Imperfect system is all that protects you from genetic parasites out to destroy your genes

DNA

We like to think of evolution as a fine-tuning process, one that whittles away genetic redundancies. The only problem is, we are not fine-tuned machines. Our bodies are chock-full of parts that either don't work anymore or are so buggy that our biology has Macgyvered a way to make it work.

Take our DNA. No, seriously, take our DNA. It's mostly garbage anyways. Fifty percent of our is comprised of genetic parasites, called transposable elements or , that usually lie dormant. When they are allowed to move around the genome, they can wreak havoc on our genes. These bundles of rogue DNA sequences, nicknamed jumping genes, can hop into an essential gene and interrupt it, leading to a variety of mutations that cause conditions like infertility.

Our reproductive cells, called germ cells, are particularly sensitive to transposons, so they rely on a system called the PIWI pathway to keep the transposons in check. Scientists have long wondered how the pathway works and why, despite its checks and balances, do transposons still make up such a large portion of our genome. Understanding the system would help scientists demystify human infertility and other diseases that result when transposons run amok.

Brandeis biology professor Nelson Lau and his lab recently published two studies on the PIWI pathway, short for P-element Induced Wimpy testis. When the pathway is blocked in fruit flies, it results in small, infertile testes and ovaries.

The pathway's main weapons against transposons are PIWI proteins and small RNA molecules called piRNAs.

Think of PIWI proteins as transposon bounty hunters and piRNAs as the wanted posters that provide vital information about the outlaw DNA. But the piRNAs don't offer a complete picture. "Germ cells do something very weird by shredding that wanted poster into a lot of small pieces," Lau says. "Instead of carrying the whole poster, piRNAs carry what might look like part of a nose, half of an eye or a sliver of a lip."

Just as a shredded wanted poster could match many faces, those small piRNAs could match many good genes, so how do PIWI proteins track down and silence transposons without silencing good genes in the process?

In a study published in RNA, Lau and his team, led by graduate student Josef Clark and former technician Christina Post, observed that PIWI proteins are careful. The proteins waited until they had a good composite picture from enough piRNAs before they clamped down on the transposon

But that doesn't mean the system is flawless. Far from it, Lau's team discovered.

In a second study published in Genome Research, Lau and postdocs Yuliya Sytnikova, Reazur Rahman and bioinformatician Gung-wei Chirn observed new transposable elements in the fruit fly cells moving to different areas of the genome, affecting nearby genes. "We all knew that the PIWI pathway was continuously active, so the conventional wisdom was that it was doing a decent job keeping these transposons under wraps," Lau says. "We stood corrected."

It turns out transposons are not so easily subdued. Many slipped past the PIWI system, landing on new genome spots and impacting surrounding genes. Some transposons could even make disguises—long non-coding RNAs that Lau thinks are meant to trick the PIWI proteins.

This may explain why transposons continue to make up such a large part of our genome, Lau says. "The PIWI pathway works just well enough to allow our to develop, but not well enough to keep all of the transposons fully redacted," he says.

This may seem an ineffective way to protect our genome—our body's most important artifact—but there may be a method in PIWI's madness. After all, transposons have evolved with every member of the animal kingdom, from sponges to humans—there must be some reason they're tolerated.

Perhaps, Lau says, a bit of genetic mischief, in the right places, is good. It ensures genetic variation and diversity, which is important for a species to reproduce and evolve.

Like so much of our biology, it's not pretty but it is effective—for the most part.


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A class of RNA molecules protects germ cells from damage, researchers show

Journal information: Genome Research

Citation: Imperfect system is all that protects you from genetic parasites out to destroy your genes (2014, November 17) retrieved 23 September 2019 from https://phys.org/news/2014-11-imperfect-genetic-parasites-genes.html
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JVK
Nov 17, 2014
... think of evolution as a fine-tuning process, one that whittles away genetic redundancies. The only problem is, we are not fine-tuned machines.


http://genomebiol...15/1/401

Excerpt: "...the interactions between pre-mRNA and proteins fine-tune alternative splicing in a manner that can gradually create new protein functionalities without the need to create additional genes and without affecting existing proteins [4-6]."

Apparently, others have realized that evolution cannot fine-tune anything via mutations and natural selection. So they describe the nutrient-dependent fine tuning that occurs via amino acid substitutions and their pheromone-controlled fixation as if it was an imperfect system.

This, despite the fact that the system links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms. For examples see: http://www.ncbi.n...24693353

Nov 17, 2014
Our bodies are chock-full of parts that either don't work anymore or are so buggy that our biology has Macgyvered a way to make it work.


And I am here to tell you, after 40 this increases exponentially with age.


Nov 18, 2014
evolution cannot fine-tune anything via mutations
well that rules out your model as well then, perfume boy
this specifically means that your model CANNOT fine tune anything nor can you support it as being a viable model refuting evolution because, IN YOUR OWN WORDS :
Captain Stumpy asked jk
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
(this is the DEFINITION of mutation) to which you (jk) answered
YES!
--Thanks for asking
you you are either REFUTING your own model or you are STUPIDLY not able to see how your model causes mutaitons

GO TROLL ELSEWHERE

your PSEUDOSCIENCE is only being pushed because your faith demands it and your perfume wants the notoriety

JVK
Nov 18, 2014
I wonder how these scientists, who accept the idea that most of the information in DNA is unnecessary, explain the fact that everything in the human and other living organisms is exactly what they need to survive...


Thanks for asking.

The facts that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via RNA-mediated events and species-specificity are included in this article and my comments to The Scientist Magazine. "Species-Specific" http://www.the-sc...pecific/

Excerpt: Scientists uncover striking differences between mouse and human gene expression across a variety of tissues.

Unfortunately, Captain Stumpy prevents intelligent discussion of facts here. Hopefully, the moderators at The Scientist Magazine will limit his presence there.

Nov 19, 2014
Ren82
I wonder how these scientists, who accept the idea that most of the information in DNA is unnecessary, explain the fact that everything in the human and other living organisms is exactly what they need to survive in their environment without excesses or deficiency?
You are showing yet again you are badly misinformed or ignoring reproductive biology.

Eg. Human females born with ~million eggs, human males ejaculate ~250million sperm, wouldnt this be correct to say its an 'excess' ?

Ren82 claimed
Why have appeared and saved as a useful for the organisms such safeguards once they stop progrеs of evolution?
Who has ever claimed evolution should or even could stop ?

Ren82 claimed
When you want to support a compromised theory, you can produce only anti science.
Like the claim a god spoke to a human & explained it was the choice of a girl (Eve) to go against god so it punished EVERYONE so badly is why we have diseases & need an immune system ?

Logic ?

Nov 19, 2014
Unfortunately, Captain Stumpy prevents intelligent discussion of facts here. Hopefully, the moderators at The Scientist Magazine will limit his presence there
the only INTELLIGENT conversation is one where all parties agree on a nomenclature, such as the one used by biologists and geneticists

as such, you REFUSE to accept the terminology even though you say you are working as a "serious scientist" in the field
you MAKE UP your own definitions, even when you've been shown the error of your ways, such as when I asked
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
(this is the DEFINITION of mutation) to which you answered
YES!
--Thanks for asking
as for "The Scientist Magazine" [sic]
they do NOT inhibit me from posting there in ANY way

so sad for you, jvk-TROLL

JVK
Nov 19, 2014
Nutrient-dependent RNA-directed DNA methylation links amino acid substitutions to cell type differentiation and differences in morphology and behavior in all primates. That is the basis for the following research.

Differentially Methylated Plasticity Genes in the Amygdala of Young Primates Are Linked to Anxious Temperament, an at Risk Phenotype for Anxiety and Depressive Disorders
http://www.jneuro...act?etoc

"To investigate the role of DNA methylation in the development and expression of AT, we performed genome-wide DNA methylation and mRNA expression analyses in Ce tissue collected from young monkeys repeatedly phenotyped for AT and its associated brain metabolism."

They are not attempting to foolishly link mutations to differences in morphology or behavior because mutations cannot be used to link genetic networks and species-specific metabolic networks. Only an idiot would attempt to link a DEFINITION of mutation into anything.

Nov 19, 2014
Ren82 for a change asked
Are you sure that women are born with millions of eggs?.
Yes, here is a fairly good explanation which also goes into degeneration & chromosomal abnormalities, this goes toward refuting your idea of intelligent design or excess etc
http://www.cledp....ith.html

You have made claims you have shown why complexity can't continue but you havent, this is the problem with religious people; they start by blindly accepting a claim then when they also make claims they consider this sufficient 'proof' - obviously its not & cannot ever be Science.

Eg. You have claimed you know what 'complex' is but cannot indicate any metric on scale.

ie. You accept formamide is naturally produced in early earth atmosphere and that Guanine arises from that. You have also stated others can be produced from simple chemistry but, you cannot describe the measure of complexity that you believe cannot occur naturally...

Nov 20, 2014
@Ren82 This is a purely mathematical probability without taking into account external environmental factors that are not in fact allow the synthesis of such a complex organic molecule by chance.
Real living systems oscillate between average and improbable, so chance of finding some new, innovative biological niche is maximized. You obviously have no idea about what you're writing

Nov 20, 2014
Ren82 has to stop LYING, actually read & learn
Do I wrote something wrong? Do scientists have an answer how did the life occure on Earth by pure chance?
Your comprehension is bad, your logic is flawed, your idea of complexity is arbitrary.

U have been told BEFORE it is NOT 'pure chance', why are U lying ???????

Its ALREADY proved atoms & molecules self assemble, its called chemistry !

Along with that; activation energy, equilibria, probabilistic interaction influenced by
temperature, pressure, excess or deficiencies of various components as all environments
have been present on Earth for a LONG time !

Have U not read or even thought, early life processes reached a stable equilibrium LONG ago & before there was enough O2 for widespread oxidation, such as in deep oceans where heat, pressure & temperature are abundant !

Be specific, U have not yet described detail when u claim 'complex' can't occur !

Define your idea of 'complex' & where it comes from - maths ?

Nov 20, 2014
Ren82 claimed
Therefore purely statistical to appear by chance such DNA in the primordial environment probability is:
1 / 1,308,759 ^ 4 = 1 / 2 933 855 533 861 496 119 446 561;
U missed the point & already been told that such 'pure chance' is inappropriate !

Can't U understand issue of foundational chemistry.

****
Start with relative equilibria of the DNA base pairs, there are literally millions of intermediate molecular combinations which R so short lived U cannot isolate them for long enough to explore all their interactions but, it is known from chemical equilibria evidence & instrumentation they occur. Eg. Very short laser pulses to probe high speed uncommon reactions which are proven to OCCUR which U R ignorant of.
****

Ren82 - What is your definition of 'complex' ?

Ren82 - WHY should U think it stops at arbitrary point because a god claimed it to Moses ?

Your god IS very nasty, punishing the innocent continuously (for ever) because of a girl.

Yuck !

Nov 20, 2014
Ren82 claimed
This is a purely mathematical probability without taking into account external environmental factors that are not in fact allow the synthesis of such a complex organic molecule by chance.
No. U are wrong, because U cannot know all the quantum detail of ANY environment in which permutations of arrangements occur, that must be damn obvious even to people of average IQ.

Why can't u see that ?

See my earlier post re intermediate molecules & think self assembly !

Ren82 claimed
Not consider the complex protein molecules that need to occur simultaneously with the DNA to be able to read and translate this information.
Wrong. They don't NEED to occur "simultaneously" at all.

Why are U not expanding your reading in biochemistry or chemical equilibria or combinatorial activation energies of short lived intermediate molecular interactions.

Atoms self assemble to molecules to structures etc, why SHOULD it stop anywhere & THEN need a god to step in ?

Nov 20, 2014
Ren82 missed the point
... simplest possible form of life allows only one unique DNA or RNA, which will match up to its chemical structure and functions in order to provides its metabolism.
What U didn't think about is BEFORE organisms continue progression by reproduction, there are components (short lived) which enable the foundational scaffolding I have described.

Because U can't see intermediate molecules does not mean they don't have means to assemble greater complexity which, due to issues of activation energy & equilibria, allow the more complex forms (seen) to be (more) stable.

Ren82 glossed over early steps
Even the simplest of organisms are uniquely complex.
To a degree (but clones) but, you havent noticed I'm offering comment about earlier in that process long before organisms as a whole replicate independently.

Self-assembly of less complex molecules U accepted (Guanine), if your definition of complex is an organism, U go too far on this step !

Nov 20, 2014
Ren82 claimed
You constantly miss the fact that such organism need complex DNA and many different proteins at the same time in the same place to begin to exist and to support its metabolism.
No I have not missed that. This is far beyond addressing my earlier point in response to your assertion life can only come about by massive simultaneity.

YOU missed the point; BEFORE an organism can replicate independently through evolution its constituents can readily self-assemble & do so by way of intermediate molecules which are very short lived but observed.

Ren82 claimed
But probability to occur in one place so different complex organic molecules is virtualy zero.
Because your maths IGNORES HUGE permutation space ie Arrangements

Ren82 claimed
..will disintegrate very quickly thank to adverse factors of this environment.
Evidence please, especially in the deep oceans where oxygen is very low for oxidation ?

U accepted self-assembly of DNA base pairs !

Nov 20, 2014
@Ren82 "Real living systems oscillate between average and improbable,.."

Is there any sense in this sentence?
Real living systems become novelty seeking at all levels from cellular to psychological. Then they revert to an average mode to incorporate their discoveries into their memory. You are taught to fear evolution and do everything humanly possible to prevent it in your personal life. Even stupid robots and smartphones can upgrade themselves now. You're more akin to fossilized dinosaur turd

However a chrostopath such as yourself is taught to never ask questions or seek novelty, so you only orbit about the average, become defensive about figments of your script that are non-adaptive, and grow more irrelevant with time like a fossil

JVK
Nov 20, 2014
Thanks Ren82

I was beginning to think that intelligent life did not exist among the participants at phys.org news

Have you read this: http://www.biorxi...0/010884
Excerpt: ...a substantial fraction of the RNA content in mammalian cells remains remarkably constant across large biological and evoluionary scales."

The focus is on RNA-mediated events that differentiate cell types via amino acid substitutions, not the pseudoscientific nonsense of population geneticists who never connected genetic networks to metabolic networks.

Nov 20, 2014
Ren82 claimed
I stick to the laws of physics and the facts of the observations and experiments in the fields of science such as physics, microbiology, genetics, biochemistry, Informatics.
No.

Don't believe U !

Only way U "could", if U were expert in ALL these areas WITH formal studies AND kept informed of several 1000's peer reviewed papers, a HUGE amount of time, ie. none for prayer !

Then U claim to have uni qualifications in; Physics, Microbiology, Genetics, Biochemistry, Informatics ?

Evidence U lie is clear, U conceded elsewhere U didn't understand complexity of Activation Energy (chemistry), it's pre-requisite for uni; biochemistry, microbiology etc

Had U studied biochemistry U would also know about intermediate reactions.

U should know probability & statistics also pre-requisite for ALL above, yet in your facile attempt at probability calculation U completely ignored permutations & arrangements & with respect to time.

Your claims appear deluded !

Nov 20, 2014
Ren82 with proof of delusion
I stick to the laws of physics and the facts of the observations and experiments in the fields of science such as physics, microbiology, genetics, biochemistry, Informatics. These facts strongly deny even the slightest possibility of self organization of matter on sufficiently complex level, allowing the emergence of life and its gradual development.
Look at what U have said in above two sentences.

First:- U claim to have (wide) knowledge of many science fields & be complete would demands formal studies ie. uni qualifications AND constantly reading 1000's of journal articles as so many in all these fields are published often.

Second:- You claim "The facts..."

You FAIL dismally in logic & cognition. You cannot ascribe a claim to knowledge as 'facts'.

U have NO facts, U are ONLY claim, U have NO evidence complex self-assembly STOPS at some arbitrary point - I have asked U to ascribe a metric - U ignored that question.

TBC

JVK
Nov 20, 2014
Darwin 2.0: Scientists shed new light on how species diverge
http://phys.org/n...rge.html

Dizzying heights: Prehistoric farming on the 'roof of the world'
http://phys.org/n...oof.html

Those who think they know anything about physics, chemistry, or molecular biology can now tell the rest of us how birds and humans evolved when there is only evidence that links ecological variation to ecological adaptation.

Nov 21, 2014
JVK claimed
Those who think they know anything about physics, chemistry, or molecular biology can now tell the rest of us how birds and humans evolved when there is only evidence that links ecological variation to ecological adaptation.
Given we have only had microbiology for ~200yrs U would have to agree we have made great strides in advanced understanding of biological processes, especially molecular biology. Now we have advanced instrumentation that ffers micro scale NMR & femto lasers to observe dynamics of intermediate molecular interactions which scaffold to larger structures then its clear it will only be a matter of time before such questions as U ask can be addressed.

In the meantime it would be helpful for U & your creationist buddies to read this:-
http://en.wikiped...mergence

U would have to agree atoms/molecules self-assemble (SA) according to several rules.

So what is your idea as to when a level of complexity in self-assembly stops ?

JVK
Nov 21, 2014
Thanks for not being afraid to ask stupid questions that can readily be answered by a medical laboratory scientist who spent the last two years of a 40 year career in the microbiology department of a hospital laboratory.

Re: the ignorance of emergence vs my claim.

Evolutionary theorists and other pseudoscientists don't seem to realize that self-assembly starts with nutrient-dependent metabolism and stops when the thermodynamic cycles of protein biosynthesis and degradation are stabilized by RNA-directed DNA methylation and RNA-mediated events. The events link nutrient-dependent amino acid substitutions to the stability of DNA in organized genomes. Theorists attribute species diversity to 'emergence' or evolutionary events that cannot possibly be linked from ecological variation to ecological adaptation in species from microbes to man via conserved molecular mechanisms that must involve the bio-physically constrained chemistry of protein folding.

Nov 22, 2014
Ren82 missed the point
@Mike_Massen
no, he didn't miss the point, he ignored it completely, Mike!
he is a creationist, like jk... they ignore evidence that refutes their religion
he has already been given tons of links to sites and studies showing him how evolution works, mutations, biology and more
he ignores it because it doesn't jibe with his religion and thus it doesn't exist for him/them

just report them as trolls

I stick to the laws of physics and the facts of the observations and experiments
@dumb&dumber-ren
no, you do NOT
you IGNORED every study that i linked which proved you wrong
then played STUPID with the rest
you are not "asking naughty questions"- you are championing a religion and failing to make your point
there is benefit in playing "devils advocate", but all you are doing is denying science

Nov 22, 2014
medical laboratory scientist who spent the last two years of a 40 year career in the microbiology department of a hospital laboratory
at least you are not trying to claim experience in diagnostic medicine again...
Evolutionary theorists and other pseudoscientists don't seem to realize
actually, it is YOU who doesn't realize how stupid you are
case in point: your failure to correctly utilize the nomenclature/lexicno while claiming "40 years" experience
also, you claim your model somehow transcends evolution theory when you don't comprehend that it actually SUPPORTS it
why?
because your model causes mutations (and you've already admitted it)
your even failed when you tried to "interpret" other studies
So Kohl is mistaken if he is claiming that my study (or Rich Lenski's work) provide evidence AGAINST the role of mutations in evolution
epic failure for jk and the creationist team

religion inhibits thought and controls people, that's it

JVK
Nov 30, 2014
at least you are not trying to claim experience in diagnostic medicine again...


What makes you think I am not (other than the fact you are an idiot)? Of course I have that experience and expertise. I quote from my 2012 review: http://www.ncbi.n...24693349
"The gene, cell, tissue, organ, organ-system pathway is a neuroscientifically established link between sensory input and behavior. Marts and Resnick (2007) stress the importance of this pathway in the context of a systems biology approach to pharmacogenomics."

http://medicalxpr...ome.html
"It's amazing how precisely the 60:40 ratio is maintained. It occurs in the genome of every individual – almost like a magic formula," says Hoehe. The 60:40 distribution ratio appears to be essential for survival. "This formula may help us to understand how gene variability occurs and how it affects gene function."

https://www.youtu...G_9EEeeA

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