Rethinking junk DNA

Source of information was referenced (reference 2, read...).
Information describes a fact.

Stole? Another lie. Stealing facts? Oh no, call the police, I stole the text "The earth revolves around the sun" without referencing the text.

Lol, everytime the words become a bit to big, you and your pointless toadies shout "plagiarism". Just because a sentence that describes a fact is a bit more complex than "The earth revolves around the sun", does not mean I plagiarised the fact or the text. In this case it is referenced as well. Shame man, pick up that biology textbook. Educate yourself.
 
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Phronesis:

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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Human Endogenous Retrovirus HERV-K14 Families: Status, Variants, Evolution, and Mobilization of Other Cellular Sequences:

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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Copyright © 2005, American Society for Microbiology
Aline Flockerzi,1 Stefan Burkhardt,2 Werner Schempp,3 Eckart Meese,1 and Jens Mayer1*
 
I suggest you write a complaint and watch how they laugh at your compaint about a fact that has been referenced. ROFL, you are scraping low.

Source of information was referenced (reference 2, read...).
Information describes a fact.
 
Phronesis said:
I suggest you write a complaint and watch how they laugh at your compaint(sic) about a fact that has been referenced. ROFL, you are scraping low.

Source of information was referenced (reference 2, read...).
Information describes a fact.
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Not referenced here, old boy - passed off as your own words, rather.

plagiarize or plagiarise
verb

take (the work or an idea of someone else) and pass it off as one's own.

DERIVATIVES
plagiarism noun
plagiarist noun
plagiaristic adjective
plagiarizer noun

ORIGIN
C18 (earlier (C17) as plagiarism): from Latin plagiarius 'kidnapper'.
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- my COED.

:eek::eek:
 
Trying to be funny now? That sentence is from my blog, where it is referenced. Do you want to have references for every sentence? Then I suggest you start doing the same for every little fact you give.

Now you are really scraping low. But, like I said, I suggest you write a complaint and watch how they laugh at your compaint about a fact that has been referenced.

Look, if you can't discuss plain facts (as a result of not understanding simple facts) and try to sling mud at other people, I suggest that you rather not participate in a discussion because it is just plain evident that you just can't do anything BUT troll. You can't discuss ANYTHING that is even remotely related to science without trolling, that much is evident.
 
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Phronesis said:
Trying to be funny now? That sentence is from my blog, where it is referenced. Do you want to have references for every sentence? Then I suggest you start doing the same for every little fact you give.
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Words that belong to others must be attributed and acknowledged, not passed off as one's own. There is reference neither to the original source of the words ( necessary ) nor to your blog ( irrelevant ) in the plagiarising post as it stands.

Phronesis said:
Look, if you can't discuss plain facts (as a result of not understanding simple facts) and try to sling mud at other people, I suggest that you rather not participate in a discussion because it is just plain evident that you just can't do anything BUT troll. You can't discuss ANYTHING that is even remotely related to science without trolling, that much is evident.
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Attempting to justify your plagiarism by stating that it references something you hold to be true is of no relevance. The quotes stand, and demonstrate clearly that you copied someone else's words. If you are unable to articulate the claim in your own words then either say nothing or acknowledge authorship.

I don't troll ( most of the time ). I point out lies and muddled thinking. Your own understandings of philosophical concepts ( intentionality ) and scientific concepts ( Brownian motion ) are often inaccurate or confused. This needs to be pointed out, as does your penchant for slipping creationist insinuations ( design, artificial selection ) into supposedly scientific posts.

I would pass a sarcastic comment as usual, but refrain because of moderatory warnings.
 
Oh puhlease, I wrote a sentence from my blog that is well referenced. Write a complaint if the original text bothers you so much. Just to irritate you, I will repost it (science pisses you off shame) to show how completely and utterly irrelevant you are to a discussion and that all you can DO IS TROLL.

Stop trolling. You still have not shown you even understand intentionality, nor Brownian motion, nor any other scientific fact for that matter. You just say others don't understand it. No surprise really because your "**** happens" philosophy does not really allow you to understand anything because... well your understanding is just more **** that happens according to your own philosophy.

Tell you what rainman old chop, why don't you show that you actually have a basic understanding of junk DNA and what it is since this is a thread about junk DNA...
 
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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 (Flockerzi et al., 2005)

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:


Flockerzi A, Burkhardt S, Schempp W, Meese E, Mayer J.Human endogenous retrovirus HERV-K14 families: status, variants, evolution, and mobilization of other cellular sequences. J Virol. 2005 Mar;79(5):2941-9.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 (Flockerzi et al., 2005)
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Now you are learning. Try just using their words as is and quote them, in the correct fashion. You might look at some of the rest of your post, as there appear to be more unattributed passages viz some stuff from:

Role of Endogenous Retroviruses in Autoimmune Diseases
Infectious Disease Clinics of North America, Volume 20, Issue 4, Pages 913-929
I. Colmegna, R. Garry

No doubt I could dig up more. Try to be honest in what you quote now please.

PS Where is your "blog" referenced in your original post, as you claim?
 
Oh puhlease, coming from MyBB Nr 1 troll and habitual liar himself. Run along now. Btw, I put in the reference delibuirately to show you just how irrelevant it is. It has been referenced at my blog. but you knew that and is again just trolling. Amazing, and your BS is tolerated here...
 
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Phronesis said:
Oh puhlease, coming from MyBB Nr 1 troll and habitual liar himself. Run along now. Btw, I put in the reference delibuirately to show you just how irrelevant it is. It has been referenced at my blog. but you knew that and is again just trolling. Amazing, and your BS is tolerated here...
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I'll take that as the expected "nowhere". No need to get personal and rude now.

PS I don't read your blog.
 
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Me personal and rude? ROFL, coming from you, that is hilarious. You are welcome to stop trolling now.

Love your new signature btw. Just shows how dishonest and hypocritical you are by quotemining me. Meh, more trolling.
 
Wow rwenzori, I see you are still misrepresenting and quotemining me in your signature... Oh well, guess that is expected from someone that is unable to discuss a topic at hand.

Aanyway as seen here:
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.

And now:

Spare Gene Is Fodder For Fishes' Evolution

ScienceDaily (Sep. 8, 2009) — Scientists have suspected that spare parts in the genome—extra copies of functional genes that arise when genes or whole genomes get duplicated—might sometimes provide the raw materials for the evolution of new traits. Now, researchers report in a study published online on September 3rd in Current Biology, a Cell Press publication, that they have discovered a prime example of this in fish.
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Phronesis said:
Wow rwenzori, I see you are still misrepresenting and quotemining me in your signature... Oh well, guess that is expected from someone that is unable to discuss a topic at hand.
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Seeing as you insist on repeating your bogus argument beyond ad nauseam to 100 metres down the sewer, allow me to repeat the counter:

In evolutionary biology and molecular biology, junk DNA is a provisional label for the portions of the DNA sequence of a chromosome or a genome for which no function has been identified. The term was introduced in 1972 by Susumu Ohno[1], but is as of 2008 somewhat outdated, being used mainly in popular science and in a colloquial way in scientific publications. If DNA does not seem to have a function now it may have had a function in the past or may yet have a function in future.
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It took you 7 pages to dig up that?

Now tell that to all your other lackys who keep using this argument from ignorance.
Stomp the words "provisional label" into their heads.
 
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