'Junk DNA' drives embryonic development

These are differentiating mouse embryonic stem cells (green = mesoderm progenitor cells, red = endoderm progenitor cells). The microRNAs identified in this study block endoderm formation, while enhancing mesoderm formation. Credit: Sanford-Burnham Medical Research Institute

An embryo is an amazing thing. From just one initial cell, an entire living, breathing body emerges, full of working cells and organs. It comes as no surprise that embryonic development is a very carefully orchestrated process—everything has to fall into the right place at the right time. Developmental and cell biologists study this very thing, unraveling the molecular cues that determine how we become human.

"One of the first, and arguably most important, steps in development is the allocation of into three germ layers—ectoderm, , and endoderm—that give rise to all tissues and organs in the body," explains Mark Mercola, Ph.D., professor and director of Sanford-Burnham's and Regeneration Program in the Sanford Children's Health Research Center.

In a study published in the journal & Development, Mercola and his team, including postdoctoral researcher Alexandre Colas, Ph.D., and Wesley McKeithan, discovered that microRNAs play an important role in this cell- and germ layer-directing process during development.

MicroRNA: one man's junk is another's treasure

MicroRNAs are small pieces of genetic material similar to the messenger RNA that carries protein-encoding recipes from a cell's genome out to the protein-building machinery in the cytoplasm. Only microRNAs don't encode proteins. So, for many years, scientists dismissed the regions of the genome that encode these small, non-protein coding RNAs as "junk."

We now know that microRNAs are far from junk. They may not encode their own proteins, but they do bind messenger RNA, preventing their encoded proteins from being constructed. In this way, microRNAs play important roles in determining which proteins are produced (or not produced) at a given time.

MicroRNAs are increasingly recognized as an important part of both normal cellular function and the development of human disease.

So, why not , too?

Directing cellular traffic

To pinpoint which—if any—microRNAs influence germ layer formation in early embryonic development, Mercola and his team individually studied most (about 900) of the microRNAs from the human genome. They tested each microRNA's ability to direct formation of mesoderm and endoderm from embryonic stem cells. In doing so, they discovered that two microRNA families—called let-7 and miR-18—block endoderm formation, while enhancing mesoderm and ectoderm formation.

The researchers confirmed their finding by artificially blocking let-7 function and checking to see what happened. That move dramatically altered embryonic cell fate, diverting would-be mesoderm and ectoderm into endoderm and underscoring the microRNA's crucial role in development.

But they still wanted to know more…how do let-7 and miR-18 work? Mercola's team went on to determine that these microRNAs direct mesoderm and ectoderm formation by dampening the TGFβ signaling pathway. TGFβ is a molecule that influences many cellular behaviors, including proliferation and differentiation. When these microRNAs tinker with TGFβ activity, they send cells on a certain course—some go on to become bone, others brain.

"We've now shown that microRNAs are powerful regulators of embryonic cell fate," Mercola says. "But our study also demonstrates that screening techniques, combined with systems biology, provide a paradigm for whole-genome screening and its use in identifying molecular signals that control complex biological processes."

More information: Colas AR, McKeithan WL, Cunningham TJ, Bushway PJ, Garmire LX, Duester G, Subramaniam S, & Mercola M (2012). Whole-genome microRNA screening identifies let-7 and mir-18 as regulators of germ layer formation during early embryogenesis. Genes & development PMID: 23152446

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Tachyon8491
1.7 / 5 (6) Dec 03, 2012
Fundamentally important proof. I am not hesitant to point out however, that intuitive understanding of "junk DNA's" role arose very long ago...
Lurker2358
1.6 / 5 (7) Dec 03, 2012
I've been telling people for years that there was no such thing as "Junk DNA," but you can't convince some of the most radical leftists that human beings are anything other than "Junk".

The structures of life are produced in a specific order, showing forward planning at every stage of the development, which means there is no junk, and clearly means it was intelligently designed at some stage of existence.

The fact some scientist is only just now figuring this out is just proof that previous "scientists" did not do due diligence, and were far too eager to accept the "life exists by accident and junk DNA proves it" lie that they fed one another for years.

Junk DNA believing atheists can spout their vitriol at "creationists," but it is the "junk DNA" believing evolutionists, and especially the hard atheist evolutionists, who now look like complete fools; as if we didn't already know that ahead of time.
JVK
2.3 / 5 (3) Dec 04, 2012
The epigenetically effected microRNA /messenger RNA balance is responsible for adaptive evolution of our brain and behavior.
Based on what's currently known, I presented an updated model of that last month: http://f1000.com/.../1092760
This model of systems biology represents the conservation of bottom-up organization and top-down activation via:
1.Nutrient-dependent stress-induced and social stress-induced intracellular changes in the homeostatic balance of microRNA(miRNA) and messenger RNA (mRNA);
2.Intermolecular changes in DNA (genes);
3.Non-random experience-dependent stochastic variations in de novo gene expression for odor receptors;
4.The required gene-cell-tissue-organ-organ system pathway that links sensory input directly to gene activation in neurosecretory cells of the brain;
5.The required reciprocity that links gene expression to behavior that alters gene expression (i.e., from genes to behavior and back).
The only good reason to believe is evidence!
Tausch
1 / 5 (1) Dec 04, 2012
Binding prevents construction. What regulates binding?
JVK
3 / 5 (2) Dec 04, 2012
Could it be, perhaps, random mutations? Isn't there some silly theory about that? What do you think regulates binding? Is there a model for it?
triplehelix
3 / 5 (2) Dec 04, 2012
Lurker, You are simply assuming a top down design approach. Things can "look" designed from a bottom up approach. An example of this would be pretty much any company these days where the work is done by the lower echelons and then presented by a senior manager as if it was all done by them and planned that way. The workings were bottom up, but it looks top down.

We use this thing called evidence. Even if Junk DNA isnt Junk, this doesnt change the fact that thousands of species have been genetically identified and they fit perfectly on evolutionary/phylogenetic trees in terms of conserved genes and when genes develop and changed etc, within predictable and known timescales, with not a single anomolous result throwing everything out of whack.

Also, the term "Junk DNA" was not popularised by most scientists, its term was coined due to the fact we didn't know its exact workings and didnt directly make proteins. Most scientists agreed it probably does have a role, but as yet unknown.
Tachyon8491
1.6 / 5 (7) Dec 04, 2012
I for one do not believe in randomicity in any form, not even in the quantal domain where a-causal quantum-indeterminacy is assumed to reign, and where random quantum fluctuations are axiomatically proposed to originate all higher forms of complexity. Compared to molecular embryologists, the morphogenetic embryologists are making a popular comeback, supported by the Gariaev phantom DNA effect and multifactorial evidence from many other fields. The function of non-epiphenomenal consciousness is completely ignored in causal evolutions: consequently all quantum physics, philosophy, metaphysics and theoretical physics, let alone the public paradigm are full of indeterministic conceptual thinking in the forms of "coincidence," "accident" "luck," "misfortune" and "acts of some deity" (the latter being geographically sensitive). Forty years of deep-going research have convinced me of a more rational (and beautiful) alternative. (author of three published books on cosmogony and complexity)
triplehelix
3.7 / 5 (3) Dec 04, 2012
Also, out of all the "Junk DNA" they have found one particular section which has a role, based on only preliminary data. You then claim all knowledge of the entire situation and state with divine confidence that every single piece of "Junk DNA" must therefore have a use...

This is at best pathetic, at worst, extremely ignorant. You're doing EXACTLY what those "atheistic scientists" APPARENTLY do. Get one or two bits of evidence and claim unknown things to be true (in your case, design and creation).

Hypocritical much?

Also no, most "atheistic scientists" did not state Junk DNA is definitely Junk DNA. Any decent scientist will say "more research is required" for any unknowns. You get the occasional few crazy ones, but they're few and far between. This one tiny development into genetics does not remove the fact that masses of genetic data still comply perfectly with evolution and a bottom up natural selection approach, not a top down designer approach.
triplehelix
3 / 5 (2) Dec 04, 2012
Tachyon, I cant speak for quantum physics as it is something I am not excellent at. Random mutations in Biology however, are for all intents and purposes-random. Yes they have chemical and physical reasons why the A became a G, and eventually led to a modified or new protein/sub species etc. However that causation is so lost in the noise of the data, that it is considered "random" macro scale wise. Its occurrence was not planned, designed, or intellectually thought out, and is on such a small and almost invisible scale as to be realistically deemed "random. If one were to score the causation between the individual genetic variations throughout environment and vertical transfer from breeding, and the score between the physical natural selection of a species due to environment, predation, etc, you would have magnitudal differences. As such, these can be classed as random mutations being directed via non random selection :D
JVK
2 / 5 (4) Dec 04, 2012
@triplehelix: Re: Random mutations being directed via non random selection??? Bottom-up nutrient chemical-dependent epigenetic changes in intracellular signaling and stochastic gene expression that is controlled by metabolism of the nutrient chemicals to pheromones that control reproduction from their top-down epigenetic effects on intracellular signaling and stochastic gene expression is not random. It represents concurrent effects of the sensory environment on molecular mechanisms that link genes to behavior and back. Is that what you're calling non-random selection (e.g., selection for food and mates)? If so, how do random mutations cause anything in the context of non-random Natural Selection for food, and Sexual Selection for mates? You lost me in the noise of your randomness. It's as if you were trying to tell us the finely tuned microRNA / messenger RNA balance results from randomness/noise. Hope you can clarify a bit. Thanks.
triplehelix
3 / 5 (2) Dec 05, 2012
Congratulations, you ignored my entire post. I said that mutations do have an underlying cause. My point was these explanations are preliminary, or not fully understood, and in comparison to the direct driving force of natural selection, it can be seen as "random". These causatives don't DIRECT that species somewhere, the mutations can be on any particular gene, no a specific given one. A mutation will affect 1, 2 or 3 of our genes. Natural selection will guarantee its survival. Hence "Random" and "Non Random". No it is not truly random, you would know I said this if you bothered to read my post. Good photographic memory parrot fashion you have there. Try understanding what you wrote and you might get further
Tausch
1 / 5 (1) Dec 05, 2012
Binding prevents construction. What regulates binding?-T

Could it be, perhaps, random mutations? Isn't there some silly theory about that? What do you think regulates binding? Is there a model for it?-JVK


"...dampening the TGFβ signaling pathway" from the random process you referenced results in chaos not order.

There is no regulation model for the binding. A non random model of regulated binding aligns more readily with the processes already uncovered.
Tachyon8491
1.7 / 5 (6) Dec 05, 2012
Hi Triple,
"Random mutations in Biology however, are for all intents and purposes-random."
I understand your point of view but differ diametrically from it. To me, the "noise" of random quantum fluctuations that then cause "random" mutation resulting in e.g. teratogenic and autoimmune phenomena, are not random at all. I also understand that this orientation cannot be empirically proven - it is a matter of intuitive, philosophical inclination but - does have evidence when a vastly bigger picture is addressed - e.g. morphogenetic fields (Weiss, Speman, etc.); phantom DNA effect; epigenetic mRNA optimisation of allelic switching; paraphysical phenomena such as NDE and OBE (van Lommel study); and more. I feel that the randomicity perspective is generated by an overwhelming many-to-one ratio between quantal entities and observer making it look "random" where such dynamics could also be explained as quantisations of consciousness from a singular collective - experimenting with potential..
JVK
2 / 5 (4) Dec 05, 2012
A non random model of regulated binding aligns more readily with the processes already uncovered.

I thought that was obvious. Bottom-up receptor-mediated stochastic gene expression driven by nutrient chemicals is simultaneously controlled by top-down receptor mediated pheromone-controlled stochastic gene expression, which makes the gene to behavior and back (e.g., to receptor-mediated behavior) non-random. It would be great if triplehelix attempted to answer my question about how random mutations could cause adaptive evolution of the gene to behavior and back model I have detailed.
Random or not, I don't see how natural selection guarantees survival of mutations; most are deleterious as everyone else seems to know.
Tausch
3 / 5 (2) Dec 06, 2012
I can not make any sense from your misapprehensions.
Try rewording your thoughts.
A stochastic process is a random process.
I suggested otherwise.
You think that is obvious.
And then dismiss both processes with "Random or not", and assume the knowledge everyone else knows with an change in topic issue.
You make no sense. You never have.
JVK
1 / 5 (3) Dec 06, 2012
From fertilization to adult sexual behavior: http://www.hawaii...ion.html made sense of the obvious link from olfactory/pheromonal input to stochastic gene expression and behavior in species from microbes to man. I detailed it further in an award-winning Neuroendocrinology Letters review: Human pheromones: integrating neuroendocrinology and ethology http://www.nel.ed...view.htm and in an award-winning journal article concurrently published as a book chapter in the Handbook of the Evolution of Human Sexuality: The Mind's Eyes: Human pheromones, neuroscience, and male sexual preferences http://www2.hu-be...kohl.htm

If you cannot understand representations drawn from award-winning publications, simply admit the problem is your ignorance, not my inability to make sense of non-random stochastic gene expression in the context of adaptive evolution. http://f1000.com/.../1092760
Tausch
3 / 5 (2) Dec 06, 2012
"...non-random stochastic..." is a oxymoron.
Your constant use of not only this but other meaningless expressions will increase your inability to make sense of anything.

You need only to post. Until the only reply from others is indifference - a response worthy of the nonsense you post.
JVK
1 / 5 (3) Dec 06, 2012
"...non-random stochastic..." is a oxymoron.


Only a moron would ignore my publication history and the ENCODE project data. But, here you are, again! You have built a straw man argument outside the context of the gene expression that drives embryonic development by taking "...non-random stochastic..." outside the context of systems biology and the requirement for non-random stochastic gene expression. Stochastic gene expression that is altered from the bottom up by the epigenetic effects of nutrient chemicals and altered from the top down by pheromones is not random (It's calibrated, standardized, and controlled). That makes it non-random stochastic gene expression whether or not you are intelligent enough to realize it.
Tausch
3 / 5 (2) Dec 06, 2012
You need only to post. Until the only reply from others is indifference ...
JVK
1 / 5 (3) Dec 06, 2012
You need only to post. Until the only reply from others is indifference ...


Indifference is difficult to distinguish from ignorance in your case.

"Systems biology meets epigenetics: A computational model explains epigenome dynamics during differentiation." December 4th, 2012.

http://phys.org/n...ion.html
freethinking
1 / 5 (3) Dec 08, 2012
Hummm, science showing a person is created at conception. If you have an abortion, you KILL a person.