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Saturday, December 11, 2010

The thinking of the made CREATIONIST. I challenge Darwinists to step up and be scientists rather than priests

"That pretty well sums up what Darwinism has become.   A bunch of religious zealots pathetically seeking for the impossible because the plausible evidence for a Creator God is distasteful to them." - Radar


As the non-creationist information theorist Hubert Yockey observed over 30 years ago (and he has not revised his opinion since):
Research on the origin of life seems to be unique in that the conclusion has already been authoritatively accepted … . What remains to be done is to find the scenarios which describe the detailed mechanisms and processes by which this happened.
One must conclude that, contrary to the established and current wisdom a scenario describing the genesis of life on earth by chance and natural causes which can be accepted on the basis of fact and not faith has not yet been written.’

Reference

Yockey, H.P., A calculation of the probability of spontaneous biogenesis by information theory, Journal of Theoretical Biology, 67:377–398, 1977; quotes from pp. 379, 396.

 Chloe at full gallop

I had to listen to Derek and the Dominoes Layla and Other Assorted Love Songs today, just had an urge to hear something I had not heard for awhile.   My Bloodhound/Shepard mix turns her head straight back behind herself and looks at me, wondering why the petting has stopped?  She realizes I am typing on my laptop and she gives up, content to lay down next to me on the couch.   I turn the surround sound up to 59 and am content with the mix and I am in a time machine.  I remember college days, when everybody who was cool had ELP and King Crimson and Neil Young with Crazy Horse and Layla...  Ah to be 19 and stupid and immortal again...and yet all the mistakes and wrong turns...naw, you can't go back you can never go back.

We are the generation who has Deadheads sticker on our Cadillac.   We were the Woodstock generation and now we are The Man.   It boggles my mind.  We are being elected to political office, we are heading up corporations and we were watching the Beatles when they played on Ed Sullivan and now we can access a world-wide database via our laptops far beyond the contents of any library.  My generation was born in a world of radio and prop airplanes and now it has been over forty years ago since we walked on the Moon.  Much has changed. 

19th Century suppositions that have been falling apart from within have no place in our world now.   Empiricism demands that logic be followed.   Occam's Razor.  When natural causes fail, the supernatural must be considered.   Historical evidence points to the Genesis account as being plausible based on what we know about rock layers and organisms...far more plausible than a self-creating Universe with a self-creating biosphere so well designed we are still trying to catch  up to the superior designs within organisms, trying to copy them and learn from them.

I wonder how many of my readers can grok this...there is love in the world because God made the world with love and He made it good.   We humans can feel love and be loving even without knowing God but to be consistently loving goes beyond feelings and transcends even actions, it must be integral to your being to be consistent and true.   Love with no God becomes selfishness and bitterness in the end.  

From Super Seventies

One of the great comments in rock journalism, as emotional and committed as the music itself, was penned by Dave Marsh for The Rolling Stone Illustrated History of Rock and Roll. Writing about Clapton, Marsh observed "there are few moments in the repertoire of recorded rock where a singer or writer has reached so deeply into himself that the effect of hearing them is akin to witnessing a murder, or a suicide... to me, 'Layla' is the greatest of them." 

A more strictly accurate analogy would be with an account of a road accident described by the person critically injured. Clapton managed to bawl out his pain over frustrated love with raw emotion. A superb team helped him complete his masterpiece. The duelling guitar introduction with Duane Allman is thrilling, and the lengthy duet with pianist Jim Gordon is gorgeous. Gordon's fellow Dominos Carl Radle and Bobby Whitlock offered admirable support.

Playing this album reminded me of another kind of love...like Eric Clapton and George Harrison and Pattie Boyd.   They both loved her, both cheated on her, both hated themselves for it, both did it anyway, and she was the inspiration for many of their songs.   Ironically both Harrison and Clapton play on the Beatle's song, While My Guitar Gently Weeps and they were friends of the sort that can do cocaine together one day and hit on the other one's girlfriend the next.  This album plays and I remember the joys and the fun but I can feel the pain in my soul for all the people I hurt and abandoned and cheated, too.   The 70's were a decade for excess and intoxication until God reached down to get my attention.

Now my life is much better.   When I look into the eyes of my wife I see real love and I love her so much, she is my girlfriend and my best friend and my dear companion.   We study and pray together.   We both love music.   I write blog posts and articles and she makes art.   I have the love of my life and I have great children and grandchildren and family and life is much better as a Christian even as a beat up old guy because I have peace and love and understanding and life is never boring and I am always sure that there is purpose and intention at work.  I am here to love people and help them and make sure that God gets a seat at the table of worldviews.   I am here to support my family, keep a roof over them, pay the bills.   I am here to serve my customers, help them make good choices about their IT security and equipment and help them when support is needed.   Today I spent two hours on the phone with a client in California helping with a uninstall/reinstall on a set of virtual servers.  Yesterday I made four sales.  Every day is a new day.

If you have heard this Layla album, the first three tracks are done without Duane Allman and then the rest include him.   Sometimes it is hard to figure out which lead is Clapton and which is Allman, but to my ear Clapton's solos sound sharper or sparkier and Allman's more rounded.  Music is such a subjective thing, lots of people don't even like this album.   Now the philosophy of the songs is, to me, sophomoric at best and largely dreadful but the music is a part and parcel of my soul. 

There is the funny thing.   Jesus took my dead spirit and made it alive.  He came alive inside of me and changed things radically in a dramatic and general way on the very first second of His arrival within me but in a gradual and specific set of ways as the years go by.   I still love rock, but a lot of my rock music is Christian rock and trust me, Phil Keaggy and Rex Carroll and Paul Jackson and Tony Palacios and guys like that could shred and rock out with the best of them.   I listen to White Cross far more often than I listen to Jimi Hendrix but there is a time for Hendrix and a place in me for him and for my memories of an old life.

Jesus changed me, but He did not undo me.   He did not turn me into a robot and my old memories did not disappear.   I didn't suddenly hate smoking pot, I just realized that I didn't need it and it wasn't legal so I just quit.   When God came into my life, he gave me the power to overcome sin within me and live a different life.  Commenters love to call me a liar but in fact I do not lie on this blog, I just say things they do not like.  I point out that Darwinism is unscientific and driven by religion.   Darwinists do not like to hear this because they know it is true or, if they do not know it, they fear it.   The more we learn about the Universe and life, the more design we find.   

When I became a Christian my worldview began to change.   My commenters who are of the Darwinist persuasion are very often guilty of the sin of not knowing themselves.   I know myself.   I know and speak the truth when I say that I did believe in macroevolution long after I became a Christian and that, when I began to study the subject, I did so by reviewing the evidence and did not bring the Bible into the process often at all.  I considered the rock layers, the fossils, the makeup of organisms and I realized that the Genesis account COULD be literal.   Therefore I set forth to find out for myself whether I was willing to accept that Genesis was literal based on evidence I could tangibly grasp in my hands or comprehend of scientific papers and treatises.   My faith was not challenged by the task.  I knew that Christ was my Savior.   No matter what I discovered about origins that would not change.  I just wanted to know the truth.

Faith at full gallop

Now I have put Electric Ladyland on.  Chloe the Shephound has run away in fright from the first track and Faith the Alaskan Husky has jumped up next to me to fill the void.    That opening track sounded like thunder to Chloe, I suppose.  Me and Jimi both have/had a little Cherokee blood in common.  Not much else alike, but man that guy was creative with that guitar in his hands!   This is the album in which he wonders if in 1983 a Merman he should turn out to be.   But he didn't make it to 1983.   Heck, he didn't make it to 1973.  That "1983" song was the song playing the first time my first hit of acid kicked in.   I was at a party already toked up when somebody offered me some LSD and I thought, why not?  It was in 1972 and I was at a friend's place in Monterey and suddenly I was seeing things not there and I was under the ocean and multi-colored girls were dancing in the sky and the walls were flickering like a dying TV tube and then they were gone and space was stretching out before me...Jimi was singing "Straight Ahead" and I was trying to see what was at the end of space in the LSD world.  If you have tripped you will understand that I do not remember much of it particularly well but I wanted to do it again and again.   I was trying to find the supernatural, trying to comprehend the eternal by way of psychoactive drugs. 

Creationism versus Darwinism


I have been continually studying the subject for thirty years now.   Because I have been so long in study I can clearly see some things that commenters often miss:


All of you are believers.   You may believe in meditation,  in Allah, in God or in notgod.   No matter what it is you believe, you believe it and live according to that belief.   I don't know whether to laugh or cry when a commenter claims that he doesn't bring his beliefs into his science.   When you say that, I say to you, know thyself before you start saying foolish things.   An atheist believes with all his might that there is NO GOD.   That is a worldview and that is a religion.   Atheism is a religion.  Science does NOT automatically exclude supernatural causation, it merely seeks material solutions first.   Darwinists cannot see beyond the material no matter what.  Therefore they make bad scientists and give us bad science.   The people who are doing the best work are paying no attention to Darwin at all and just learning from the world around them ways to make life better for people. 

Jimi sang - "   Not to be die but to be reborn, free from lands so battered and torn...forever "

Darwinism has injected religion into science.  The skirmish in the comments thread about the Law of Biogenesis reveals this to be true.  Pasteur proved conclusively that there was no spontaneous generation and that life does not come from non-life.   Science accepted this as a law.   But as Darwinism became popularized, scientists decided that they did not want to accept this law anymore even though it is testable and repeatable and has never been broken.   Think about that.   Here was an established law as established as gravitational law and yet scientists decided to cast it aside for religious purposes.   How hypocritical can you be?  You pretend to be scientists and yet to take an established law and throw it away because it doesn't fit your pet religion?   Shame on you!   

I do grieve for you, those of you who do not see.   Socrates through Plato called men who did not perceive the divine as, per this site: 

"In the beginning of the Allegory of the Cave Plato represents man’s condition as being “chained in a cave,” with only a fire behind him. He perceives the world by watching the shadows on the wall. He sits in darkness with the false light of the fire and does not realize that this existence is wrong or lacking. It merely is his existence — he knows no other nor offers any complaint.

Plato next imagines in the Allegory of the Cave what would occur if the chained man were suddenly released from his bondage and let out into the world. Plato describes how some people would immediately be frightened and want to return to the cave and the familiar dark existence. Others would look at the sun and finally see the world as it truly is.

They would know their previous existence was farce, a shadow of truth, and they would come to understand that their lives had been one of deception. A few would embrace the sun, and the true life and have a far better understanding of “truth.” They would also want to return to the cave to free the others in bondage, and would be puzzled by people still in the cave who would not believe the now “enlightened” truth bearer. Many would refuse to acknowledge any truth beyond their current existence in the cave."

I wanted the Sun.  I took drugs to find the Sun.   I chanted and meditated.  I studied philosphy and read sacred books from many cultures.  The concept of the man and the cave was something that drove me and, when for a time I thought I could never know the truth, it turned me into a "drink harder, party harder, leave a good-looking corpse" kind of guy.

I found the Sun when I found the Son.  I want to lead people out of the cave.  I feel bad for people in the cave who think the shadows are bright lights and caress their chains.   But it angers me when they impose those chains on others by deception and censorship and propaganda.   So this is a fight. 

Jesus said that the Pharisees, who were the ruling elites of the Jews, were like "blind leading the blind."  Jesus Christ never sinned and He was a man of truth and love, but he had harsh words for those who were leading others to destruction and called them whited tombs and vipers.   God clearly is angry with those who hinder others from finding their way out of the cave.   Mark 9:42:  - “But whoever causes one of these little ones who believe in Me to stumble, it would be better for him if a millstone were hung around his neck, and he were thrown into the sea."

So I identify organizations such as the NCSE as evil because they are hard at work keeping people from knowing truth.   Here is truth:   Darwinism is built on suppositions and while it might have been plausible in 1870, by 1970 scientists knew entirely too much about organisms to believe they came about by chance and yet they have continued to allow their vain religion to keep them from making logical decisions about what we see in the world around us.   It has been over a half a century since we discovered DNA and we are still learning more about how it works.  The idea of Junk DNA turned out to be a complete failure, for in fact DNA does far more than we first knew.   At the bottom of this post I am going to give you a semi-technical paper concerning transposons in DNA.  Just think about the fact that there are thousands upon thousands of technical, semi-technical and reader-friendly articles and documents being produced by real scientists who believe in a Designer and do great science without lugging the horrendous weight of the Dead Darwin around with them.   Real science will have to abandon Darwin eventually.   It may be a few of the high priests of Darwin will have to change or kick the bucket before the ruling paradigm shifts.  But it will.

To the Darwinist taking a walk, he sees rocks and understands they could have gotten to their place by natural causes.   He sees trees and understands that they grew from, say, acorns.   But when he gets to a barb-wire fence, he begins to speculate on how the post shrub grew and then developed long, hard, spiked tendrils that join fellow post shrubs together and he spends long hours writing a story of how this may have happened and then applies for grant money to study the evolution of the barb-wire fence shrub.   He will not for a second consider the relatively obvious observation that someone made the fence and erected it on purpose.   That pretty well sums up what Darwinism has become.   A bunch of religious zealots pathetically seeking for the impossible because the plausible evidence for a Creator God is distasteful to them.

So don't you tell me that the Law of Biogenesis is no longer a law until you can falsify it.   It has already been tested and retested.  

Don't you tell me that information comes from natural sources until you identify one.  Go ahead and show us what you know, Darwinist!   Where does information come from?   Do not insult us with an answer like "mutation" since you have to have information to mutate.   Do not claim that natural selection produces information because selection decides to select from a menu of information.  

~~~~~~~


Transposon amplification in rapid intrabaraminic diversification

Transposons are wide-spread mobile genetic elements that make up a huge part of the genomes of species. They are so named because of their ability to jump from one place in the genome to another. Often, they are given whimsical names, such as gypsy, Mariner, Tourist, or Pack-MULEs, which reflect their mobility. Barbara McClintock discovered the existence of these elements after witnessing the phenotypical change they brought about after jumping around in the maize genome. Due to evolutionary bias, transposons have generally been regarded as parasitic “junk DNA”, using the host’s genetic machinery to propagate. However, the actual functionality, diversity, and high abundance of transposons justify a revision of this viewpoint. Such rapid transposon accumulation puts the mechanisms for rapid speciation (given a recent creation and subsequent Flood-induced genetic bottleneck) into a new perspective, and may lead to a further development of a scientific basis for baraminological research. This paper deals with the distribution and dispersal of transposons in the light of evolutionary models as well as a creationist reinterpretion. Some calculations of transposition rates are given which support recent creation and rapid intrabaraminic variation. The importance of transposons is discussed in regard to mapping baramin life-histories.

Transposons in general

Basic types of human transposons.
Table 1. Basic types of human transposons

In the higher species (eukaryotes), two basic types of transposons can be distinguished: Class I and Class II. Class I transposons replicate through an RNA intermediate, and are therefore called retrotransposons, and end in sequences called long terminal repeats (LTRs). Class I transposons are located in areas where recombination between genes takes place. Members of Class I are short and long interspersed nuclear elements (called SINEs and LINEs, respectively); these make up a major part of the repetitive elements present in eukaryotic genomes. Class I transposons are usually located further away from the coding region of genes than the Class II transposons. LINEs can contain ORFs (open reading frames) from a few genes, such as reverse transcriptase or integrase, and are capable of transposing autonomously. They end up in LTRs. SINEs are much shorter elements which do not contain any coding sequences. Alu elements are examples of SINEs.

Class II, or DNA transposons replicate autonomously, using their own genes and proteins to copy their own sequences, and insert themselves into other parts of the genome. In this way they are capable of moving parts of the host’s genome along within themselves. They are located closer to genes (for example MITE sequences in cereal genomes) as opposed to Class I type transposons. Class II transposons can be divided into many different families and subfamilies, and bear names such as Activator, Mutator, or Helitron. Class II transposons are present in a few hundred or thousand copies per genome at most, and are sparser than Class I type transposons.1-5 Basic types of transposon elements are depicted in table 1.

Why transposons are a problem for evolutionary theory

Introductory thoughts on the effects of transposons on the genome

The naturalistic view of life assumes that the first “simple” genome of a living organism emerged from a chemical soup. Through selectable mutations accumulated over several billion years, this original genome evolved into all the intricate genomes we observe today. However, genome research in the past 10 years presents a picture of a far more dynamic genome that has been shaped and sculpted to a significant degree by transposable elements.6 We can see in table 2 that transposons make up a large percent of the genomes of different organisms.
Table 2. Genome sizes and content of repetitive elements 
in some well-known organisms.
Table 2. Genome sizes and content of repetitive elements in some well-known organisms.

For example, evolutionists claim the maize genome acquired virtually all retrotransposons (which make up about 80% of the maize genome: see table 1) in the last 6 million years.3 This statement is quite profound. First, it raises a question related to species stability. If it really took 6 million years for the maize genome to quadruplicate in size, then how could acquiring such a great quantity of genetic material keep maize the same species for such a long time? Maize was derived from teosinte, a plant hardly recognizable as modern maize. Teosinte was domesticated by the Amerindians over the past few thousand years, making rapid diversification by intelligent selection a more plausible explanation as to how the maize genome changed in such a way.

Evolutionists contend that, as in the case of transcription factor binding sites, random base substitutions can cause the appearance and disappearance of regulatory sequence elements. With transposons inflating the genome in such a manner, large chunks of raw genetic material would appear out of which new kinds of genes or other genetic elements could be formed. This is similar to how Arabidopsis is supposed to have acquired a major part of its genes. 60% of BAC sequences covering 80% of the Arabidopsis genome were found to contain duplicated segments, but yet it remained the same species.7
 
Since it is commonly accepted that transposons rapidly spread within the genome after colonizing the germ line (when the delicate developmental program is active), this is strongly discouraging to the idea that transposons are only harmful in their phenotypic effect. Actually, some functions of transposons can be assigned to repetitive elements; for example, certain structural functions and recombination sites, as well as genome rearrangement through transpositioning of genetic elements. Transposons can also react to abiotic stresses by regulating expression patterns of genes through cis-regulatory elements inserted by moving transposons.8 Other functional examples include induction of alternative splicing, or changing the expression patterns in certain tissues or even the subcellular location of proteins.9 It looks as though researchers will have to rethink the “junk DNA” theory10).

The concept that transposon-induced gene inflation is not only not producing junk DNA, but that it is also beneficial and strategic could be taken a step further. An interesting technique for studying the phenotypic effect of multiple genes has been developed in recent years by a Canadian research team involving the synthesis of a mammalian artificial chromosome (MAC) construct. It has been shown that MAC constructs persisted stably throughout several mouse generations. The interesting thing here is that even with the MAC carrying a whole array of novel genes (each with a potential to severely affect the phenotype) the mice are expected to remain mice. The researchers do not predict that they will evolve into a new species!11,12
 
Lacking observational evidence, evolutionists can always fall back on the argument that such acquisitions of raw genetic material may indeed give rise to new species and claim that “ … the rice genome would be, in effect, ‘the wheat genome without the repetitive sequences’.”3 This implies that changes in the transposon content are sufficient to give rise to new species. However, this would still not answer how the coding regions of the wheat/rice genome came about; it only deals with regulatory or contextual changes.13-15 A study done by Kalendar et al. dealing with the copia-type BARE-1 retrotransposon in barley shows that transposable elements can spread rapidly in response to microclimatic divergence.16 In this study, the copy numbers of BARE-1 ranged from 8,300 to 22,100 per haploid barley genome within a 400 m long gorge at Evolution Canyon in Mount Carmel, Israel. Such changes surely could not have taken millions of years because the wild barley that was studied exhibited retrotransposon replicative spread variability assumed to be correlated to sudden stress due to microclimate variations within the gorge and other climatic factors.
Figure 1. Model of transposon accumulation. The equation 
used  for calculating the number of transposons as a function of time 
is.
Figure 1. Model of transposon accumulation. The equation used for calculating the number of transposons as a function of time is n(t).

Evolutionary models dealing with the rate of transposition state that the distribution of transposons within host genomes can take place in short “bursts”, the accumulative effect of which could eventually lead to “genomic obesity”. Afterward, genetic material could be slowly lost (although the mechanism remains unclear). It is reasonable to propose that unequal cross-over recombinations or deletions of different sizes may be the underlying mechanism. If so, larger genomes could be expected to contain transposons younger than those in smaller genomes, because the latter could already be diminished in size due to deletions.

A study by SanMiguel in 1998 dealing with a number of plant species (such as Arabidopsis, rice, lotus, sorghum, maize, barley and diploid wheat) showed that even by evolutionary standards the studied retrotransposons are all thought to be about the same age.17 It should be noted, however, that the age of the LTR sequences is calculated by the gamma-corrected Kimura 2 method and depends on the substitution rate of nucleotides in the LTR sequences. In this model, the age of an LTR sequence is calculated from the substitution rate, but the substitution rate is based on the estimated time to the divergence between the species. It is an obvious case of circular reasoning.17,18-23
 
With many thousands of copies of transposons within the genome, genomes should have grown quite quickly during a very short period relative to the evolutionary timescale.

The number of LTR sequences in barley was also shown to correlate with altitude and temperature.24 Parallel to this, the differences in the repetitive content of the wheat/rice genome could shed light on how intrabaraminic variation could occur, as these two species belong to a single holobaramin.25 Considering these observations, it is clear that a mechanism to induce rapid variation makes more sense in a creationist framework (where new species arise almost instantly) than in the evolutionary model (where it supposedly takes hundreds of thousands of years for novel species to arise).

Consequently, it would be a stretch of the imagination that different species persisted for millions of years without having their genomes affected. For example, genome size variation has been observed within the progeny of Helianthus annuus, where the difference in genome size was 14.7%. This would mean 441 Mb (which is larger than the genome of rice itself!) of the 3,000 Mb genome of sunflower.26 With many thousands of copies of transposons within the genome, genomes should have grown quite quickly during a very short period relative to the evolutionary timescale. Contrary to this, evolutionists estimate that according to gene loss models, it would take around 1.5 billion years for maize to get rid of the same amount of this excess genetic material.27

Model of transposon accumulation in genomes

Transposons are capable of adding large tracts of DNA to the genome, and it would be of great importance to formulate a mathematical model describing the rate of transposon amplification within a genome. The model presented below is completely hypothetical in nature. Research is required to elucidate the exact way in which transposons accumulate and may validate or reject the proposed model.

Since the numbers of new transposons which arise within the genome are proportional to the number of transposons capable of replicating themselves, we may say that

Equation 1 
That is, the rate of spread of transposons n’(t) within the genome is proportional to the function f(t) of the number of transposons n(t) capable of replicating after t transposition events. From this we can deduce that
Equation 2
where n(t) is the number of transposons after t transposition events, C’ is a constant, and F(t) is the primitive function of the function f(t) which is characteristic of the rate of transposon accumulation within the genome.
From this we may deduce one of two possible things. If the primitive function F(t) of f(t) is constant, that is

Equation 3 
 
meaning that the number of transposons in a genome after t transpositions grows exponentially. If so, it would lead to an exponential explosion relatively quickly. This would lend support to the creationist model, which predicts large numbers of transposons accumulating in genomes only recently (that is, with a short period of time allowed for accumulation to occur). It would also be in line with evidence from other fields of science that support the recent creation/worldwide Flood model (for example: high mutation rates are observed, yet the number of mutations that have occurred since mitochondrial Eve is too small if we assume long ages; also extremely high rates of radioactive decay are suggested by the creationist RATE team).28,29
 
In the evolutionary framework, the model implies a runaway / out of control accumulation of transposons in the genome a long time ago. Since we see genomes still intact, this means that runaway transposon accumulation has not yet occurred in the relatively short time since creation.

However, if the function f(t) is not constant, then the rate of transposon accumulation may change during time. A further investigation of the function f(t) reveals important characteristics about the dynamics of transposon accumulation. We know that the lower and upper bounds of the function f(t) are 0 and ln 2, respectively:

Equation 4 
The lower bound 0 would mean a complete stasis in the accumulation of transposons within the genome, resulting in no increase; i.e. no transposition and/or amplification. Therefore, f(t) is always greater than zero. Since after any t number of transposition events the maximum number of transposons within the genome is n(t) = 2t , then
Equation 5
If we take the function f(t) to decay exponentially, we get
Equation 6
However, when the variable t (= transposition events) increases, e-gt/g decreases and tends to decline to 0. The remaining function n(t) = eht, however, still describes an exponential growth of transposon copy acquisition. However, if in equation 6 h is equal to 0, we arrive at an equation for a sigmoidal curve. According to this model, transposon accumulation lags off after an exponential burst in a later phase. This means that after an initial burst phase of transposon accumulation, a lag phase follows, characterized by a shutdown of transposon activity. This is noteworthy, because it fits with certain aspects of the AGEing hypothesis of Todd Wood,30,31 who contends that genetic rearrangement occurred during a certain period of time after the Flood in the genomes of organisms to allow the rapid phenotypic change necessary for adaptive dispersal via genetic variation.

In figure 1 we can see a hypothetical situation where the number of transposons is calculated as a function of transposition events. The equation n(t) = 100000 •e–e–1 (if we assume that g = 1) gives a sigmoidal curve of the form n(t) = a •e–e–1, where e–e–1 ranges from 0 to 1. Therefore, a would denote the maximum number of transposons in the genome.

The obvious question is that if the number of transposons has already reached a plateau, then how long has this plateau condition persisted? Evolutionists could argue that it has continued for an indefinitely long time. This would mean that all transposon activity has had ample time to shut down completely. Contrary to this, some transposons have been shown to be active in a number of organisms, such as humans.27,32 However, very few plant retrotransposons have been shown to be transcriptionally active (one is BARE-1 in barley).1,8,33 MITE sequences in plants have not been shown to excise, except for the rice mPing element, also indicative of their low transposase activity.1,9
 
This would mean that we are presently at the top shoulder of the sigmoidal curve, where transposon activity is slowly dying out. This is marked by the presence of many defective transposon sequences within genomes.

The importance of transposons in baraminology studies

Many repetitive sequences are either species or genera specific in bacteria, plants and animals, and are thought to promote speciation.34 This is good news for baraminologists, since transposons can therefore be used as a sort of signature to identify members of a baramin. This would mean that transposons could be used as a diagnostic tool to determine whether or not a species is a member of a given baramin.
Average number of LTR sequences in thousands per barley 
genome. The average number of LTR sequences is shown in the H, Y and I 
genomes of barley for species listed in table 3. The number of LTR 
sequences for tetraploid genomes was divided by two. The data was taken 
from Vicient <em>et al</em>., ref. 33. Data for 
<em>genome X</em> was not used because it was only from a 
single species.
Figure 2. Average number of LTR sequences in thousands per barley genome. 
 The average number of LTR sequences is shown in the H, Y and I genomes of barley for species listed in table 3. The number of LTR sequences for tetraploid genomes was divided by two. The data was taken from Vicient et al., ref. 33. Data for genome X was not used because it was only from a single species.

By counting the number of the various transposons in the genomes of different species that belong to the same baramin, we can get a picture of the life history of a given baramin. In other words, by following the change in the number of a given transposable element, we can estimate which species originated from a particular baranome (see refs. 14 and 15). For example, particular MITE sequences can be found at the same position in the genomes of different plant genomes because of their relative stability.1 Therefore MITEs can be used as landmark or reference sequences to mark the inflation or change of a certain baranome. Also, the BARE-1 transposon element is widespread and specifically found in a number of grass species (such as wheat, rye and oats), each with slightly diverged sequence, whereas it is absent in other species. This may indicate that BARE-1 is a baramin-specific transpoable element.24 A similar diagnostic transposon element is the RIRE-1 element in rice.1
 
The number of BARE-1 elements in a genome can be approximated by the number of LTR, in and rt sequences within the genome. According to Vicient et al.,33 the number of copies of these element decreases in the Y, H and X genomes of different barley species (Hordeum spp.) as compared to the I genome of barley, and may reflect the spreading of the transposon during the life history of the Hordeum monobaramin (see figure 2). In the genus Hordeum, the I genome is the most representative of barley, and contains the most sequences. The Y, H and X genomes are characteristic of other barley species, and contain a decreasing number of these elements, Y having the highest. Furthermore, Vicient et al. also found that genome size was negatively correlated (r = –0.593) to genetic distance from barley, meaning that the genomes of the Hordeum species may have inflated parallel to their acquisition of transposable elements.
Table 3. Number of LTR sequences in different species of 
barley.
Table 3. Number of LTR sequences in different species of barley.

Table 3 is a list of barley species with different types of genomes (H, Y and I) and the 1,000s of LTR sequences they contain, which are supposedly equal to the number of BARE-1 transposons in the genome. In addition, table 3 shows that barley genomes roughly fall into three groups: group I contains the highest number of LTR sequences; group Y has an intermediate number of LTR sequences; and group H has the lowest number.

According to mainstream evolutionists, the wheat genome equals the rice genome but without the repetitive elements. Since transposon activity adds large tracts of DNA to the genomes of organisms, and because they do not easily back-mutate, transposons may be a tool to track back the “life-history” of baramins. For the rice and wheat genomes, which belong to the same baramin,30 it would be an interesting endeavour to map species relationship as a function of transposon content.
Table 3. Number of LTR sequences in different species of 
barley.
Figure 3. Model of the life history of baramins following transposon amplification. According to this model, genome size expands in time after Creation/Flood along with transposon content. The archebaramin is at the base of the baraminic tree, and represents the original genome with little or no transposon content. At different intervals, transposon invasion and amplification can occur, causing large-scale intrabaraminic diversification (represented by the large branches). At different branch points, monobaraminic variation can occur, as seen in the genus Hordeum.33

In this respect it is interesting to determine whether species with the same gene content and colinearity all classify as members of the same holobaramin. For example, microcolinearity has been shown to exist between certain parts of the genome in rice and members of the tribe Triticeae, even though the distance between genes may be up to at least sevenfold.35 Similarly, species with about the same transposon content may be members of the same monobaramin, such as species in the genus Hordeum, which show intrabaraminic (and even intraspecies) variation. The nature and degree of variation would obviously be helpful in determining ancestry. In contrast, species with the same gene colinearity but with different transposon content could be members of different monobaramins. This is because different numbers of transposon would have accumulated after speciation occurred.

Furthermore, microcolinearity is proof of a young age for plant species since, if they really are millions of years old according to evolution, then the order of their genes should become scramble past recognition.

Because of the widespread dispersion and conserved LTR termini, molecular studies such as REMAP (Retrotransposon-Microsatellite Amplification Polymorphism) and IRAP (Inter-Retrotransposon Amplified Polymorphism) may be useful tools in tracking the spread of transposons within baramins.36 Given their large difference in genome size, rice and wheat could be members of different monobaramins. Moreover, species in a given baramin with small genome size could be members of the archebaramin, representing the original state of the baranome before the amplification process started. This model is presented in figure 3.

The life history of a baramin undergoing transposon amplification is analogous to an uninflated balloon on which a number of dots/bars are drawn and connected to each other by lines (see figure 4). The dots represent different genes, whereas the lines represent the intergenic spaces. Inflating the balloon is analogous to an increase in transposon content: The further the dots move from each other on the surface of the balloon, the greater the length of the intergenic regions become.

This is in accord with a study in rice, sorghum, and maize, which showed significant differences in a certain segment of the Adh1-F locus between the three species, although the genes in this region were mainly colinear. In this case, homologs of the Adh1 and u22 genes were 50 kbp apart in sorghum, but 120 kbp apart in the larger maize genome. The gene density in this region was approximately one gene per 9–12 kbp in rice and sorghum, whereas the density was one per 30–80 kbp in maize, which shows intrabaraminic variation due to transposon amplification.37 This shows that determination of gene colinearity in related species such as cereals could be of great help in exploring the boundaries of baraminology.38,39 Furthermore, microcolinearity of genes is proof of a young age for plant species since, if they really are millions of years old according to evolution, then the order of their genes should have become scrambled past recognition.
Genome model of gene colinearity and retrotransposon

        markering.
Figure 4. Genome model of gene colinearity and retrotransposon markering. In this model, six species are represented by six concentric circles of different line thicknesses. The six circles represent chromosomes with genes at specific intervals. The first five chromosomes starting from the centre of the circles, represent species belonging to a specific baramin (e.g. the grasses), while the outer circle represents a genome belonging to another baramin (e.g. Arabidopsis). Here we can see that genes (black dots/bars) are colinear in the case of the first five circles/chromosomes/species, since they belong to the same holobaramin. The concentricity of the circles also illustrates baramin-specific transposon amplification. We can see that the 2nd and 3rd circles contain three elements (grey bars) denoting specific transposon elements that are monobaramin-specific. The 4th and 5th circles contain light grey elements that are also monobaramin-specific.

When gene colinearity was studied between Arabidopsis (Brassicaceae) and rice, it was found that ESTs (expressed sequence tags) from rice had very low homology with genes on the chromosomes of Arabidopsis, even at the protein level. This was interpreted by our evolutionary friends to indicate that the genomes of the both plants had “eroded” too much for a successful comparison. In other words, gene colinearity and order were unrecognizable.40 In a separate study of rice, wheat and Arabidopsis, researchers found that out of 46 types of rice copia elements, only two (Adena and Osr8) were present in Arabidopsis, and even the Osr8 element was thought to be in silico contamination.41 Similarly, a computer analysis of Tourist and Stowaway rice short inverted-repeat elements in the non-coding regions of 413 Arabidopsis genes failed to identify a single repeat longer than 30 bp.9 It is most interesting to note that Moore et al. have found that the genomes of a number of grass species can even be circularized (formed into a circle) around one another and divided into 19 colinear rice linkage segments that are all representative of the ancestral grass genome (in our case the genome of the archebaramin).42 This mode of representation of the genomes of a single monobaramin may even be adapted to all baraminology.

Contrary to mainstream assumptions, the expansion of genomes via transposon amplification is much faster than anticipated by the evolutionary model. Neither is the type of speciation of the kind that is required to evolve from microbe to man.

Furthermore, when comparing mammalian and plant transposons, we find that SINEs and LINEs are more common to mammalian genomes, whereas MITEs and LTR retrotransposons are more common to plant genomes. We can take these transposons as marker elements common to the mammalian and plant apobaramins, respectively. These would be examples of baramin-specific transposable element markers.
Creationists could interpret this observation to support the notion that colinearity of genes is evidence of interbaraminic relationships; for example, lack of colinearity of genes between Arabidopsis and rice demonstrates the discontinuity between the monocot grasses and dicot Brassicaceae, thereby assigning these two plant groups to separate baramins.

Conclusion

The process of genome expansion by means of transposable elements as observed in several plant species shows that genomes can be moulded quite dynamically without crossing evolutionary boundaries. Contrary to mainstream assumptions, the expansion of genomes via transposon amplification is much faster than anticipated by the evolutionary model. Neither is the type of speciation of the kind that is required to evolve from microbe to man. In addition, the rapid spread of transposable elements within these genomes shows that genomes are recent. Variation induced by accumulation of transposable elements and fast-track speciation events are very rapid phenomena and fit nicely with the biblical timescale. A large number of transposable elements also give support to the Wood model of rapid baraminic diversification after the Flood followed by subsequent widespread deactivation. Furthermore, the distribution of certain transposable elements shows that they can be used as marker elements in baraminology studies. Considering the increasing body of evidence that transposable elements induce variation in baranomes, and may even be involved in post-Flood speciation events, they should be renamed variation-inducing genetic elements (VIGEs; as proposed by Borger, ref. 14).

Glossary

BAC sequence: bacterial artificial clone.
Copia element: a common type of retrotransposon with retrovirus-like sequence organization.
EST: expressed sequence tags used to determine gene transcripts. Usually short in length, covering only part of a gene.
gag/prt/pol/env proteins: a number of proteins coded for by Class II type transposons and which are necessary for transposition.
Gamma-corrected Kimura two method: a substitution model for calculating genetic distances between DNA sequences.
in sequence: a domain within the BARE-1 element encoding the integrase protein and needed for replication.
LTR: long terminal repeat—a type of sequence belonging to LINEs and involved in the insertion of the transposon.
MITE: miniature inverted-repeat transposable element: short transposon of several hundred bps which are restricted in transposition. May contain genetic regulator elements.
ORF: open reading frame—that part of a gene which can be potentially translated into peptides/proteins.
rt sequence: a domain within the BARE-1 element encoding the reverse transcriptase protein and needed for replication.

Acknowledgments

I would like to thank Aladár Pettkó-Szandtner and Levente Bendegúz Szűk for their critical reading of the manuscript as well as Tamás Varga for his help in describing the mathematical model behind transposon accumulation. I would also like to thank Eszter Cserháti for proofreading the text.

Related articles

Further reading

References

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  2. Mao, L., et al., Rice transposable elements: a survey of 73,000 sequence-tagged-connectors, Genome Res 10(7):982–990, 2000. Return to text.
  3. Moore, G., Cereal chromosome structure, evolution, and pairing, Annu Rev Plant Physiol Plant Mol Biol 51:195–222, 2000. Return to text.
  4. Bureau, T.E. and Wessler, S.R., Mobile inverted-repeat elements of the Tourist family are associated with the genes of many cereal grasses, Proc Natl Acad Sci USA 91(4):1411–1415, 1994. Return to text.
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9 comments:

Jon Woolf said...

"Where does information come from?"

When you take a new deck of cards, shuffle it thoroughly, and then deal five poker hands, where does the 'information' in Player 3's straight flush and Player 5's full house come from?

You read the words, Radar, but you fail to understand their meaning.

"Such rapid transposon accumulation puts the mechanisms for rapid speciation (given a recent creation and subsequent Flood-induced genetic bottleneck) into a new perspective, and may lead to a further development of a scientific basis for baraminological research."

There was no Flood, therefore the author is thoroughly biased and his conclusions worthless. However, just for laughs I read the article. I'm no geneticist, and for all I know his mathematics are screwy, but it looks to me like if you strip away the author's preconceptions of creationism, 'baramins', and other such nonsense, what you get is a potentially-useful analysis of transposon dynamics. Of course, he fails utterly to realize that his analysis shows transposon changes are genetic mutations and therefore subject to all the rules that govern such mutations. According to creationists, one such rule is Haldane's Dilemma, which says that beneficial evolution is impossible.

So we see that as usual, this attempt by a creationist to sound like a real scientist succeeds mainly in shooting still another hole in creationism.

highboy said...

I'm curious radar as to how a carving of a stegosaurus ends up on the temple of a tribe living 700 years ago, when the dinosaur supposedly lived 65 million years ago?

I'm also curious as to how someone who only ascribe to empirical scientific evidence from which to draw their conclusions can conclude that life was indeed an act of random chance, given that there is absolutely no way to test for that either. No matter how you slice physical reality up, you have a reality that has no explanation for itself found within itself. Whether its God or chance the answer is outside the realm of natural phenomenon.

radar said...

Woolf manages to entirely dodge both questions again. Random series of cards are data, not intelligence. If we, using our intellect, draw conclusions from data then we are able to generate information.

The wind is not intelligent. Intelligent men have developed machines to measure the wind for velocity and direction. The machines accumulate data. We can use intellect to draw conclusions from the data.

But cards do not generate information and neither does the wind. There is no correlation between your answer and the question of where information comes from.

radar said...

No, transposons are pre-existing information that moves within the gene pool. You seriously think you are more qualified to speak to the subject than the author?

Your religion does not allow for the Flood, which is why your view of geology is so badly skewed. It is you who is too religious to consider evidence clearly. Almost every culture has a flood story and the rocks are a testimony to a world-wide flood. So you are the one unqualified to make any reasonable statements concerning origins as a religious zealot who is thoroughly brainwashed.

Jon Woolf said...

"There is no correlation between your answer and the question of where information comes from."

Correction: you don't see a correlation. But the correlation exists anyway. A deck of cards, whether it's being used to play poker, or bridge, or whist, or blackjack, or chemin-de-fer, is a perfect basic demonstration of the statistical principle that order can arise from random processes. And what do we call an ordered sequence of bits that carries some sort of meaning or message? Why, that's information, Gracie.

Chemical reactions can have the same result. Order from disorder. Meaning from randomness. Information where none existed before.

"Almost every culture has a flood story"

Almost every culture has stories of magicians, talking beasts, theriomorphs, and a long list of other fantastic things. Does that mean all those things were once real?

"and the rocks are a testimony to a world-wide flood."

Except where they aren't -- which is the point of that long list of questions I keep posting and you keep avoiding. None of those things has a rational explanation under Flood geology. Sane and sober scientists know this. That's why they abandoned Flood geology two hundred years ago.

Anonymous said...

"Random series of cards are data, not intelligence."

Interesting Freudian slip there, Radar. Nobody claimed that a random deck of cards was synonymous with intelligence. Oops.

Information is organized data. The organizing principle may or may not be intelligent unto itself.

Anonymous said...

"Your religion does not allow for the Flood, which is why your view of geology is so badly skewed."

1. What is Jon Woolf's religion, Radar?

2. What is Paul Pavao's religion, Radar?

How would, for example, atheism (I have no idea if Jon Woolf is an atheist, but it seems you're presuming he is) not allow for a global flood?

You're basing this claim of a global flood mostly on a religious text while at the same time dismissing every other religious text as evidence. Why would that be?

But since you're claiming it was an actual event that took place, there must be physical evidence for it.

Incidentally, atheism would not be opposed to a global flood approx. 6K years ago - it's just that no evidence for it has ever been found, so there is no reason to believe it occurred.

And no, special pleading is not evidence. It's a logical fallacy. Why do you think your religion should be afforded special treatment?

For starters, what would be the arrangement of fossils in rock strata if a global flood had actually occurred?

Could LIPs have occurred if a global flood had actually occurred?

The evidence speaks against it, and your alleged claims for it are extremely patchy.

Are you willing to go where the evidence leads?

radar said...

Jon Woolf said...

"There is no correlation between your answer and the question of where information comes from."

Correction: you don't see a correlation. But the correlation exists anyway. A deck of cards, whether it's being used to play poker, or bridge, or whist, or blackjack, or chemin-de-fer, is a perfect basic demonstration of the statistical principle that order can arise from random processes. And what do we call an ordered sequence of bits that carries some sort of meaning or message? Why, that's information, Gracie.


So wrong. First of all, where did the cards come from, and the information on the cards? In the Darwinist scenario, you need a naturalistic source for the cards and the information that is on them. It was no slip on my part to point this out. It is silly for you to try to use this as an example, though.

Secondly, the "order" of the cards can very tremendously but for anyone to perceive any order to them, he must be intelligent. It requires an intelligent source to devise and print the cards. It takes an intelligent source to read the cards. A deck of cards is meaningless to non-intelligence.

I presume Woolf is an atheist, in part because of the nature of his comments and also because of his website. I took a look and noticed that, while he is a big sci-fi and fantasy fan, he doesn't recommend the Lord of the Rings or the Narnia series, two of the most prominent fantasy series of all time. But they had Christian authors, so it would seem that he just doesn't like the concept of God. His choice is his own.

Atheism does not want to admit to a global flood because the Bible says that we had one. Atheism doesn't want to admit that organisms are designed because then you need a Designer.

Jon Woolf said...

Gee, Blogger is being remarkably twitchy about deleting comments ... the one I put here last night lasted several hours before mysteriously vanishing, instead of just a few minutes like comments hit by the Mystery Deleter usually do.

"I presume Woolf is an atheist,"

You presume wrongly.

"I took a look and noticed that, while he is a big sci-fi and fantasy fan, he doesn't recommend the Lord of the Rings"

I have an entire page about the works of Tolkien. I have nothing posted about C. S. Lewis, it's true, but then I have a lot of books that I just never added to the site. Both fiction and non-fiction.