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Author Topic:   Are mutations truly random or are they guided?
herebedragons
Member (Idle past 18 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 1 of 134 (548531)
02-27-2010 11:46 PM


The purpose of this thread is to discuss the evidence regarding mutations and whether they are really random or whether they are directed and guided by the cell or the organism and influenced by the environment.

This initial post is not intended to present evidence for either assertion, but to establish the basis for my challenging the accepted norm of RM + NS = Evolution. I feel there is sufficient reason to question whether mutations are truly random and that randomness is sufficient to explain the diversity of life we have here on Earth. So, in this post I will describe some of the observations that got me thinking about this subject and then we can discuss the experimental and observed evidence and see where it leads.

French zoologist Pierre-Paul Grassé believed that

quote:
To explain evolution he instead thinks that you must look at the internal dynamics of living things.

So let’s begin with a brief description of what goes on within a living cell. I have heard living cells compared to the most advanced factories on Earth, but the more I learn about the cell the more I see that as an understatement. Part of what makes the cell so incredible is the scale. All these biochemical functions happen in a “factory” less that 1mm in size. Many cells are invisible to the naked eye yet carry on processes so complicated that there is still much we don’t know.

Proteins are manufactured by ribosomes using mRNA. Each protein is made up of an exact sequence of amino acids brought to the ribosome by a specific tRNA. Each protein has a specific function and is specifically suited to that function. The Golgi apparatus can then modify the protein, creating a molecular tag that is used to target the protein to a specific cellular location.

DNA replication is very critical and extremely precise. It uses a complex system of proteins, enzymes, and polymerases to break the DNA strands apart, create daughter strands and correct any errors. The process is exceptionally accurate, with less than 1 error every 1 billion nucleotides.

ATP is produced in precisely the quantities needed for cellular operation and is not stored by the cell. If the cell is deprived of the resources it needs for cellular respiration, it will die in a matter of just a few minutes. Protein pumps move resources, such as Na+ in and out of the cell. Cells throughout the organism can communicate with one another, ensuring resources are available where and when needed.

The DNA contains all necessary information for the growth and development of the organism. Look out over a cornfield and you will see that all the plants are about the same height, have developed in the same sequence and mature at about the same time. This is a highly regulated process. Even when hundreds of cell types are involved in an organism, they still manage to organize into tissues, organs and systems with incredible precision.

These cellular processes are taught in freshmen level biology and, of course, I have greatly abbreviated them. Advanced courses, such as Cellular Biology, spend the entire semester (sometimes two) discussing only cellular processes. What I have concluded is that cells are highly ordered and regulated. None of it is random or left to chance. When something goes wrong with the process it is detrimental to the cell and therefore to the organism. How do we rely on “mistakes” to produce improvement?

This is not an argument about irreducible complexity and I am not saying “God-did-it”. What I am suggesting is that random mutations may not be the all powerful driving force of evolution that they have been thought to be. Instead, it makes more sense that mutations, (and therefore adaptation) are directed by the cell and by cellular processes.

So, I would like to discuss the experimental and observed evidence for and against the idea that mutations are random and yet can still provide the needed resources for evolution to occur.

Defendez-vous bien!


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Adminnemooseus
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Message 2 of 134 (548543)
02-28-2010 12:52 AM


Thread Copied from Proposed New Topics Forum
Thread copied here from the Are mutations truly random or are they guided? thread in the Proposed New Topics forum.

    
ZenMonkey
Member (Idle past 2797 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


(1)
Message 3 of 134 (548547)
02-28-2010 1:23 AM
Reply to: Message 1 by herebedragons
02-27-2010 11:46 PM


Argument from incredulity.

To be honest, herebedragons, are you really interested in the answer to your question? (And there is an answer, quite a good one, which has been gone over in multiple ways repeatedly in this forum.) Are you willing to listen to a genuine explanation, or have you already decided that you won't accept it? Do your have any basis for your doubts other than you have been led to believe that science conflicts with your religion, and so science must therefore be wrong?

Before continuing, would you go over to the Berkeley Evolution 101 website, read through it carefully, and really try to understand their explanations? Are you actually interested in learning something?


I have no time for lies and fantasy, and neither should you. Enjoy or die.
-John Lydon

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slevesque
Member (Idle past 2927 days)
Posts: 1456
Joined: 05-14-2009


Message 4 of 134 (548551)
02-28-2010 2:20 AM
Reply to: Message 1 by herebedragons
02-27-2010 11:46 PM


You speak french ?

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Stagamancer
Member (Idle past 3202 days)
Posts: 174
From: Oregon
Joined: 12-28-2008


(2)
Message 5 of 134 (548553)
02-28-2010 3:27 AM
Reply to: Message 1 by herebedragons
02-27-2010 11:46 PM


How do we rely on “mistakes” to produce improvement?

Happens all the time, just look at many of the serendipitous advancements in science and technology. Wikipedia has quite a list.
Some examples on the list:
1. LSD
2. Silly Putty
3. Discovery of Helium
4. Penicillin
5. Viagra
6. Mechanism for inkjet printers
7. Microwave oven

Granted, most of the time, if you make a mistake while doing science, you'll probably just end up ruining your experiment. However, there will be the occasional time when you accidentally put B in with C instead of A and you get something no one has seen before. The chance of this happening to an individual at any given point in time is small, but the number of scientists and experiments is high enough that accidental advancements have been made numerous times. The same is true for mutations in DNA. The cellular machinery is remarkably good at what it does, but those few mistakes it makes, when you look at an entire population over the amount of time life has been around adds up to a LOT of mistakes. And the thing about beneficial ones is that once they arise they tend to stick around.

it makes more sense that mutations, (and therefore adaptation) are directed by the cell and by cellular processes.

How exactly would this work? How could a cell know to direct mutation? The only instance I can think of that is anything like this is bacteria that have increased mutation rates during stressful times. The idea is that with a higher mutation rate, the chance of coming across a beneficial mutation is higher. However, the mutation is still undirected and relies on chance. The ability to induce mutation is also, in an of itself mutation that arose by chance and the was selected for.

When you say "it makes more sense..." have you really thought about it? How would an individual cell possess the forethought to make the correct mutations? I think it makes more sense that mutations arise randomly.


We have many intuitions in our life and the point is that many of these intuitions are wrong. The question is, are we going to test those intuitions?
-Dan Ariely

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Percy
Member
Posts: 18872
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.4


(1)
Message 6 of 134 (548562)
02-28-2010 6:36 AM
Reply to: Message 1 by herebedragons
02-27-2010 11:46 PM


herebedragons writes:

This is not an argument about irreducible complexity and I am not saying “God-did-it”. What I am suggesting is that random mutations may not be the all powerful driving force of evolution that they have been thought to be. Instead, it makes more sense that mutations, (and therefore adaptation) are directed by the cell and by cellular processes.

Most mutations are deleterious, so your conclusion that the cell guides processes that usually hurt or kill it makes no sense.

The true driving force behind evolution is natural selection, the originator of adaptation. Random mutation is merely one source of variation that natural selection draws upon as it molds populations of organisms toward better adaptation to their environment through successive generations.

--Percy


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RAZD
Member
Posts: 20156
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 4.1


(1)
Message 7 of 134 (548565)
02-28-2010 8:18 AM
Reply to: Message 1 by herebedragons
02-27-2010 11:46 PM


Hi again herebedragons,

Just a small comment:

The DNA contains all necessary information for the growth and development of the organism. Look out over a cornfield and you will see that all the plants are about the same height, have developed in the same sequence and mature at about the same time. This is a highly regulated process. Even when hundreds of cell types are involved in an organism, they still manage to organize into tissues, organs and systems with incredible precision.

And yet no two plants are identical even though they come from highly controlled seed production in today's fields. You will find some "runts in the litter" that do not do as well in growth and production of corn (survival and reproduction), and you will find some that grow and produce more than the average ones.

Those differences are due to mutations. We can eliminate environmental effects on development when the whole field would experience the same effects, so we are left with differences in the DNA to produce the differences observed.

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
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AZPaul3
Member
Posts: 4640
From: Phoenix
Joined: 11-06-2006
Member Rating: 4.5


(1)
Message 8 of 134 (548582)
02-28-2010 10:34 AM
Reply to: Message 1 by herebedragons
02-27-2010 11:46 PM


Round and Round We Go
I shouldn't be surprised by this OP. Most people just do not do the research to find out if these things have been answered.

The data may be presented in a few dozen forum messages here but it still takes months of research to comprehend.

This is not a new question. In fact it is 300+ years old at this point and a “guided” or “directed” mechanism has already been found: Natural Selection. Only the "guiding" is blind to the population and the "directing" is brutal to the individual.

Two points to be addressed:

Randomness of mutation. Before you can assess the random nature of mutation you must first understand the mechanisms of mutation. A small start might be here. Note the “randomness” studies, google these for additional information, follow the links and learn.

Acquired Characteristics. The “directed” mechanism you may be looking for is called Acquired Characteristics. Traits acquired by the individual during its life or from the environment around it are passed on to its offspring. For this to occur there, of course, must be some kind of feed-back mechanism into the genome of the individuals germ cells so that these new characteristics are inherited by the offspring.

Start with Jean-Baptiste Lamarck. Do the research and learn how these ideas have been so thoroughly refuted. As you get deep into it you might be surprised at the lack of some overarching "world view" that directed the research. There is no identifiable feedback mechanism from environment to DNA of the individual. The only identified mechanism is Natural Selection which operates its feedback at the level of populations. Now, unless one wants to posit some kind of magic, other-dimensional or divine mechanism this is the totality of the present science.

If you want to see an example of the effects of ignoring the science on this subject then research Trofim Denisovich Lysenko.


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Dr Adequate
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Posts: 16107
Joined: 07-20-2006
Member Rating: 8.0


(2)
Message 9 of 134 (548598)
02-28-2010 2:21 PM
Reply to: Message 1 by herebedragons
02-27-2010 11:46 PM


Instead, it makes more sense that mutations, (and therefore adaptation) are directed by the cell and by cellular processes.

Except that the requisite cellular processes don't exist. How could they? These processes would have, in effect, to be able to think. The mechanisms in a bacterium, for example, would have to be able to look at the chemical structure of a novel antibiotic, look at the metabolism of the bacterium, and figure out what changes needed to be made to its genetic code to make its metabolism invulnerable to the antibiotic --- a question so difficult that no human geneticist would undertake to figure it out a priori.

I would not completely rule out a scenario in which an organism had a mechanism for performing some specific act of genetic engineering on itself in response to long-standing fluctuations in the environment. But it is beyond belief that the cell could have a general mechanism for making appropriate changes to its genome.

So, I would like to discuss the experimental and observed evidence for and against the idea that mutations are random ...

One point which has already been made is that most mutations are not particularly useful. Now you might suggest that only one cell in a million has the intelligence to figure out what the right mutation is, but it seems simpler to imagine that they all mutate at random and one cell in a million is lucky enough to get it right.

(By analogy, the fact that some people win the lottery does not particularly persuade me that people have psychic powers allowing the winners to divine the correct numbers --- since dumb luck will in fact explain the frequency with which people win.)

... and yet can still provide the needed resources for evolution to occur.

I would draw your attention to the existence of genetic algorithms and genetic programming. We know that these processes work, and we know exactly how these processes work, and there is not a chance that the random number generator of a computer somehow knows how to solve every problem that computer scientists throw at it. In this case we can be utterly certain that there's no intelligence in the mechanisms --- but the random variation is indeed sufficient.


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Taz
Member (Idle past 1578 days)
Posts: 5069
From: Zerus
Joined: 07-18-2006


(1)
Message 10 of 134 (548608)
02-28-2010 4:55 PM
Reply to: Message 1 by herebedragons
02-27-2010 11:46 PM


herebedragons writes:

This is not an argument about irreducible complexity and I am not saying “God-did-it”. What I am suggesting is that random mutations may not be the all powerful driving force of evolution that they have been thought to be. Instead, it makes more sense that mutations, (and therefore adaptation) are directed by the cell and by cellular processes.

So, I would like to discuss the experimental and observed evidence for and against the idea that mutations are random and yet can still provide the needed resources for evolution to occur.


Of course, your entire post is a straw man. You briefly mentioned natural selection and then completely ignored it in the rest of your post. But then you also blow up the role of random mutation to imply that random mutation is the main driving force of evolution.

Random mutation is only part of evolution. And I would argue that in the great scheme of things it is a very small part of it. The main beef of it all are all the mechanisms that take full advantage of the variations that invariably result from mutation. But you failed to take that into consideration at all.

So, it leads me to wonder why you started this thread. Since you are aware of natural selection, I doubt that you are either ignorant or genuinely seeking out knowledge. What's the alternative? Only the gods and you know.


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Bolder-dash
Member (Idle past 1916 days)
Posts: 983
From: China
Joined: 11-14-2009


Message 11 of 134 (548661)
02-28-2010 10:20 PM
Reply to: Message 10 by Taz
02-28-2010 4:55 PM


I had given up posting on this forum anymore, because its clear the rules for moderation are not applied equally (thus most on the other side of this debate all quickly leave this site)-however as I browse through here, I see the evolutionists are up to their same old tricks-which I couldn't just let slide.

Once again you and Perry and others are trying to run away from the random aspect of the entire ToE, as if natural selection all by itself can do anything. The fact that you can neither adequately demonstrate the accuracy of either the random mutations aspect of it, nor the natural selection aspect of it, does not prevent you from claiming that the random mutations part is a "very small part of it." How bizarre this aspect of your argument really is. Natural selection says absolutely nothing other than some organisms live more than others-yet you want to claim that the actual changes from one generation to the next are a small part of populations changing. Your talking points are made for dopes.

You side claims it takes too long to "see" evolution and that's why it is hard to demonstrate it scientifically, you claim your theory can make predictions but don't know what they are, you claim the mechanisms for all of the variation are still not clearly know yet you are sure they are random, you say you don't know how it all started but are working on that, and now you want to say that well, look let's not get all hung up on the small matter of how the changes happen in a species, let's just concentrate on the fact that once the changes happen, animals survive better (or maybe not, we are still working on that too, perhaps its all just lucky horizontal drift!).

For a scientific theory that wants to preclude consideration of all other ideas, its not much of a theory. Or I am just arguing from incredulity again?

From the incredulity that you have the right to call something so vague and unverifiable a theory. And from the incredulity that your side thinks that just because your theory is hard to prove and impossible to show, and full of gaps of explanation and empirical evidence-that if someone has another theory that is equally unable to be proven, since it can't be seen yet, it has no business being considered.


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herebedragons
Member (Idle past 18 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 12 of 134 (548664)
02-28-2010 10:34 PM
Reply to: Message 4 by slevesque
02-28-2010 2:20 AM


Non, je ne parle pas français
You speak french ?

No, I don’t. I just thought it was a very appropriate closing line to use for this forum so I decided to use it. It is the equivalent of “Take care of yourself” or “You be careful”. Literally translated it means “Defend yourself well”. (But you probably knew that already)

Defendez-vous bien!


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herebedragons
Member (Idle past 18 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 13 of 134 (548665)
02-28-2010 10:39 PM
Reply to: Message 5 by Stagamancer
02-28-2010 3:27 AM


serendipity???
Hi Stagamancer

serendipitous advancements in science and technology

Point well taken. However, there is a difference between accidently discovering something while looking for something else and relying on mistakes for advancements. You would be very unlikely to make any significant discovery by just randomly mixing chemicals, for instance. You begin in a specific direction and keep your eyes and mind open for serendipitous results.

quote:
The French scientist Louis Pasteur also famously said: "In the fields of observation chance favors only the prepared mind."

How exactly would this work? How could a cell know to direct mutation?

When you say "it makes more sense..." have you really thought about it?

Yes I have thought about it and honestly, I don’t have a good answer yet. That’s why I am on this forum - that’s why I am asking the question.

How would an individual cell possess the forethought to make the correct mutations?

Let me put the question back to you. How does the individual cell know how to do any of the cellular functions it carries out? Do you understand the extreme complexity of cellular processes? How does the cell have the “knowledge” to keep itself functioning? If we consider the amount of “knowledge” a cell does have, why can we not conceive that it also has the knowledge to make changes to itself in order to survive?

Keep in mind, I am not overly confident that my assertions are true, but I think they are worth investigating. I would like to see experimental evidence (I already have looked at the Luria-Delbruck case)

Defendez-vous bien!


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Taz
Member (Idle past 1578 days)
Posts: 5069
From: Zerus
Joined: 07-18-2006


Message 14 of 134 (548667)
02-28-2010 10:42 PM
Reply to: Message 11 by Bolder-dash
02-28-2010 10:20 PM


Bolder-dash writes:

Once again you and Perry and others are trying to run away from the random aspect of the entire ToE, as if natural selection all by itself can do anything. The fact that you can neither adequately demonstrate the accuracy of either the random mutations aspect of it, nor the natural selection aspect of it, does not prevent you from claiming that the random mutations part is a "very small part of it."


Random mutation and natural selection don't just apply to biological life. It's also a very useful method to understand physical problems in physics. Hint: monte carlo method.

Random mutation is a small but significant part of evolution. Parameters (selective pressures) are then applied to weed out the undesired results and keep the desired results. Through time, small but significant results are accumulated to give rise to new characteristics. And so on and so forth. But my point in this thread is random mutation isn't the start all end all thing that drives evolution. It's a significant piece, but just a piece nonetheless.

You side claims it takes too long to "see" evolution and that's why it is hard to demonstrate it scientifically

Incorrect. Evolution is very easy to demonstrate. But it also depends on who's receiving the information. And right now as it stands, you seem to have no clue how the mechanisms work.

you claim your theory can make predictions but don't know what they are

What are you talking about? Accurate predictions have been cited so many times on this forum, I've lost count.

you claim the mechanisms for all of the variation are still not clearly know yet you are sure they are random

Huh? When did I or anyone say this?

you say you don't know how it all started but are working on that

What, and you claim to know it all?

and now you want to say that well, look let's not get all hung up on the small matter of how the changes happen in a species, let's just concentrate on the fact that once the changes happen, animals survive better (or maybe not, we are still working on that too, perhaps its all just lucky horizontal drift!).

You seem to have a gross misunderstanding of evolution based on these words.

For a scientific theory that wants to preclude consideration of all other ideas, its not much of a theory.

Incorrect. If you have a better view, please by all means publish your experiments and results in peer review.

Do you or do you not agree that mutation invariably happens? If you do not, please explain why and give us examples. If you do agree, then I don't understand what the argument is here.

And from the incredulity that your side thinks that just because your theory is hard to prove and impossible to show...

Again, the theory is quite simple to understand and demonstrate. The problem lies in the audience. Your words demonstrate that you don't even understand the basics of biological evolution. Just because you can throw in words from a high school biology text doesn't mean you understand them.

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herebedragons
Member (Idle past 18 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 15 of 134 (548668)
02-28-2010 10:43 PM
Reply to: Message 9 by Dr Adequate
02-28-2010 2:21 PM


Hi Dr. Adequate

I would not completely rule out a scenario in which an organism had a mechanism for performing some specific act of genetic engineering on itself in response to long-standing fluctuations in the environment. But it is beyond belief that the cell could have a general mechanism for making appropriate changes to its genome.

This is probably closer to what I am thinking. (I wonder why you put it in such a small font size?) For example, a plant would not need to respond to novel food sources, but they would need to respond to climate changes, altitude changes and the like. So a general mechanism would not be necessary, but a specific mechanism would allow the organism to respond appropriately to changes in environment.

One point which has already been made is that most mutations are not particularly useful. Now you might suggest that only one cell in a million has the intelligence to figure out what the right mutation is, but it seems simpler to imagine that they all mutate at random and one cell in a million is lucky enough to get it right.

I do realize that there are mutations that are random, being caused by errors in replication. I noted the error rate that seems to be accepted - 1 error in 1 billion nucleotide replications. As you noted, most are not particularly useful. Then add into it that the mutation must happen in the germ cells and then be the lucky germ to be fertilized (or involved in fertilization) and the odds are beyond my liking. I think your comment about being “simpler to imagine” fails to recognize the incredible complexity of cellular processes. Nothing that goes on within the cell is simple. Nothing about the cell is “simple to imagine”.

I would also add that I am not overly confident that my assertions are true, but I think they are worth investigating. I would like to see experimental evidence (I already have looked at the Luria-Delbruck case). I have some things of my own that I will present for discussion as soon as I get a chance.

Defendez-vous bien!


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