Epigenetics- exploring

[lemit]

Of course, the thing those species are responding to doesn't exist, so those changes are completely random. There must be other species demonstrating the opposite changes in range and breeding cycles. Does anyone have data on them?

 

Thanks.

 

--lemit

[Michaelangelica]

Of course, the thing those species are responding to doesn't exist, so those changes are completely random. There must be other species demonstrating the opposite changes in range and breeding cycles. Does anyone have data on them?

 

Thanks.

 

--lemit

Now you are just being silly and perverse --LOL

[Essay]

Of course, the thing those species are responding to doesn't exist, so those changes are completely random. There must be other species demonstrating the opposite changes in range and breeding cycles. Does anyone have data on them?

 

Thanks.

 

--lemit

 

 

Phenology: The Effects of Climate Change on Ecosystem Health | EarthTrends

Phenology:

The science that deals with annually or periodically recurring natural events is called phenology. Examples of phenological observations include flowering, ripening of fruits, unfolding leaves, hatching eggs, and bird migrations. Correlations between these seasonal events (or phenophases) and the changing climate have been suggested by scientists for a long time. A recent study of more than 542 plant and 19 animal species in 21 European countries confirmed a popular but previously unproven assumption: the leafing, flowering and fruiting of more than 75% of all plant species had advanced as a result of rising temperatures. Spring and summer now arrive 2.5 days earlier each decade, and it seems that our natural environment has responded quickly.

 

USA National Phenology Network | USA National Phenology Network

"The network harnesses the power of people and the Internet to collect and share information, providing researchers with far more data than they could collect alone."

 

You too could be a phenologist!

[HydrogenBond]

To me life makes more sense, if there is a two way control system. One aspect of the control system starts at the DNA, and feeds forward ,right from the beginning of a cell's life, to get the foundation genes and proteins up and running. The other aspect of the feedback system should be connected to the environment, via the cell membrane and other proteins. That way the DNA can be induced to react quickly to real time changes within the environment, rather than depend on a single feed forward system that is trying random things until something works. If I get cold my body shivers. This is feedback to the DNA rather than DNA feedforward making me hot and cold randomly trying to predict the weather.

 

In a controlled environment, only feedforward from the DNA might be needed, since things are very predictable. If I was always in a hot environment, the DNA could set my body to warm at birth and be right. This would look like feedforward is enough. In the lab, where tests need to be repeatable, we have to set up a controlled environment. But in the real world, things are not always so predictable.

 

One observation for a feedback system, which always comes to mind, is the duplication of the DNA. During this duplication process, the DNA is off-line, with respect the cell's control system, yet the cell doesn't shut down. Although all these systems stemmed from the DNA, once in the field, they have an autonomy apart from the DNA, since the DNA is off-line, and they keep working.

 

The next question becomes, are there others systems which have levels of autonomy, apart from the DNA, after they are produced by the DNA? These would be a good place for a feedback system, to the DNA, since these systems are not fully tied into the bias of the DNA feedforward, and could offer some independent feedback, leading to such things as epigenetics.

 

An analogy for a cell with only DNA feedforward, is a boss who likes to micro manage all the employees. He has to make every decision and controls everything so he won't really listen to feedback that contradicts the boss. The alternative is an office environment, where the boss sets general policy and goals, but gives autonomy to the employees, with each employee one of his trusted protegee.

 

The first scenario will always bias the work of the employees to the boss and not allow much independent feedback. The other scenario has a boss who respects the ideas of the employees, since they are trusted in the field, fighting the battles, and have a level of autonomous competence.This office environment allows the employees to go to meetings with the boss, adding their observations, helping to shape the direction of the new policies which can better meet the real time supply and demand.

[HydrogenBond]

One of the my favorite organelles within the cell are the mitochondria. The mitochondria are argumentatively a basic unit of life. They are able to self replicate and metabolize. This makes them ideally suited as part of the cell's feedback system. The mitochondria are the engines of the cell, providing ATP needed to run the cell. They are the straw that stirs the cellular drink.

 

For example, if the mitochondria decided to go on strike and stop ATP production, the cell would shut down. Cell cycles are dependant on an increase in ATP production, to run the energy intensive process. If the mitochondria decided to be lazy, and not increase ATP at the right time, the cell cycle would run slower, maybe stop short of full replication, or maybe never run at all. This could effect the pace of evolution.

 

If the mitochondria decided to really crank up the ATP, to beyond anything seen by the cell, during cell cycles, it is conceivable that the DNA would be tripping over its own two feet, making more mistakes during replication. That last part is only speculation, but this revenge of the mitochondria is interesting to consider as a source for the Cambric explosion. It could have been the final battle for dominance between the mitochondria and the DNA, with the DNA winning.

 

One thing that has always crossed my mind is why didn't the mitochondria become the center of the ancient cell. They control the energy and therefore could have evolved a way to meter out energy favoring their own selfish genes. Evolution could have lengthened their DNA, slowly adding new protein features, extrapolating control over cellular functions farther and farther from the energy center, until the mitochondria became the dominant player in the cell. But instead, they stayed simple and more or less ignored the pace of evolution that other DNA realized.

 

The mitochondria, besides being energy moguls, are also the entropy moguls of the cell. Without ATP, most things would just sit there looking pretty. With ATP, the enzymes experience more degrees of freedom, able to do their enzyme things. With the mitochondria the moguls of energy and entropy, they have global ways to alter global dynamics within the cell at the time time. The mitochondria may not lead this control system, but once in motion the energy and entropy mogul's output sets a potential, since everything needs energy and/or entropy.

[freeztar]

First of all, this post does not address the topic as far as I can tell. Nonetheless, some things need to be addressed.

 

The mitochondria are argumentatively a basic unit of life.

 

This is incorrect. The first sentence of the wikipedia article on mitochondria states "In cell biology, a mitochondrion (plural mitochondria) is a membrane-enclosed organelle found in most eukaryotic cells". So, mitochondria are not present in all life. They are not found in prokaryotes and they are not found in all eukaryotes.

 

They are able to self replicate and metabolize.

 

This is a bit misleading. It's better, imho, to say that they replicate via binary fission. This replication is tied to cell processes though and is not autonomous of the cell.

 

This makes them ideally suited as part of the cell's feedback system.

 

How so?

 

For example, if the mitochondria decided to go on strike and stop ATP production, the cell would shut down. Cell cycles are dependant on an increase in ATP production, to run the energy intensive process. If the mitochondria decided to be lazy, and not increase ATP at the right time, the cell cycle would run slower, maybe stop short of full replication, or maybe never run at all. This could effect the pace of evolution.

 

Correct, though it's important to denote what scale of evolution you are talking about.

 

If the mitochondria decided to really crank up the ATP, to beyond anything seen by the cell, during cell cycles, it is conceivable that the DNA would be tripping over its own two feet, making more mistakes during replication. That last part is only speculation,

 

I don't think the percentage of mutations would increase, but the number of mutations might, just from the increase in the number of mitochondrial fissions (with or without a complete cell cycle). In any case, a higher number of mutations would be expected simply because they occur frequently and do not have the same error checking ability as nuclear DNA.

 

Mitochondrial disease - Wikipedia, the free encyclopedia

 

but this revenge of the mitochondria is interesting to consider as a source for the Cambric explosion.

 

I'm not sure what you mean by "revenge". Do you have any sources to support your idea? Have you looked?

 

It could have been the final battle for dominance between the mitochondria and the DNA, with the DNA winning.

 

It's important to note that mitochondria have mitochondrial DNA, which is different than the DNA kept in the cell nucleus. So in a sense you are saying that the two DNAs are battling it out, which is not the case. The nuclear DNA codes for the mitochondrial DNA (mtDNA). The mtDNA codes for enzymes necessary for the mitochondrian's function within the cell. The two work together and are not competing in healthy cells.

 

One thing that has always crossed my mind is why didn't the mitochondria become the center of the ancient cell.

 

Since the nuclear DNA codes for the mtDNA, how would this be possible?

 

The mitochondria, besides being energy moguls, are also the entropy moguls of the cell. Without ATP, most things would just sit there looking pretty. With ATP, the enzymes experience more degrees of freedom, able to do their enzyme things. With the mitochondria the moguls of energy and entropy, they have global ways to alter global dynamics within the cell at the time time. The mitochondria may not lead this control system, but once in motion the energy and entropy mogul's output sets a potential, since everything needs energy and/or entropy.

 

That last paragraph is very confusing and I'm not sure what you are trying to say. For example, what are "global ways"?

 

HB, you continue to make claims and false statements without supporting your ideas. As a science site, we place very high value on support for ideas.

 

In general, I recommend following these three logical steps when making a post.

1. Screen your ideas - Are they new or has someone thought of them before? If so, who? Is this idea valid and does it corroborate with known scientific data?

2. Research - Read up on the subject and find sources that either directly or indirectly support your ideas.

3. Post links - Once you have gathered supporting evidence, incorporate this into the expression of your ideas. There are various ways of doing that and I give you a couple examples in this post. However you do it, the important part is that the sources you used to create or support your ideas need to be easily accessible to those reading your post. Web links are best, but book or journal citations are ok if the info is not freely available online.

 

If you do this, your posts will become better and more appreciated and you will enjoy an extended stay here. If you do not, or can not, do this, you are in violation of the rules and the result should be obvious.

[CraigD]

... if the mitochondria decided to go on strike and stop ATP production ... If the mitochondria decided to really crank up the ATP, to beyond anything seen by the cell, during cell cycles ... but this revenge of the mitochondria is interesting to consider as a source for the Cambric explosion. It could have been the final battle for dominance between the mitochondria and the DNA, with the DNA winning.

If you enjoy this line of speculation, HBond, you might enjoy reading, watching, or playing one of the Parasite Eve books, movies, or video games, a horror fictional exploration of an attempted takeover of the world by mitorchondria.

 

The idea’s pure fiction, however, because of the obvious biomechanical problem that mitochondria are very small and simple, so lack any sort of nervous or other system with which to be conscious of, communicate with, or plot taking over, the world. Parasite Eve’s writer solves this problem by imagining that a subtle, dispersed consciousness is embodied in human mitochondria, which due to human evolution having reached a ideal point in the form of a individual woman, “wakes up”, takes over her mind, causes her to die in a car crash, then takes over the mind of ... oh, well, you’d better read the book or watch the movie (and good luck trying to figure it out from that!), as the plot gets pretty complicated!

[HydrogenBond]

The point of the discussion was epigenetics. Rather than talk about effects, I was trying to see if I could infer aspects at the level of cause. My main point was the mitochondria are the engines of the cell, producing ATP energy. Some of my detours were off base, not due to me trying to misinform, but due to lack of working knowledge. I appreciate the help trying to keep me moving down the middle.

 

The mitochondria are the engines of the cell. As far as I can remember, the main user of mitochondria ATP energy is the cell membrane, with neuron membranes using up 90% of the ATP, if my memory is serves me right. As such, I would infer that the membrane is the secondary leg of the energy system, due to its high energy proportion.

 

To make where I am heading easier to see, picture a hypothetical pseudo-cell (this is not real but for visualization) with only mitochondria (including basic support) and a cell membrane, which contains all the bells and whistles one normally sees within a working membrane. The rest of the internal volume is just water.

 

The mitochondria output ATP energy and send it to the membrane adding energy into the membrane. The membrane uses much of that ATP for ion pumping creating potential energy within the membrane, which we measure as membrane potential. This potential energy is used for active transport into the cell, with the mitochondria constantly sending ATP energy to maintain the potential.

 

The materials being transported, enter the empty pseudo-cell and begin to fill the aqueous cavity. In essence, the engine of the cell, is using ATP energy, via the membrane, to increase the entropy within the volume. Now there another potential.

[Essay]

... is using ATP energy, via the membrane, to increase the entropy within the volume. Now there another potential.

That sounds like a good working model....

 

But do you mean "to lower the entropy..." -as the ATP's energy is used to segregate potassium from sodium, or calcium from magnesium, or pumping anything (such as H+) against a gradient - which raises the electrical potential (but transitionally lowers the entropy)?

 

~ :)

 

p.s. ...and what about epigenetics?

[HydrogenBond]

I was trying to stay simple. The separation of ions into a gradient will lower the entropy of the ions. They would prefer increase entropy to form a uniform solution. But we will add ATP energy for a work cycle, via enzymes, to lower ionic entropy. When entropy lowers, energy is given off. This energy becomes part of the potential energy within the gradient, i.e., once irretrievable energy was retrieved. The second law says that entropy needs to increase. So we need to release the potential energy within the gradient. This is set up to transport materials. The cell can't help but be fed according to the second law, since the membrane is trying to violate the second law, temporarily, using work. But the second law wins again by feeding the cell.

 

Part of the increasing entropy goes into the inner volume, contained within the degrees of freedom of the influx molecules. What I would like to add are hypothetical enzymes that have the lock and key feature, but no energy yet to turn the key (we won't yet use ATP to turn the key at this time).

 

What we have in this hypothetical case are molecules moving within the volume enjoying degrees of freedom. If they stick onto an enzyme, they lose degrees of freedom by being bound. This will lower their entropy. In the above situation, although our simple enzymes initially help lower entropy, by simply binding influx molecules, they will eventually saturate, such that a continued influx will eventually increase entropy again.

 

Now there is a building potential, for the low entropy enzyme-key composites to increase entropy. If the key is not a good fit, entropy increasing separates it easier. The best fit can hang on longer, being more stable, until increasing entropy only allows the best fits to hang in there. Even without being specific, the entropy boost will sort of define what is specific by what hangs in longest.

 

Spontaneous change leading to grinding down larger key molecules into smaller things requires less energy than building up, since there is already a potential in the volume to increase entropy. Making more small things from bigger things moves in the direction of the increasing entropy. Building up and lowering entropy is less likely, using only spontaneous change, since the enzymes would have to act against the entropy increasing. The main point is some rough digestion is more likely to follow the increasing entropy potential set up by the membrane. This loops back to the mitochondria.

 

An interesting set of observations, along these lines, are that neurons don't undergo cell cycles. The mitochondria also give up to 90% of their ATP to the neuron membrane, which favors digestion and metabolism. It is possible cell cycles don't work very well under the high internal entropy conditions created by the membrane. This might explain why neuron stick with RNA production.

 

If we took a double helix of DNA and the same size double helix of RNA (hypothetically to start), the DNA will remain that way, but the RNA won't, because it has more degrees of freedom built into it. The RNA could separate in part, loop back onto itself, etc. If neuron don't make DNA very often, it is possible the cellular entropy stays too high to make more of this lower entropy DNA state. This is speculation but follows logically using the basic lay of the land.

 

Regardless, the second law is still in effect, especially at the neuron membrane, trying to increase the entropy of this highest membrane potential state. This can be done with neuron firing, since this will help the membrane cations move toward the coveted uniform solution. But ATP will constantly reset the potential. Once neurons evolved, life could not help but begin to become conscious, due to the second law. Neuron firing is just another way to enforce the second law. The ATP constantly restores the potential, setting the renewable second law potential for continuous consciousness. Sort of like feeding the cell but feeds the mind.

 

This is still not epigenetics, but I trying to work my way to the DNA.

[Essay]

I was trying to stay simple.

Oh well, maybe next time....

===

 

I did read this ...with some difficulty.

 

You seem to be learning a lot about cellular biology and biochemistry, and physiology too; and you have a great facility for connecting all these things up to see the overall dissipative structure... but about entropy....

...it just isn't what it used to be....

 

I think it's important to point out that changes in entropy are usually very small compared with the other "free energy" effects of electrical, chemical, and paramagnetic forces that occur during chemical/biochemical reactions.

 

p.s. I don't think the keys get "ground down," but just other keys come along until one fits well enough (though I suppose other keys only "come along" if some other "key" or substrate is getting modified in some way).

 

~

[HydrogenBond]

I would like to talk about water and entropy by using a simple example. If we mix gasoline with water, like will attract like, (polar-polar and nonpolar-nonpolar) and the two components will separate out. The water sinks to the bottom and the gasoline floats to the top. Relative to degrees of freedom for entropy, both components have freedom to move within their respective phases. However, they don't have the same freedom to move about as freely within the other phase.

 

In winter, one common problem is water in the gas. The water will phase separate, as little drops at the bottom of the tank. For the most part, the entropy of the water is limited to these little drops. If we add dry gas or methanol, this polar organic solvent, becomes sort of a liaison, allowing the water to dissolve into the gasoline. The methanol increases the degrees of freedom of the water, relative to it not being there, by allowing it to move throughout the entire tank.

 

If we go back to our membrane transporting materials, the entropy within the volume is not just associated with the degrees of freedom within the influx materials, but is also connected to the entropy impact on the water. These are adding additional degrees of freedom to the water.

 

Below is a diagram showing information transfer within water, where water has new degrees of freedom, due to various things within the water.

 

 

Hydrogen bonding carries information about solutes and surfaces over significant distances in liquid water. The effect is synergistic, directive and extensive. Thus, in the diagram below, strong hydrogen-bonding in molecule (1), caused by solutes or surfaces, will be transmitted to molecules 2 and 3, then to 5 and 6 and then as combined power to 8.

 

Hydrogen bonding in water

 

The point being, this information transfer reflects more degrees of freedom within the water, since water would not do these things, unless there is a surface or substrate to get the informational entropy into motion. Since water is in contact with nearly everything within the volume, the entropy information created within the water, by substrates and surfaces is being broadcasted, even as things move. The information doesn't extend beyond about 2 nanometers, but it will still reaches surfaces and substrates before these come into actual contact. The water entropy is not needed for the discussion, but was introduced to show influx entropy is more than just the influx.

[HydrogenBond]

I would like to go back to the basic hypothetical scenario. We have a hollow membrane volume, with mitochondria, and a functional cell membrane. The ATP going into the membrane is segregating cations, lowering cationic entropy. The second law is in effect trying to increase entropy through material transport, which causes the cations to blend again. Inside the volume, I added enzymes which can attach things entering the cell, which helps to lower the degree of freedom of the influx, but only until things gets saturated. What I would now like to add is ATP active groups onto the enzymes.

 

The impact of ATP ,on the enzymes is to increase their degrees of freedom or entropy. Without ATP functionality, an enzyme would attach a molecule and the composite would sit there looking pretty. They will be some wiggle room and some spontaneous change in the direction of entropy. But once we add the ATP, there are more degrees of freedom, allowing additional bending, rotating, bond breaking, even transformation into new things, etc.

 

Among these extra degrees of freedom, for some enzymes, are actions which can lower entropy. For example, the Na+, K+ pumps would just sit there looking pretty without ATP. But once we add ATP, there are now additional degrees of freedom, allowing the pumps to wiggle and exchanges cations, against the entropy of a uniform solution. There are also other uses for the enhanced degrees of freedom offered by ATP, which can, paradoxically, lower configurational entropy, such as on the DNA. ATP gives the degree of freedom needed to polymerize, restricting the smaller monomers, taking away degree of freedom that they once had. The second law is in effect, and will impact this.

 

I would now like to look at ATP.

 

The potential within ATP is expressed by transferring the terminal phosphate group (far left) to the enzyme. This phosphate group is an electron acceptor, and typically accepts electron density from an -OH group on the enzyme. Because ATP is an electron acceptor, it actually has more in common with O2, than glucose, wood, methanol, gasoline, etc, all of which are electron releasers. I tend to view ATP as the mini-me of O2. This is not exactly a perfect analogy, but it keeps the mind in the right place.

 

As the O2 mini-me, ATP is connected to the same side of the potential that drives metabolism, which burn things down to lower energy and higher entropy, i.e., CO2, water and energy. ATP will also increase degrees of freedom of the enzyme (check). However, it is not strong enough to burn things down by breaking covalent bonds (such as in fire). But what ATP can burn, are hydrogen bonds, giving the enzymes degrees of freedom they need to break covalent bonds. These H-bonds can reform, for another cycle.

[HydrogenBond]

I would like to move from the membrane, to the DNA, and look at some basic DNA configurations, as a function of entropy. If we pack the DNA double helix, with histone proteins, the linear DNA will lose degrees of freedom, since it is induced to wrap in a systematic way around histone balls. As we increase the order of packing even further, more degrees of freedom are lost, until upon its final packing, the DNA is in the specific configurations we call chromosomes.

 

If we start with chromosomes, and increase the configurational entropy of the DNA, the process reverses until we reach unpacked DNA double helix. The entropy generated within the cell, favors unpacking of the DNA, since this reflects entropy increasing. This is done with enzymes, which unpack the DNA, so there are the additional degrees of freedom needed for activity on the DNA.

 

There is one additional degree of freedom, which also uses enzymes, which separates the DNA double helix into two. This usually begins at places with the bases sequence ATA or TAT, which non-coincidentally make use of the root of ATP. From a practical point of view, these base pairs form only two hydrogen bonds, instead of three, and are therefore easier to separate or increase degrees of freedom.

 

If we took a fixed length of DNA double helix and the same length of RNA double helix, and places these within water, the DNA would remain a double helix, while the RNA will not remain this way for long, since it has others degrees of freedom, including being able to exist as a single helix. This implies RNA has higher configurational entropy than DNA. Cells that use RNA as the genetic material, exist at higher genetic entropy than cells that use DNA.

 

If we start with monomers and make a polymer, the entropy or degrees of freedom will decrease. A simple way to see this is to take ten blocks, that are attached like a little train and throw them on the table. Although they can form many shapes, they are under the constraint, that they have to fall within a circular area, that has to be less than or equal to the length of the ten unit polymer. With single blocks, one can theoretically mimic these shapes, with random throws, but can also form single block distributions, where the blocks can exist beyond the length circle of the polymer. The longer the polymer, the more limit there is placed compared to the same length of many smaller units. Based on this simple analysis, rRNA, by being longer than mRNA, has less configurational entropy than mRNA. One could infer this from fewer ATA starter regions per length.

 

Within the nucleus, the lower entropy of the rRNA is increased with proteins to form the nucleolus. It is a shape of increasing entropy. When the entropy increases to a critical level, ribosome precursors bud off. This is similar to a configurational polymer of sorts, which is breaking the bulk configuration into the smaller units, implicit of the ribosome precursors. These have more degrees of freedom and can leave the nucleus. The straw that stirs the drink or mitochondria is setting a global potential. The hierarchical steps from the DNA, follow the most probable path using this entropy constraint.

[freeztar]

Unless you are building towards epigenetics, HBond, I think it would be best to move the last several posts to their own thread.

[HydrogenBond]

I am moving in that direction, but I am trying to be careful. The next step , is to consider the hypothetical situation of polymerizing animo acids and nucleotides, but without templates.

 

With nucleotides, since there are four bases for RNA and DNA, random polymerization works using the odds within four different units. Because there are twenty amino acids, if we polymerize these randomly, the distribution will be based on odds using 20 distinct units. In essence, the final distributions, for any given number of monomer units, is like having a dice with four sides and one with twenty sides, with the twenty sided dice having more distinctions. In this hypothetical situation, the proteins have more degrees of freedom than RNA or DNA.

 

In nature, these three polymerizations are not random, since this is done with template relationships. The DNA and RNA uses proper base pairing, while proteins use codon sequence of three bases. In both cases, the entropy within the hypothetical situation, lowers substantially. Making that improvement, from random to templates, went opposite the second law, which would like to always increase entropy.

 

Since the DNA and RNA uses a single base pair relationship, while the proteins use three base codons, the relative entropy within the random polymerization of proteins was reduced proportionally higher. I haven't done the math, but this would help narrow the entropy bandwidth between them.

 

The next thing we need to look at are the configurational entropy differences between proteins, DNA and RNA. This has to do with degrees of freedom in terms of final shapes. DNA has less freedom than RNA, as was shown earlier, while proteins have more shape freedom than RNA. Protein can form linear, globular and even random looking shapes, which is not common to DNA or RNA. The monomers of RNA and DNA, share a common phosphate and sugar, while their bases are loosely similar, creating this tighter distribution of shapes, matter how we randomly polymerize. The animo acids, have -R groups, that differ widely, allowing more degrees of freedom within the final shape if we randomly polymerized. This is just another reflection of the entropy hierarchy, going from less to more, in a general way, from DNA, to RNA, to protein.

 

Nature has lowered the degrees of freedom of the protein even further, by the way these are designed to be made. With DNA, we can start almost anywhere on the DNA (using the starter regions), but it does not matter what base comes next. We get still get close shapes within the mRNA. On the other hand, we can't start in the middle of proteins, and get the same final shape, since it will begin folding where we start, with polar and organic groups starting things differently. This choice by nature reflects entropy within building proteins, reduced; get repeatable shapes.

 

Going from DNA to RNA to protein is moving in the direction of the entropy field of the straw that stirs the drink and the second law. While the means of production for these basic configurations have evolved in a way that have lowered the entropy within each, relative to the probability of randomness. Epigenetics is based on changes on the DNA, some will lower and some will increase entropy. Lowering entropy would be anything that packs it longer, prevents separating the DNA or making RNA, etc. Higher entropy will have the opposite impact.

[HydrogenBond]

I would like to talk about a basic aspect of epigenetics, which has to do with gene placement. The easiest way to discuss this is with an example of hypothetical DNA with only genes for two classes of proteins. These protein classes will be packing proteins and unpacking proteins. As was shown, packing proteins lower the degree of freedom of the DNA and lower the configurational entropy of the DNA. Unpacking proteins will increase the configurational entropy by offering more degrees of freedom.

 

Depending on what unpacks first on packed DNA, will have an impact on the final configurational entropy of the DNA. If we place the unpacking genes so they unpack first, the DNA is able to increase configurational entropy, as more and more of unpacking proteins are fabricated, creating an unpacking chain reaction. Eventually, the unpacking reaches the packing genes, which then begin to compete with the unpacking.

 

If we placed the packing protein so they are the first to unpack, using a few unpacking enzymes to get the ball rolling, the packing proteins will compete at the very beginning keeping the configurational entropy of the DNA low. We have altered the response of the DNA using only gene placement.

 

Unpacking the DNA is loosely analogous to a child looking for a toy in his toy box. If the toy is on the top, the toy will be the first thing he grabs and he is ready to play. If the toy he wants is at the bottom, he will have to pull other toys out of the box, and maybe scatter them on the floor. If the packing proteins came out first, it would be like his mother picking up the toys behind her child, refilling his toy box. He might continue unloading the box, but may never get to the toy he needs at the bottom. Proper placement of the genes in the box, is a epigenetic failsafe, making sure the cell gets what it uses most of the time, even if mother puts the toys back.

 

The cell cycle makes use of this toy box principle, making it possible to create what appears to be an entropy paradox. During cell cycles the metabolism increases, therefore one would expect high configurational entropy within the DNA. This does occur, with genetic unpacking and activity very high and occurring all over the DNA. DNA production even begins with RNA primers.

 

But making DNA instead of RNA, implies the type of molecule being made is one that defines lowering configurational entropy, compared to RNA. This is compound further when the DNA packs, during a very high entropy time in the cell. The way the cell does this is by placing the needed configurational entropy lowering proteins, such as packing proteins, at the bottom of the toy box. The high entropy within the cell is moving the DNA into high configurational entropy mode, reaching the bottom of the toy box. At the level of synthesis from DNA to RNA to protein, we are still following the increasing entropy. However, once the DNA dependent proteins take shape, their impact becomes the entropy lowering needed to create the paradox, i.e., DNA production and packing into very low entropy against the push of high metabolic entropy. The double DNA eventually needs to follow the high background entropy, dividing the DNA.