and there are a lot more things happening than we expected,” said Ewan Birney of the European Molecular Biology Laboratory-European Bioinformatics Institute, a lead researcher on the project.

In one of the Nature papers, researchers link the gene switches to a range of human diseases — multiple sclerosis, lupus, rheumatoid arthritis, Crohn’s disease, celiac disease — and even to traits like height. In large studies over the past decade, scientists found that minor changes in human DNA sequences increase the risk that a person will get those diseases. But those changes were in the junk, now often referred to as the dark matter — they were not changes in genes — and their significance was not clear. The new analysis reveals that a great many of those changes alter gene switches and are highly significant.

“Most of the changes that affect disease don’t lie in the genes themselves; they lie in the switches,” said Michael Snyder, a Stanford University researcher for the project, called Encode, for Encyclopedia of DNA Elements.

And that, said Dr. Bradley Bernstein, an Encode researcher at Massachusetts General Hospital, “is a really big deal.” He added, “I don’t think anyone predicted that would be the case.”

The discoveries also can reveal which genetic changes are important in cancer, and why. As they began determining the DNA sequences of cancer cells, researchers realized that most of the thousands of DNA changes in cancer cells were not in genes; they were in the dark matter. The challenge is to figure out which of those changes are driving the cancer’s growth.

“These papers are very significant,” said Dr. Mark A. Rubin, a prostate cancer genomics researcher at Weill Cornell Medical College. Dr. Rubin, who was not part of the Encode project, added, “They will definitely have an impact on our medical research on cancer.”

In prostate cancer, for example, his group found mutations in important genes that are not readily attacked by drugs. But Encode, by showing which regions of the dark matter control those genes, gives another way to attack them: target those controlling switches.

Dr. Rubin, who also used the Google Maps analogy, explained: “Now you can follow the roads and see the traffic circulation. That’s exactly the same way we will use these data in cancer research.” Encode provides a road map with traffic patterns for alternate ways to go after cancer genes, he said.

Dr. Bernstein said, “This is a resource, like the human genome, that will drive science forward.”

The system, though, is stunningly complex, with many redundancies. Just the idea of so many switches was almost incomprehensible, Dr. Bernstein said.

There also is a sort of DNA wiring system that is almost inconceivably intricate.

“It is like opening a wiring closet and seeing a hairball of wires,” said Mark Gerstein, an Encode researcher from Yale. “We tried to unravel this hairball and make it interpretable.”

There is another sort of hairball as well: the complex three-dimensional structure of DNA. Human DNA is such a long strand — about 10 feet of DNA stuffed into a microscopic nucleus of a cell — that it fits only because it is tightly wound and coiled around itself. When they looked at the three-dimensional structure — the hairball — Encode researchers discovered that small segments of dark-matter DNA are often quite close to genes they control. In the past, when they analyzed only the uncoiled length of DNA, those controlling regions appeared to be far from the genes they affect.

The project began in 2003, as researchers began to appreciate how little they knew about human DNA. In recent years, some began to find switches in the 99 percent of human DNA that is not genes, but they could not fully characterize or explain what a vast majority of it was doing.

The thought before the start of the project, said Thomas Gingeras, an Encode researcher from Cold Spring Harbor Laboratory, was that only 5 to 10 percent of the DNA in a human being was actually being used.

The big surprise was not only that almost all of the DNA is used but also that a large proportion of it is gene switches. Before Encode, said Dr. John Stamatoyannopoulos, a University of Washington scientist who was part of the project, “if you had said half of the genome and probably more has instructions for turning genes on and off, I don’t think people would have believed you.”

By the time the National Human Genome Research Institute, part of the National Institutes of Health, embarked on Encode, major advances in DNA sequencing and computational biology had made it conceivable to try to understand the dark matter of human DNA. Even so, the analysis was daunting — the researchers generated 15 trillion bytes of raw data. Analyzing the data required the equivalent of more than 300 years of computer time.

Just organizing the researchers and coordinating the work was a huge undertaking. Dr. Gerstein, one of the project’s leaders, has produced a diagram of the authors with their connections to one another. It looks nearly as complicated as the wiring diagram for the human DNA switches. Now that part of the work is done, and the hundreds of authors have written their papers.

“There is literally a flotilla of papers,” Dr. Gerstein said. But, he added, more work has yet to be done — there are still parts of the genome that have not been figured out.

That, though, is for the next stage of Encode.

This article is written from the perspective of research

scientists and it has an emotionally mixed message.  On 

the one hand there is a certain excitement that this huge 

new source of possibly helpful information is now 

available, and on the other hand there is a sense of 

frustration.  It's like they thought they almost had their 

arms around this monster (the human genome) and now 

they find the problem is thousands, perhaps millions, of 

times more complicated than they had originally thought.


I remember reading a comic when I was a kid which 

featured Scrooge McDuck.  If you don't remember, Scrooge

was Donald Duck's impossibly rich and incredibly stingy 

uncle.  One day Scrooge heard some noise from the street 

in front of his mansion.  A parade was in progress hailing 

some sultan as 'the richest man in the world."  After the 

parade,  they installed a large marble statue of the sultan in 

the town park on a pedestal on which was carved "the 

richest man in the world."  Now Scrooge took great offense 

at this (although why he should have, being a duck, did not 

occur to me at the time I first read it), so Scrooge quickly

built a much larger statue right near the sultan's proclaiming 

Scrooge McDuck as "the richest man in the world." Of

course the sultan responded with an even larger statue; 

McDuck built a silver statue; the sultan built a gold statue;

McDuck, a platinum statue, and so on, and so forth.  In the 

end the poor sultan dressed solely in a barrel (if you are too

young to remember, wearing only a barrel was a symbol of 

abject poverty dating back to the Depression Era), the 

sultan came knocking on Scrooge McDuck's door and was 

let in to a huge vault, the size of an Olympic swimming 

pool, that had merely a few piles of coins lying about.  

"Ah, ha," exclaimed the sultan, leaping for joy, "so you're 

broke, too!" "Don't be ridiculous," responded Scrooge 

McDuck, "this is only my petty cash vault," and he led the 

sultan through another door at the far end of this vault 

into a chamber the size of a football stadium where there 

were literally acres of cash and gold coins piled to the 

ceiling.


The sultan was dressed down for his arrogance in thinking 

that he had more money than any one in the world, when 

he had merely a fraction of McDuck's fortune.  What of the 

arrogance of evolutionary theorists who are constantly 

trying to 'simplify' the creation of life and the  

transcendent complexity of living organisms so that it can 

fit into their sad little theory of life being the outcome of 

a linear series of random replication 'mistakes?'  Darwin, 

without any modern optic technology available to him, 

thought that a cell, and therefore a single celled creature, 

which he considered to be the beginning of life, was an 

undifferentiated sac of albumen. 


Are you aware of the complexity of a living cell? Of a single 

celled creature, which has a genetic system and

which transcribes, translates its genetic code and which 

folds and manufactures and delivers the resultant proteins 

with the same precision that we do ours? Which senses its 

environment, has a way of distinguishing what is to be 

approached and eaten from what is to be avoided? Which

digests food, eliminates wastes, has a complete metabolic 

system that makes all these processes possible, replicates, 

and grows, and has a gene sharing system which is 

available to it when necessary and is so wondrously 

complex that it rivals anything that we humans accomplish 

biologically today (please read my posts 'Wonder' and 

'Evolution'), and which has, within its membranes,

thousands upon thousands of protein molecules, molecules

which this cell manufactured itself, each and every one of

which is, itself, a high tech, biological machine whose 

precisely engineered shape, precise pattern of charges, 

and precisely arranged chemical components allows it to 

do an absolutely specific task necessary to the survival of 

the cell.


And this, according to all geological evidence, was the very 

'simple' beginning of life, that Darwinists refer to, and 

occurred at the moment that the surface of the planet was

cool enough (below the temperature of boiling water) to 

sustain microbial life. There is no evidence whatsoever of 

so-called pre-biotic pools of organic matter slowly 

accumulating over millions of years to form such a cell. 

How could organic matter accumulate into this 

synchronized complexity?  In fact, there are no traces  of 

organic matter at all prior to these four billion year old 

traces of microbes. How could there be? In the boiling 

hot, meteor bombarded, tornado infested environment of early earth,

organic material would last no longer than it would take to

boil an egg (a raw egg, by the way, is precisely that, 

unprotected organic matter).  Even in our much more stable 

environment, organic matter of all life is protected from the 

elements by membranes and systems to control internal 

temperature and nutrient and water levels.


This is the same community that celebrated when it was 

discovered that only three thousand stretches of nucleotides 

were actual genes and which was eager to pronounce the

rest, close to three billion nucleotides, 'junk.'  Their theory is 

laughably inadequate to explain the complexity of life as we

know it, and much more inadequate to explain the 

complexity of life as 'they' know it.  This is why, I believe,

this amazing complexity is not taught in basic biology 

classes.  It is not hard to understand.  You can get it simply 

by knowing the number of molecules, and the precision of 

these processes, without having to memorize all the 

thousands of names that researchers have assigned to 

every chemical and organelle involved. The problem is not

that it is difficult to grasp, but that  it is wondrous, and 

evolutionary biologists who are committed to the idea that

everything about living organisms including their origin is

explainable by simple scientific laws and by the slow but 

random accumulation of accidents, do not want students to

feel overwhelmed, wondrous or awestruck by the 

transendent complexity of their own bodies......Too bad!

It was this community that announced with glee that they 

had found God and God was the genetic code; that the 

code consisted of only three thousands strands of 

nucleotides among the three billion found in each cell, and 

that as soon as they had figured out the sequencing of the 

human genome, they would complete their understanding of

the mechanics of life.  Sorry, my neo-Darwinist friends, you

thought you had found God, but you had only found his 

petty cash drawer.  Yes, the genetic system is magnificently

complex and magnificently coordinated; but the timing

system of the firing of those genes is exponentially more

so. Every different organ of your body, every different

organelle within each cell, every stage of development from

a fertilized ovum to an adult, is dependent on this firing 

system; not just on the genes, but on which genes are fired 

and when they are fired.


When scientists study the firing of genes they look at an

adult organism and study all the stimuli that are responded 

to by gene firing which leads to enzyme production.  We eat

something, or we do a physically demanding task, or we 

experience a big drop or rise in temperature.  These stimuli 

trigger a whole series of reactions which lead to a 'trigger' 

molecule bonding with a nucleic acid molecule within the

nucleus of the cell leading to transcription, translation,

protein folding,and protein delivery.  A system that is very

complex, absolutely precise and brilliantly constructed.  But 

all this pales compared to the firing of genes involved in the 

development of an organism from fertilized egg to new born.  

In this process billions of genes are fired every day in 

absolutely precise and coordinated sequences.  It is so 

impossibly complex that researchers dare not even 

approach it. 



So let's look again at the information uncovered in this 

article. There are three billion nucleotides folded, or coiled in 

each cell in the body.  There are one hundred trillion cells.

When the DNA strand of each single cell is unspooled that 

will yield an impossibly thin string (only a few atoms wide) 

that is, according to the above article, ten feet long.  I had 

previously heard that the strand was about a meter long. In 

that same article it said that if all the strands from every cell 

in a human body, in your body, were arranged end to end,

 that would create a strand that would stretch to the sun (not 

the moon) and back.  If, indeed, each individual cellular 

segment is ten feet rather than a meter, that would make

the accumulated length long enough to stretch to the sun

and back three times. That would be 558 million miles of

nucleotides, or, going in the other direction, a strand that

would stretch past Jupiter and half way to Saturn.

Understand, I am not talking about the accumulated DNA of 

humanity, which would be seven billion times as long (or 

slightly less than seven hundred thousand light years), but

just the DNA strands in your own individual body.  


Now I knew that the strands were coiled differently in

different cells. Why?  The protein 'trigger' molecule must 

find the right nucleotide to bind to in order to begin the 

process of transcription.  The ten foot strand of three billion

nucleotides have to be coiled so tightly that  there is still

room within the nucleus for the trigger molecules to float

around in the nuclear fluid. However, because of the 

tightness of the coil, only a small percentage of the genes 

and their triggers are accessible.  In, for instance, cells of 

the adrenal glands, the genes that carry the code for 

adrenal cortical hormone must be easily accessed.  In 

salivary glands, the genes for salivary enzyme must be 

accessible.  Each type of cell has its own special function

and manufactures a particular set of proteins unique to that

type; so the DNA must be folded in a way that makes all 

the genes and all the trigger nucleotides for the genes that

are commonly manufactured by that cell easily accessible

to the trigger protein molecules for those genes. There are

over two thousand types of cells; therefore there are at 

least two thousand different folding patterns.  Further

research may discover that the folding patterns may be

more specialized than that, and may be related not just to 

the specific type of cell, but to it's location in the body and 

the unique genetic demands that are made on that particular 

cell.


What I didn't realize, that I learned from this article, is that 

the triggers for certain genes may be thousands or even 

millions of nucleotides away from the actual gene, but 

because of the way the strand is folded, that trigger winds

up, although on a different portion of the strand, right next

to, or even abutting the gene.  That means that these, at 

least two thousand different folding patterns of, I remind 

you, three billion nucleotides, is so specific that the triggers

found perhaps several feet from the gene, wind up, after 

the coiling, right next to or abutting the gene; and they must 

abut the gene or the whole transcription process could not 

move forward.


What kind of a task would that be, to precisely fold one 

hundred trillion sets of three billion nucleotides?  If we 

assigned every person on the planet, say seven billion 

people, to work on this task, and we blew up the nucleotide 

strand several thousand times so that it was a size that

people could see, say the thickness of a pearl necklace 

with each nucleotide being a pearl, and since there are four 

different types of nucleotides that make up DNA, let's say

the pearls come in four different colors, white, black, pink 

and grey; then each person on the earth  would be given 

fifteen thousand necklaces (their one seven billionth share 

of the one hundred trillion strands found in each of the one 

hundred trillion cells of your body) each three billion pearls 

long.  Do you think that each person ,if there were room on 

the surface of the earth for all these enormous pearl 

strands, which there would not be (if the pearls measured 

fifty pearls per foot, then each of the fifteen thousand 

strands for each of the seven billion people on earth would

be over eleven thousand miles long!), do you think that

anyone would be able to fold fifteen thousand three billion 

pearl necklaces in an absolutely precise folding pattern if 

they devoted their entire lives to the endeavor?  Of course 

not.  They would have to fold one entire three billion pearl

necklace, an eleven thousand mile strand, each day for

forty-five years. I don't see how they could accomplish the 

precise folding of one necklace in a lifetime. And I remind 

you that these fifteen thousand strands, each eleven 

thousand miles long for every one of the seven billion people 

on this planet, represents the DNA folding, not for all of 

humanity, but just for one person, for you.


And that is just the physical impossibility of the task.  What 

of the precision?  Don't forget, the three billion pearl strand

has to wind up with exactly the right sequences on the 

outside of the coil to provide access to the right genes and

the right trigger molecules.  The folding must be absolutely 

precise, otherwise, when the strand gets folded over and 

over again the necessary sequences of gene pearls and

trigger pearls will wind up in the wrong place.  So no human 

could undertake such an endeavor without a plan, a design,

to follow; and you could imagine how complicated a plan for

folding a strand of three billion pearls, or nucleotides, or 

anything, would be.  So where is this plan?  It must be 

there.  Three billion nucleotides don't just fall into the exactly

right patterns of folds and turns randomly; and what over 

arching level of organization is there that distributes at least 

two thousand different folding patterns among the one 

hundred trillion developing cells?   There must be a 

guidance and that guidance must originate in a non-physical

idea and then materialize either directly into these different 

patterns, or into an intermediate, or astral, body of just 

positive and negative, or yin and yang energies, which 

guides the strands into place.


How could a spiritual idea simply manifest into something

physical? I can't explain it but I can point to a corresponding 

process where a spiritual, or non-physical idea or desire 

manifests into something physical. Every time you want to 

do something, that wanting, which is a non-physical, non-

measurable experience, the precise  thousands upon 

thousands of neurons  are fired, which begin a cascade of 

processes that winds up with you actually doing what you 

wanted to do. In the same way that human behavior and 

human creativity begin with a desire or an idea which is then

materialized; living beings, themselves, are the 

materialization of an idea which comes from a transcendent 

intelligence.


We all begin, at least all our equipment, our biological

apparatus, begins, from that one fertilized ovum.  The DNA 

in that ovum is folded in only one way.  As the genes 

mitotically divide so that that one egg becomes hundreds,

then thousands, then millions of different cells, what is the

governing principle behind the two thousand different 

foldings of the DNA?  Could the DNA, itself, be governing 

this?  Of course not.  DNA has to do with material, not 

shape.  Basically the same material that is in your arm

bone, is also in your  ribs and the bones of your big toes. 

How are the shapes of the 206 different bones of your body

determined?  It's the same material, made not only from 

the same genome, but from the same specific genes of that

genome.  The whole genetic system including the 

unfathomably complex firing system is the system by which

all the building materials get to exactly where they need to

be at the time they are needed during the development of 

the embryo.  How all that material is shaped into the bones

and eyes and hearts and livers and organelles within the 

cells, and blood vessels, and neurons and villi and sweat

glands, etc., etc., etc., is beyond the province of the genes.

So, by the way, is the amazing pattern of foldings, 

involutions, convolutions, twists and turns of the entire 

embryonic mass as it begins to develop.  Yes, each species 

goes through its own particular set of embryonic 

gymnastics, so that an ovum with a human genome will go 

through its own special set of acrobatics, and a chicken egg 

will go through its very different set.  These acrobatics then,

crucial to the entire shaping of the adult body, are related 

to the particular genome, but how could anyone say they 

were caused by that genome?


Isn't the fact that the genome is folded into two thousand 

utterly precise and different patterns in each of the one 

hundred trillion cells of our bodies, clear proof that there is a

higher level of organization to the human body, or any living 

body, than the genes themselves?  Isn't it so clear from this 

that the material of a living body does not cause the shape 

of that body; anymore than the shape of the body causes 

the material within it?  Isn't it obvious that both the shape

and the material originate and are caused by an idea, an

idea that comes from the cosmic consciousness, from the 

Godhead, from the mind of God, or from whatever you want

to call it; but from something that transcends both material 

and shapes, something that is spiritual and that far, far 

surpasses in its ability to conceive and create, both human

intelligence and human technology?


I wish ENCODE the best of luck.  I hope they make 

discoveries that will cure a thousand diseases.  I hope they 

all win Nobel Prizes and make billions of dollars for their

respective pharmaceutical companies.  For me, what is

most wonderful about these discoveries, is how it reveals 

the utterly amazing biological equipment that we all share, 

the transcendent brilliance and technological mastery of the 

creator of this equipment, and the increasing clarity with 

each new discovery of modern research, of how laughably 

inadequate our pathetic little evolutionary theory of 

sequences of random replication errors is to explain the 

true majesty and brilliance of living organisms.



Please comment!    

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.