Rethinking junk DNA

Originally Posted by Phronesis View Post
Problem is, certain people came to the conclusion the our existence must have been badly designed if it was designed (basically a massive argument from ignorance, stupid and self-refuting)
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If you could calm down and write your sentences out rationaly perhaps more people would be able to understand you better.. I have no idea what you are trying to communicate. It looks a little mad.
 
Lol, coming from MyBB's favorite mad little anti-religious bigot. Do you want it spelled out again?

To come to the conclusion that our existence must have been badly designed if it was designed is just one massive argument from ignorance. It is stupid and self-refuting and there is about as much philosophical substance in that assertion as there is in the philosophy of those who think **** just happens.

Got it?

It is amazing that there are so many anti-religious bigots here on MyBB, when in fact they should be anti-idealists. Religion does not divide and suppress, ideals do. We all have ideals and we can't live without it. Religions have their sets of ideals, anti-religionists have theirs, democrats have theirs and republicans have theirs etc. As long as people have ideals, there will be strife. Get used to it.

However, having ideals presupposes that there exists a perfect world where these ideals are played out in harmony. Heaven on earth you might say. Funny how religionists and anti-religionists can agree on the idea of an ideal reality for which scientists might argue "there is no evidence for an ideal reality". Does that stop people from believing in whatever ideals they have?
 
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Phronesis said:
However, having ideals presupposes that there exists a perfect world where these ideals are played out in harmony.
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What rot! Even for you, Phroners, old bean. You been smoking something funny as part of your religious rituals?
 
Trolling again rainman? How do you do it.... typing all that tripe and saying exactly nothing? Wu wei not working and now you are trying to say something constructive? I suggest you try again because your "**** happens" philosophy makes about as much sense as... why you... What is the matter, having daddy issues again today and now you are all cranky? Grow up old chop.
 
Phronesis said:
Trolling again rainman? How do you do it.... typing all that tripe and saying exactly nothing? Wu wei not working and now you are trying to say something constructive? I suggest you try again because your "**** happens" philosophy makes about as much sense as... why you... What is the matter, having daddy issues again today and now you are all cranky? Grow up old chop.
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Lollers @ Phroners. :D You really need to dream up some new insults - you're showing a distinct lack of imagination.

Besides, you are the one making the wild assertions about some bizarre "ideal" world - you defend your claims, or at least justify them a li'l bit.

What's this hangup about daddies? You projecting? You seem to have some "issues" here. What happened - your daddy spank you when he caught you w@nking? Was it painful? Is that why you find the need for some "perfect daddy in the sky" - maybe he'll be less cruel to you LOL! :p

But remember - Ceiling Cat watches you masturbate. :D:D
 
It seems you just don't quite get the idea that humans have ideals and what that means. Pity, guess that is what wu wei and "**** happens" philosophy does to you.
rwenzori said:
Besides, you are the one making the wild assertions about some bizarre "ideal" world - you defend your claims, or at least justify them a li'l bit.

What's this hangup about daddies? You projecting? You seem to have some "issues" here. What happened - your daddy spank you when he caught you w@nking? Was it painful? Is that why you find the need for some "perfect daddy in the sky" - maybe he'll be less cruel to you LOL! :p

But remember - Ceiling Cat watches you masturbate. :D:D
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Now now, no need to show the world your hang ups with your poppa and your fiddling... But, like you said, lucky for you and your "long-dead earthly one". No more pain, just unfinished issues for you now. Ag shame, it shows.
 
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Correction. You are the daddy of all trolls and have the mother-of-all daddy issues :p.
 
If you don't have junk, you will probably go extinct...
Shaking up the theory of evolution
Murdoch University scientists have developed an improved theory of evolution – a groundbreaking hypothesis which finally reconciles evolutionary theory with the fossil record.

Developed by PhD student Keith Oliver and Program Chair of Biomedical Sciences Dr Wayne Greene, the “Genomic Drive” hypothesis, potentially represents one of the biggest advances in evolutionary theory since the 1930s.


DNA "junk"

In a co-authored report, due to be published in the prestigious BioEssays journal, the researchers argue that transposable elements (TEs) – or what is colloquially termed jumping genes, selfish or junk DNA, have a critical role in ensuring the survival of biological lineages.

Without this DNA junk, a species is effectively frozen and faces eventual extinction.

On the other hand, species with genomes with high TE activity or strong presence of identical TEs possess a greater ability to evolve, diversify and survive.

Take for example humans, rodents and bats.

As primates some 46 per cent of the human genome is comprised of TEs while other mammals such as rodents and bats are known to possess around 40 per cent.

These TE’s are generally suppressed in the ordinary body cells of most species but are allowed to reactivate in reproductive cells for the potential benefit of the next generation.

Their activity can also be triggered when they suddenly hop between species or by stress.

TEs do their survival work by reformatting and rearranging DNA genomes to sometimes create significant adaptive mutations that undergo natural selection.


Current theory doesn't tally with fossil evidence

Dr Greene, a Senior Lecturer in Molecular Genetics, said current evolutionary theory, which assumed biological lineages evolved by the slow accumulation of adaptive mutations, did not tally with the fossil record.

However, the “Genomic Drive” theory provided a significant explanation for the way new species arose abruptly and periodically.

The theory also fitted with fossil records which showed intermittent and long periods of stasis – where many species stood still or remained the same.

Mr Oliver said the hypothesis argued that significant evolution could not take place without the activity of TEs.

“Although we are standing on the shoulders of others that have worked on TEs, we believe this is the strongest and most comprehensive case ever put forward on the role of TEs in evolution,” Mr Oliver said.

“If our theory proves correct it would be one of the biggest advances in evolution since the 1930s when Darwinism and Mendelism were reconciled in NeoDarwinism.”


Species without junk DNA risked extinction

Dr Greene said species that were devoid of TEs were more at risk of extinction because they simply lacked the capacity to adapt, change and diversify.

“If you don’t have this junk in your genome then you can’t evolve and are stuck, thereby remaining in what is termed evolutionary stasis,” Dr Greene said.

“This would explain why almost all species control their TEs rather than eliminate them.

“And of course having these TEs in a genome doesn’t mean a lineage will necessarily diversify. What it does mean is that it has a much greater potential to do so.”

Mr Oliver said an example of evolutionary stasis occurring in species without TE activity could be seen in the living fossil, the coelacanth, once thought to be extinct for 63 million years.
.
The coelacanth, which had been found off the coast of South Africa and Indonesia, had inactive or low levels of TEs and had been in stasis for 400 million years.

In another example he referred to the tuatara, where just two species had been found off the coast of New Zealand.

Like the coelacanth, the tuatara was characterised by very few jumping genes and has been unchanged for 220 million years.


An explanation for many unanswered questions

Dr Greene said Genomic Drive theory provided an explanation for many unanswered questions such as why species suddenly appeared in the fossil record, why some groups of organisms were species rich and others species poor and why some species changed little over millions of years.

Successive waves of TE activity in a lineage potentially explained alternations of rapid evolution and stasis.

He said some species - such as bats which “came out of nowhere” in the Eocene Period – suddenly appeared in the fossil record.

This was in keeping with evidence that TE or jumping gene activity occurred in sudden episodic bursts.


Improving the ability to diversify, adapt and survive

Dr Greene said an example of how TE activity affected the richness of a lineage was seen in rodents and bats.

These were species-rich orders of mammals and, unusually for modern mammals, both harboured highly active TEs.

Although there wasn’t enough data yet, the presence of TEs could also help to explain why one order of birds, commonly known as the Songbirds, (the Passeriformes) accounted for over half of all bird species and why the Perciformes accounted for 40 per cent of fish species.

While jumping gene activity in the 235 species of primates had quietened down a lot since its peak about 40 million years ago, the high presence of identical TEs in the primate genome pointed to an improved ability to diversify, adapt and survive.

By comparison a cousin of the primate, the Flying Lemur, lacked a key TE that primates had in abundance and only two species of it remained.
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Have junk....will survive. But hey, if all this junk was designed it was a bad design right? Pffff or maybe not :D.

Some of the sequences in the proposed Universal Genome in the Origin of Metazoa might have no immediate effect on fitness, but still have a function by acting as a reservoir of genetic material on which variation inducing mechanisms such as sequence duplication, somatic hypermutation, gene conversion and homologous recombination can act upon during periods of selection. Intracellular quality control mechanisms then act as selection mechanisms to keep the sequences in tact as a result of optimal systems within cells...like quality control systems.

Cells and cellular systems can be viewed as active entities that search random space for solutions during times of selection pressure. The intrinsic quality control systems are seen to act as selection mechanisms to constrain the random search and thus bias the output of a random search. Once again showing how how artificial selection plays a role in the biased trajectory of evolution.
 
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"Design"??? "Artificial selection"??? My crap-detector is nearing boiling point LOL!

Besides, "artificial selection" DOES NOTHING, don't you know? :p
:D
 
rwenzori said:
"Design"??? "Artificial selection"??? My crap-detector is nearing boiling point LOL!
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Is there any surprise really? I mean your utterly unscientific "philosophy" that "**** happens" does not really allow you to see anything but crap. I guess your poppa had the same philosophy.

rwenzori said:
Besides, "artificial selection" DOES NOTHING, don't you know? :p
:D
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Back here in the real world, articicial selection does this, this, this etc.
 
About 8% of the human genome mass consists of sequences of retroviral origin and it is thought that in the evolutionary past, exogenous retroviruses formed proviruses in the genomes of germ cells of ancestral primate species.

It was (perhaps still is) commonly believed that ERVs are just junk elements that randomly integrated into genomes and caused havoc in the past, then these shared errors were propagated in future generations. As research progresses in this area, it is becoming more and more apparent that some of these elements bare some functionality (believed to be co-opted) and are actually crucial for certain processes. More and more functions are being found for ERV elements and LTRs. It may very well turn out that ERV elements are the crucial elements that make us human.

Interesting research:
Virus Enzymes Could Promote Human, Animal Health
ScienceDaily (Aug. 31, 2009) — Could viruses be good for you? Scientists with the Agricultural Research Service (ARS) have shown that enzymes from bacteria-infecting viruses known as phages could have beneficial applications for human and animal health.
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Newly designed benefits of viral enzymes.

But, our own viral genome mass does in fact have functionality (see post #71). Not only is it good for the survival of future generations, it has other functions as well including:
1) Independent envelope genes from unrelated ERV families regulate trophoblast differentiation and syncytia formation during synepitheliochorial placentation. Are there examples of Eutheria that are capable of reproduction without ERVs?
Humans (primates): HERV-W and HERV-FRD
Mice (Rodentia): Syncytin-A and -B
Sheep (Artiodactyla): enJSRV

2) Retroelement formatting of the genome.
System architectures formatting by retroelements and other repeat elements possibly have an effect on morphological, physiological and reproductive function.

3) LTRs play a fundamental role in gene expression
Independently acquired LTRs have assumed regulatory roles for orthologous genes.
An LTR is the dominant promoter in the colon, indicating that this ancient retroviral element has a major impact on gene expression.
LTR class I endogenous retrovirus (ERV) retroelements impact considerably on the transcriptional network of human tumor suppressor protein p53 (guardian of the genome).

4) Role in autoimmunity.
Disease associations have been established, however there is as yet no proven definite causative association between HERVs and disease.
a) Human endogenous retroviruses can encode superantigenic activity
b) Transcriptional activation. HERVs may act as insertional mutagens or cis-regulatory elements causing activation, inhibition, or alternative splicing of cellular genes involved in immune function.
c) Molecular mimicry. Production of neo-antigens by modification of cellular components.
d) Epitope spreading.
e) Activation of innate immunity through pattern recognition receptors.

References:
von Sternberg R, Shapiro JA. How repeated retroelements format genome function. Cytogenet Genome Res. 2005;110(1-4):108-116.

Romanish MT, Lock WM, van de Lagemaat LN, Dunn CA, et al. Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution. PLoS Genet. 2007 Jan 12;3(1):e10.

Dunn CA, Medstrand P, Mager DL. An endogenous retroviral long terminal repeat is the dominant promoter for human beta1,3-galactosyltransferase 5 in the colon. Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12841-12846.

Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, et al. Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18613-18618.

Colmegna I, Garry RF. Abstract Role of endogenous retroviruses in autoimmune diseases. Infect Dis Clin North Am. 2006 Dec;20(4):913-929.
 
Phronesis said:
About 8% of the human genome mass consists of sequences of retroviral origin and it is thought that in the evolutionary past, exogenous retroviruses formed proviruses in the genomes of germ cells of ancestral primate species.
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More pathetic plagiarism by Phrony:


About 8% of the human genome mass consists of sequences of retroviral origin (16). It is thought that in the evolutionary past, exogenous retroviruses formed proviruses in the genomes of germ cells of ancestral primate species.
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Oh dear rainman. It is really pathetic to accuse someone of plagiarism if you can't even comprehend the sentence you are accusing the person of plagiarising... But, as you know, that sentence is from my blog, well referenced, and describes a fact and does not misrepresent the fact. But hey, this is an old tactic from the pointless posse. If they haven't got a clue, they just try and drag the other person down to their level with a bit of mudslinging. No discussion of simple facts because the genes for constructive exchange and comprehension of facts are....missing.
 
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Phronesis said:
Oh dear rainman. It is really pathetic to accuse someone of plagiarism if you can't even comprehend the sentence you are accusing the person of plagiarising... But, as you know, that sentence is from my blog, well referenced, and describes a fact and does not misrepresent the fact. But hey, this is an old tactic from the pointless posse. If they haven't got a clue, they just try and drag the other person down to their level with a bit of mudslinging. No discussion of simple facts because the genes for constructive exchange and comprehension of facts are....missing.
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You blog is this article then:

Copyright © 2005, American Society for Microbiology
Human Endogenous Retrovirus HERV-K14 Families: Status, Variants, Evolution, and Mobilization of Other Cellular Sequences†
Aline Flockerzi,1 Stefan Burkhardt,2 Werner Schempp,3 Eckart Meese,1 and Jens Mayer1*
Department of Human Genetics, University of Saarland, Homburg,1Max-Planck-Institut für Informatik, Saarbrücken,2Institute of Human Genetics and Anthropology, University of Freiburg, Freiburg, Germany, 3
*Corresponding author. Mailing address: Department of Human Genetics, Building 60, University of Saarland, 66421 Homburg, Germany. Phone: 49 6841 1626627. Fax: 49 6841 1626186. E-mail: [email protected].
Received June 8, 2004; Accepted October 8, 2004.
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Or is it that because you plagiarised that article in "your" blog and then copied said blog here, it's not really plagiarism?

You see, we know you struggle to put simple English sentences together, so articulate outbursts "by you" must be copied from others.

You thieve, lie, and plagiarise. And you are boring, which is perhaps the bigger sin.
:eek::eek:
 
Talk about boring mudsling tactics.

Source of information is referenced.
It describes a fact.

Get over it and while you are at it, get a biology book to describe you simple facts.
 
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Source of information was referenced.
Information describes a fact.
 
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