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Natural Selection

Yes - in order to be heritable, a change must be made to the DNA (no other change will do) of the egg/sperm cells of the individual.

This is an overstatement.

As an example, we are well-aware of pathogens that pass from mother to child either in utero, in the birthing process, or through breast milk -- HIV is just one example among many. But, of course, the only way we know about these pathogens is because they do bad things to us which is why we were looking for them; there may well be unknown symbiotic "pathogens" that are passed down in this way. A change in these symbiotes -- say, someone decided to snack on penicillin for most of her life, and made her symbiotes penicillin-resistant -- would be acquired and passed down to children.

Fifty years ago, someone might have written "in order to be heritable, a change must be made to the nuclear DNA of the egg/sperm cells," not realizing that mitochondrial DNA is also inherited. But if there are any RNA-only protein templates (something we've not been able to confirm), those would also be inherited maternally. We know there are self-reproducing protein templates (they're called prions) and these could also be inherited if they managed to get into the egg cell.

The problem is that we know of no method to "learn" any of these changes. In theory, any of these methods could provide a method for Lamarckian inheritance if we could figure out a way for a creature to learn how to make a particular strand of RNA....
 
DrKitten, Shadron, jackalgirl, Subduction zone, temporalIllusion, cj23, Gord in toronto, TX 50, I Rant, Ziggurat, MG1962:

You folks are incredible. Thanks for sharing your insight.
Very fascinating.

1) So, pathogens can make changes in the nucleus of a cell - in DNA.
Radiation can also alter my DNA, Correct?
One part of my body then might have infected (altered) DNA but other part of my body might have the original one. Correct?

2) How can one tell (looking at which part of the cell? What state?) if a cell is dead or not?

3) A segment of DNA must also have timer (clock) I suppose? We do not know where the timer is yet, I presume.

4) What makes DNA to mutate in the first place?
This must have something to do with radio-active decay. Atom and even proton do decay. DNA mutation must be a macroscopic result of microscopic changes as dictated by quantum mechanics.

5) My background is computer science. To me life forms looks like a sophisticated computer with quantum uncertainty effect. Body and brain in that sense is a computer - obviously, everything follows laws of nature.
 
Mutation could come from more than one source. Of course there is the old science fiction favorite, nuclear radiation. Actually I am sure there are different sources of ionizing radiation that could change a DNA molecule. Then there is something as simple as copying errors. If a gene is not copied perfectly it could result in a mutation. When you think of the million? or so genes in a genome it is not unreasonable to expect an occasional error in reproduction. I am sure there are other possible sources of mutation besides these.
 
Makes you wonder how the non-standing-erect monkeys we see behind bushes today managed to survive.

Several ways suggest themselves:

- Many smaller monkeys have taken to tree-climbing to avoid ground-bound predators and (at least to an extent, as many of them live in forests) gain a better view over large distances. Even on the savannah, where trees may be scarce, monkeys may be found resting in or near trees for this very reason. Other natural structures that would help elevate the monkey above the line of grass are also put to use, such as termite mounds.

- Baboons and relatives have grown stronger and fiercer than many other monkeys, and thus are able to drive predators off, especially as they often work in groups where the males protect the rest of the flock.

- In some cases, monkeys team up across species-borders to form multi-species "scouting parties". There was a documentary hear a few years ago when the filmmaker was inside one of these groups which contained about a dozen different species, moving at different heights in the canopy. Some warned for eagles, other for snakes, and yet others for predators on the ground. All species reacted to these warning signals, and helped out each other. Naturally, similar relationships can be found between monkeys and grass-eating mammals (which by their height can see over the grass) in grasslands.

- Many monkeys, as you may know, are considerably faster than humans, and (hopefully) also than their predators, and thus outrun them.

- Other monkeys (geladas, for instance) are of sufficient height to see over the grass themselves.

- And, of course, over the course of evolutionary time, many monkey populations that have not found a way to solve this problem have simply become extinct.

So now you don't have to wonder anymore!
 
I want to thank all of you who replied to my question and explained. Yes, it helped.


Ziggurate wrote: <quote>A giraffe does not change its genes by stretching its neck. </quote>

I think that is the answer I was looking for.

then the next question comes in...

since genetic mutation takes place randomly then evolution can take two step forward and then a step backward as well. Yes, I can see that overall there will be forward pressure.
Um , hmmm, Welcome to the Forum!

There are mechanism other than random mutation for natural selection to work upon, variation within the existing genome for example.

Beware the dangers of ]i]progressivism[/i] , the theory of natural selection through reproductive success would be blind to the future.
But it feels like to me that 3.5 billion years is not sufficient to evolve human being.\
Really?

That is a very long time for example say we have a one in a million cahnce thats omething will happen. How many times does that happen in a billion years if it happen only once a year?
1,000
Once a day?
365,000
Once an hour?
8,760,00
Once a second?
31,356,000,000

And that is just for a two member set.
I wish, similar to half-life of radio-active atoms, they had some statistical data, probability distribution on spontaneous genetic mutation. rate of genetic mutation could have been used to compute the duration it would take for an ameba to evolve to human being.
Sorry but humans didn't come from amoebas.
Is it correct to say that anything species learn either mentally (knowledge in the brain) or its body learns (growing stronger muscle) during its life time is not heritable.

Sort of there.
 
1) So, pathogens can make changes in the nucleus of a cell - in DNA.

Can they? That would surprise me (slightly), but I suppose it's possible. I can't think of any cases offhand, though.

On the other hand, since eating mushrooms can alter your DNA (mushrooms are known to be mutagenic), why not pathogens?

Radiation can also alter my DNA, Correct?

Yes, this is well-known.

One part of my body then might have infected (altered) DNA but other part of my body might have the original one. Correct?

Yes. Among other things, this is what we call "cancer."

2) How can one tell (looking at which part of the cell? What state?) if a cell is dead or not?

Roughly, the same way we can tell whether or not a person is dead; if it ain't moving, it ain't living. Even a cell that is ostensibly in one place is in continous motion internally; the cellular fluid circulates, the mitochondria drift around in it, and so forth.


3) A segment of DNA must also have timer (clock) I suppose? We do not know where the timer is yet, I presume.

Why? DNA is a chemical. Why would table salt care what time it is?

4) What makes DNA to mutate in the first place?
This must have something to do with radio-active decay. Atom and even proton do decay. DNA mutation must be a macroscopic result of microscopic changes as dictated by quantum mechanics.

Er, no. DNA mutations are chemical changes and have little to do with QM; most mutations appear to be the result of faulty copying (the enzyme grabbed a C when it wanted a T, that sort of thing, or grabbed an A a second time, yielding AA instead of A, or something like that). Sort of of like how typographic errers can sneak into a sentence if you're not paying close enough atttention.

Of course, since DNA is a chemical, you can also force mutations by chemical exposure -- yank a group of atoms off the DNA by force main, and see what happens when it tries to replicate, or alternatively mess up some of the replication enzymes directly. This is how chemical mutagens (like mushrooms) work.

Radiation works "by force main" as well; hit a molecule with enough heat/energy and it will break.

None of these effects rely on QM; they're simply chemical processes. Anything you can do to mess up a chemical can produce mutations if the chemical involved is DNA....
 
temporalillusion, I would not quite use the term directionless change. The direction of change is determined by the environment or changes in the environment that the specie lives in. For example submitting a population of bacteria to anti-biotics will induce a change into a resistant specie. But you are right in that an animal does not purposefully evolve into a giraffe.

You are right, I meant directionless with regards to the mutations or whatever process is changing the DNA.. the selection will determine the direction of the changes (as long as the mutations are providing the raw material for those changes anyway).

1) So, pathogens can make changes in the nucleus of a cell - in DNA.
Radiation can also alter my DNA, Correct?
One part of my body then might have infected (altered) DNA but other part of my body might have the original one. Correct?

Yup, check out the info on ERVs for info on changes to DNA from virii:

http://toarchive.org/faqs/comdesc/section4.html#retroviruses

In general changes have to happen to the DNA of a sex cell to be passed on, but read drkitten's post; that isn't always the case.

2) How can one tell (looking at which part of the cell? What state?) if a cell is dead or not?

Not sure.

3) A segment of DNA must also have timer (clock) I suppose? We do not know where the timer is yet, I presume.

We do. Each chromosome has sequences at the end of it called telomeres. These telomeres are like the end statement at the end of a chunk of code, except there's a lot of them instead of just one.

As a chromosome gets copied, not all of the telomeres get copied. So over time the telomeres get shorter and shorter, eventually short enough that the cell doesn't divide anymore.

This is what makes us age.

4) What makes DNA to mutate in the first place?
This must have something to do with radio-active decay. Atom and even proton do decay. DNA mutation must be a macroscopic result of microscopic changes as dictated by quantum mechanics.

Radioactivity is only one source, as Subduction Zone points out errors in copying are a common source of mutations. Try copying out the dictionary by hand, you're bound to make a few errors.

More info: http://www.toarchive.org/faqs/mutations.html#types
 
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timef, life is remarkably tenacious!
It's been around for billions of years, but only the past 500 million or so has it progressed from pond slime to the enormous variations we see or were seen in the ensuing years.
There was nothing at all of anything resembling humanity 65 million years back.
The dinosaurs kept everything from advancing because they had occupants in most of the environmental niches.
When they left, all those environmental opportunities they dominated became available to the small creepy crawlies, which then took advantage of the lack of competition from the meanies, and in the wink of an eye (which coincidentally has evolved separately many times over the eons) here we are, for better or worse.
Humanity has mostly "evolved" past the usual pressures that drive advancement, by controlling and providing its own sources of food and shelter.
It also has the very real potential of stopping just about everything in its tracks, not unlike the K-T event that freed the proto-mammals from the dinosaurs domination, but in this case taking out -everything-!
 
I am new in this field, therefore, please forgive me for my stupid ideas.

Mutation – radioactive and non-radioactive decay Connection

Subduction Zone Wrote:
Then there is something as simple as copying errors.
Drkitten wrote:
DNA mutations are chemical changes and have little to do with QM
TemporalIllusion wrote:
Try copying out the dictionary by hand, you're bound to make a few errors.

I do agree that there is copying error. I do agree that the changes are chemical. But why won’t it copy properly in the first place? In my opinion, the microscopic, underlying fundamental force that results the unexpected (unpredictable) chemical changes in cells, error in copying is the force of that is responsible for radio-nonradioactive decay (alteration of particles and atomic nucleus) and Heisenberg uncertainty principle.

Imagine a universe without the spontaneous radioactivity and no uncertainty, much like Newtonian Mechanics. In such a world there won’t be any random genetic mutation either. There won’t be any copying error. Everything would be predictable in principle.
In my opinion we must try to explain everything in terms of fundamental laws of nature. Genetic mutation is not a fundamental laws but a macroscopic result of what is happening in deeper level.

DNA clock issue

Drkitten wr
Timf1234 wrote:
Quote:
3) A segment of DNA must also have timer (clock) I suppose? We do not know where the timer is yet, I presume.
Why? DNA is a chemical. Why would table salt care what time it is?

Segment of DNA sequence coding that can be represented in informational coding similar to 10010001…) that must work to keep time. This timer results to our aging, growth with respect to time and eventually death. Tinkering with this timer we can extend not only our life but live as, say 25 years old for a long time or even forever.

Temporalillusion wrote:
Originally Posted by timf1234
3) A segment of DNA must also have timer (clock) I suppose? We do not know where the timer is yet, I presume.
We do. Each chromosome has sequences at the end of it called telomeres. These telomeres are like the end statement at the end of a chunk of code, except there's a lot of them instead of just one.

I agree.

Dancing David Wrote:
Timf1234 wrote
I wish, similar to half-life of radio-active atoms, they had some statistical data, probability distribution on spontaneous genetic mutation. rate of genetic mutation could have been used to compute the duration it would take for an ameba to evolve to human being.
Sorry but humans didn't come from amoebas.


My ignorance – I apologize.
What I meant is the common origin not necessarily ameba. I do not even know the proper term for the first lifelike object. Whatever it is, I thought (couldn’t understand), how 3.5 billion years can turn amino acid to human being. Obviously this depends on the rate of mutation and cell replication versus the genetic timer-clock. Of course, I also know that I must be wrong otherwise, I won’t be here on the Earth.

Cell movement issue.
What fascinate me how the growth of a baby take place. We eat and these food translate to my body cells and moves into different part of my body. One of my legs doesn’t grow twice as long as the other. Eye bass doesn’t show up in the back of my head. Just Amazing. Obviously, all cells must be communicating to each other.
I have no clue….

Holistic view:

I think, now we are learning about another kind of agent for change, memetic. Like genetic memetic changes life. Genetic works from bottom up whereas memetic works form top down. Although the fundamental limits of life is set by genetic but memetic, like nurture, can undo millions of years of evolution. Memetic can override natural selection, survival for the fittest. One form of memetic agent is mental virus, or informational virus that acts in neural network. Remember, contrary to evolution people do kill themselves and destroys their own civilization. Memetic can be much faster than genetics. …just a thought.
 
I do agree that there is copying error. I do agree that the changes are chemical. But why won’t it copy properly in the first place?

Because all chemical processes are semi-stochastic; there is a probability of ANY two molecules sticking together based on their configuration; it just happens that the probability is much higher for certain pairs that for others; for example C/G form a very strong bond that is easy to form and hard to break, A/T a less strong bond, and A/G less strong yet. In a suitable mixture of base pairs, the odds that any particular A should bond with a G are low, and if it does happen, it is likely to be displaced by a T in a relatively short time.

But these are merely stochastic results -- sometimes wierd things happen. The result is a mutation -- in this case, a T would be "copied" (wrongly) as a G.

In my opinion, the microscopic, underlying fundamental force that results the unexpected (unpredictable) chemical changes in cells, error in copying is the force of that is responsible for radio-nonradioactive decay (alteration of particles and atomic nucleus) and Heisenberg uncertainty principle.

Not at all helpful. Yes, if you're going to be a complete and total reductionist, the reason a football was batted down by the linebacker is not because he reached out and swatted at it, but because of QM effects.

Imagine a universe without the spontaneous radioactivity and no uncertainty, much like Newtonian Mechanics. In such a world there won’t be any random genetic mutation either. There won’t be any copying error.

Sure there would. Since these chemical reactions are taking place in a water solution, it's a matter of chance whether the A bumps into a T or a G first -- and in which orientation. This is true even in a purely Newtonian world; molecules wander unpredictably through a solution. Since we don't know what kind of molecule we'll find, we don't know what we'll bond to and you still end up with mis-bonding.

In my opinion we must try to explain everything in terms of fundamental laws of nature.

All right, we'll play it your way. I have some money down on the Tennessee Titans winning the Superbowl. Explain to me, in terms of the fundamenal laws of nature, whether or not I made a good bet.

Heck, explain to me, in terms of the fundamental laws of nature, whether or not Rothlisberger will play well next week. Part of the reason I picked the Titans, you see, is because at a macro level, the poor guy had his bell rung last week and is walking around with a concussion. I'm expecting the Steelers to lose next week as a result. Tell me how QM is going to affect his play, since I may have time to buy back my bet.

Segment of DNA sequence coding that can be represented in informational coding similar to 10010001…) that must work to keep time. This timer results to our aging, growth with respect to time and eventually death.

Except many organisms neither age nor die of aging. Cancer cells, for example, and many protozoans.

Death of old age appears to be an evolved feature of some cells, but it's hardly universal.
 
I do agree that there is copying error. I do agree that the changes are chemical. But why won’t it copy properly in the first place? In my opinion, the microscopic, underlying fundamental force that results the unexpected (unpredictable) chemical changes in cells, error in copying is the force of that is responsible for radio-nonradioactive decay (alteration of particles and atomic nucleus) and Heisenberg uncertainty principle.

You are mashing some very different concepts together here. Radioactive decay occurs because an atom isn't stable, and the uncertainty principle is a quantum level phenomenon that speaks to the measurability of values of certain pairs of conjugate variables (like momentum and position), it doesn't speak to the behaviour of the system itself.

Like drkitten says the chemical copying process isn't perfect.

Segment of DNA sequence coding that can be represented in informational coding similar to 10010001…) that must work to keep time. This timer results to our aging, growth with respect to time and eventually death. Tinkering with this timer we can extend not only our life but live as, say 25 years old for a long time or even forever.

DNA code isn't like a computer code, computer code is abstract, where DNA is not; the DNA code itself is the component necessary to generate the materials which enable life to function.

It's not as easy as tinkering with the telomeres to extend life, telomeres are a balance between a cell not living long enough and a cell living too long.. if a cell lives too long it could eventually become cancerous. We wouldn't need to just remove the part that tells a cell to die, we'd have to alter the cell to make it less susceptible to mutations so they don't become cancerous.

What I meant is the common origin not necessarily ameba. I do not even know the proper term for the first lifelike object. Whatever it is, I thought (couldn’t understand), how 3.5 billion years can turn amino acid to human being. Obviously this depends on the rate of mutation and cell replication versus the genetic timer-clock. Of course, I also know that I must be wrong otherwise, I won’t be here on the Earth.

That's basically all you need, replication, mutation, and natural selection.

What fascinate me how the growth of a baby take place. We eat and these food translate to my body cells and moves into different part of my body. One of my legs doesn’t grow twice as long as the other. Eye bass doesn’t show up in the back of my head. Just Amazing. Obviously, all cells must be communicating to each other.

That's a whole other topic, developmental biology. It's pretty fascinating and I love reading about it (though I don't pretend to understand anything about it). You might want to start another thread about it to get people who know of such things to participate. But as you say, cells communicate with each other through chemicals to turn gene expression on and off to determine what grows where and how big.
 
That it works is amazing, but it doesn't work all the time.
There's many specimens in jars with every variation one might think of in the development of a body.
It's an inexact coding, highly reliant on the environmental situation at the time.
 
Got any explanation which goes beyond speculative imagination driven by theory? You know, evidence.

In a sense evolution is very dumb.

Please explain.

I recommend checking this site for general evidence and this site for responses to creationist claims.

Please please please click. It is far and away the best scientific site I have ever seen.
 
Drkitten, temporalillusion, I Ratant, KingMerv00:

I am just thinking loud with my little knowledge that I have. I do not mean to disprove or offend anyone.

drkitten wrote:
Because all chemical processes are semi-stochastic
temporalillusion wrote:
Like drkitten says the chemical copying process isn't perfect.

Why cell copying is not perfect?
Why chemical process is stochastic?
Is there exist a deeper explanation for these imperfectness?

QM (Quantum Mechanic) has several points. The point I was making is not about unpredictability of momentum and position both with 100% accuracy but about the QM fact that, the eact timing when a single radioactive will decay is unpredictable. But half life is predictable for massive number of atom. This QM principle allows nature to play very light Russian roulette with everything, life, gene, free will, galaxy ....

Newtonian world is perfect but QM inject imperfection in a sense.

temporalillusion wrote:
DNA code isn't like a computer code, computer code is abstract, where DNA is not; the DNA code itself is the component necessary to generate the materials which enable life to function.

At higher level computer code is abstract but at lower level these codes are stored in memory in differences in voltage (charge). Computer language, English language (although imprecise), and the language of nature (such as electron has negative charge, laws of gravity, atomic properties etc.) are languages nevertheless. Our thought creates physical changes in our brain and vice-a-versa.
Nature will not tolerate illogic except small variation that is allowed by quantum mechanics.

I think the code in DNA is translatable in binary, or hexadecimal, or mathematical, or even in imprecise English language. Code and translation has to be consistent and accurate. The key word is "Consistency". Consistency is the prerequisite for the real world.

temporalillusion wrote:
It's not as easy as tinkering with the telomeres to extend life, telomeres are a balance between a cell not living long enough and a cell living too long.. if a cell lives too long it could eventually become cancerous. We wouldn't need to just remove the part that tells a cell to die, we'd have to alter the cell to make it less susceptible to mutations so they don't become cancerous.

I agree, in principle.
A lot of thing is happening at cell level. But all these reactions is happening under the supervison of current scheme of entire DNA code. It doesn't have to be like that. In principle, (may be 500 years from now) we will alter entire sequence of genetic code where a cell will not become cancerous even after living 1000 years. Or, yes, we might have to alter the cell itself.

Obviously, at this time we are just scratching the surface.

BTW, I liked your screen name, temporalillusion.
 
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This is an overstatement.

As an example, we are well-aware of pathogens that pass from mother to child either in utero, in the birthing process, or through breast milk -- HIV is just one example among many. But, of course, the only way we know about these pathogens is because they do bad things to us which is why we were looking for them; there may well be unknown symbiotic "pathogens" that are passed down in this way. A change in these symbiotes -- say, someone decided to snack on penicillin for most of her life, and made her symbiotes penicillin-resistant -- would be acquired and passed down to children.

Fifty years ago, someone might have written "in order to be heritable, a change must be made to the nuclear DNA of the egg/sperm cells," not realizing that mitochondrial DNA is also inherited. But if there are any RNA-only protein templates (something we've not been able to confirm), those would also be inherited maternally. We know there are self-reproducing protein templates (they're called prions) and these could also be inherited if they managed to get into the egg cell.

The problem is that we know of no method to "learn" any of these changes. In theory, any of these methods could provide a method for Lamarckian inheritance if we could figure out a way for a creature to learn how to make a particular strand of RNA....

You may have noticed I mentioned DNA without specifying nuclear or mitochondrial, but the rest of your observations are true. Keepin' on learning here, boss. Thanks.
 
Why cell copying is not perfect?
Why chemical process is stochastic?
Is there exist a deeper explanation for these imperfectness?
There is no need for a deeper explanation. While it's tempting to think of DNA as a printout of computer code, it's important to remember that it is biological material. It breaks, it degrades, it has flaws, and it is subject to change by outside influences, as discussed above.

Also, each of my 10 trillion or so human (as opposed to bacterial) cells that has a nucleus contains a DNA code that's about 3 billion letters long. About 2% of that is human genes. The rest is "junk" DNA. I'm a big guy and have about a kilogram of DNA bobbing around in me. If I could line up each DNA strand end-to-end, it would reach to the sun and back four times. To use a precise term, that's a crap-ton of information, all of it stored as chemicals. When I think of it that way, I'm not surprised that when that information is duplicated, mistakes can happen that may have a positive or negative effect on my survival.

My suggestion is that when you want to understand biological processes, you forget that quantum mechanics exists. QM may play a non-trivial role in some biological processes, but that area of study is in its infancy. Subatomic physics isn't needed to explain genetics.
 
Timf1234-
Further complications.
Not all DNA is germ line.
Not all germ line DNA is nuclear.
Not all reproduction is sexual. (Most creatures are bacteria, which exchange plasmids and multiply by fission).

On the point that acquired characters are not heritable- Google the term "Meme" and jump into another universal can of worms.

The basic ideas underlying evolution by natural selection are extremely simple; the detail is incredibly complicated. Most who reject it simply don't understand enough. It's immense fun!
 
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I should correct an oversimplification in my last post. I mentioned the quantity of "junk" DNA in the human genome. Scientists are discovering that some of this DNA isn't junk at all, but plays the regulatory role of switching genes on and off. Other DNA may have started as "junk" (e.g. from viruses or bacteria) but later a role evolved for it. No doubt many more such discoveries about segments of "junk" DNA will follow. Note that no quantum mechanics need be invoked to create this combination of "junk" and genes that code for human proteins.
 
Makes you wonder how the non-standing-erect monkeys we see behind bushes today managed to survive.
Because standing erect was not selected for thier particular population.

Life is not fair. The enviornment is not uniform. Any changes in any one spot could drive selection in a different direction in different populations.

That's the short answer. The longer one delves into specific pieces of evidence in the fossil record, and DNA. But, that doesn't matter. You'll just find some way to dismiss it all, and without even building an alternative theory that could explain any of it, in any detail.
 
You are mashing some very different concepts together here. Radioactive decay occurs because an atom isn't stable, and the uncertainty principle is a quantum level phenomenon that speaks to the measurability of values of certain pairs of conjugate variables (like momentum and position), it doesn't speak to the behaviour of the system itself.

At the risk of derailing and confusing timf1234, I'm going to interject and say that the above isn't true. Radioactive decay is very much dependent on the uncertainty principle (in the deltaE*deltat~hbar form). It plays a huge role in determining the lifetime of an unstable atomic nucleus against alpha and/or beta decay. Eg in alpha decay the alpha particle has to tunnel through the potential barrier of the residual nucleus. The probability of tunneling is dependent on the height of the barrier (and hence the energy that needs to be 'borrowed') and the extent of the barrier (hence the time said energy needs to be borrowed for).

Not that I think this affects the actual point you were making in any way.
 

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