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Author Topic:   Are mutations truly random or are they guided?
Bolder-dash
Member (Idle past 1889 days)
Posts: 983
From: China
Joined: 11-14-2009


(1)
Message 91 of 134 (548975)
03-02-2010 10:59 PM
Reply to: Message 90 by Coyote
03-02-2010 10:15 PM


Re: unreal expectations based on false information
Oh evidence abounds does it?

I see you are highly skilled in the Dr.A school of mental vivisection. I guess they don't call you coyote for nothing.

Let's see, there is the ongoing E. Coli experiments that demonstrate , they demonstrate hm, ...the ability of random mutations to develop, um, um.... how to say "nothing" in your school of verbal disemboweling?

Did you just pull the first thing you could find on the internet that looked scientific or had the name of a bacteria in it, and hope that no one would notice?

Yes, the evidence does abound doesn't it. Its so overwhelming we can't even see it! Sort of like the beneficial random mutations that abound everywhere around us. It sort of gives a new meaning to the word abound. In fact it does give a new meaning-whereas abound once used to mean plentiful, it now appears to mean scarce or non-existent. Quite amazing.

E Coli! Ole!!

Edited by Bolder-dash, : No reason given.


This message is a reply to:
 Message 90 by Coyote, posted 03-02-2010 10:15 PM Coyote has responded

Replies to this message:
 Message 92 by Coyote, posted 03-02-2010 11:14 PM Bolder-dash has not yet responded
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Coyote
Member (Idle past 365 days)
Posts: 6117
Joined: 01-12-2008


Message 92 of 134 (548976)
03-02-2010 11:14 PM
Reply to: Message 91 by Bolder-dash
03-02-2010 10:59 PM


Re: creationist nonsense
You must be an amazing speed reader to have sampled those papers in this short time.

Or a creationist, relying on creationist websites which have to lie as the evidence does not support their claims and beliefs.

Have you no attachment to data and facts, to well-researched theory? Have you no desire to learn what actually happened in the past?

It would seem not, as you don't present scientific evidence in your posts. You rely on ridicule in support of your dogma.

Thanks, but no thanks. I'll follow the evidence wherever it leads. And based on your posts, I certainly won't be swayed in your direction.


Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.

This message is a reply to:
 Message 91 by Bolder-dash, posted 03-02-2010 10:59 PM Bolder-dash has not yet responded

  
Meldinoor
Member (Idle past 3067 days)
Posts: 400
From: Colorado, USA
Joined: 02-16-2009


Message 93 of 134 (548980)
03-03-2010 12:36 AM
Reply to: Message 88 by Bolder-dash
03-02-2010 9:26 PM


Re: unreal expectations based on false information
Bolder-dash writes:

I assumed you could tell, because you are the one that has the theory that they exist-the basis for all of life in fact. I was so naive to think that since they are the foundation of your theory, you knew what they looked like. Touche, Docteur A! Morsure extraordinaire!

Just because we know that many small mutations can lead to large scale changes, doesn't mean we can point to a single one that is responsible for the creation of a new organ. Because that's what you want, isn't it? You want us to identify ONE mutation responsible for producing, say, a new liver or a spleen where there was none earlier. You are assuming that there is ONE starting point, when in reality, many many mutations have been involved in bringing about the structures in modern humans.

In an earlier thread RAZD and I were explaining to you how the evolution of wings or gliding membranes would have occured. You completely refrained from rebutting my post and instead engaged in a pathetic ad hominem. But that's not the point.
The point is, the evolution of wings is a good example of how new structures evolve*, because of its initial simplicity. I'm no biologist, but webbed feet and hands occur commonly enough among humans that I suspect growing some webbing is as simple as a single mutation. To a human this is hardly beneficial, but to a tree dwelling animal like a squirrel, a bit of additional webbing may boost its chances of successfully leaping to a distant tree and escaping predators. If squirrels that can leap long distances are selected for, then additional mutations may be selected for, further improving the shape and span of the web (as well as any other adaptations that make gliding easier). By the time the squirrels are gliding through the trees, it may be impossible to say exactly which mutated allelle was the starting point. It may in fact have mutated again, in which case the "starting point" is lost.

It's like going to an old temple and asking, "which stone was laid first?" We know that the temple was built by people placing stones one at a time, and the fact that we can't point to the "starting point" does not alter this fact.

Respectfully,

-Meldinoor

*More accurately, how old structures are modified

ABE:

A bit of advice. I notice how you have a persistent tendency to engage in ridicule, rather than actually discussing the points raised in the posts you respond to. I do my utmost to remain civil in my posts, and I suggest you do the same if you want people here to respect your opinion. Your posts are also a lot clearer if not phrased in a sarcastic manner. Remember, in a debate, losing one's cool is a sign of weakness

Edited by Meldinoor, : No reason given.


This message is a reply to:
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Dr Adequate
Member
Posts: 16104
Joined: 07-20-2006


Message 94 of 134 (548991)
03-03-2010 1:56 AM
Reply to: Message 88 by Bolder-dash
03-02-2010 9:26 PM


Re: unreal expectations based on false information
Whoohoo, read a biology book! Good one! Strong reply!

Perhaps so, but it was one I didn't make.

Still, it would do you no harm to familiarize yourself with the basics.

Man you got me good with that one! How long did it take you to think of that devastating rebuttal?

No time at all, since it was not what I actually wrote.

And then you back it up with even stronger rhetoric-"show me where God poofed out a magic organisms"! Powerful stuff, A! I think the media has got it all wrong, Dawkins isn't Darwin's Rottweiler, instead you are his rabies infested laughing hyena, chewing out the opposition's bloody spleens with your gnarly yellow fangs. Awesome! Who can argue with you there?

You could have saved yourself some time by just typing: "I am angered by my own inability to formulate a rational response".

But it gets better-with your biting wit, you declare-"we can show you lots of random mutations, all of them" So there!

That's not witty, that's just true.

And then your canines cut even deeper--"Please tell me how you can tell a beneficial mutation which is a starting point from one which isn't." Wow, I hadn't thought of that!

Well, next time you say something, perhaps you should try to work out in advance what it means.

Gee I don't know how one can tell-because I have never seen one. I assumed you could tell, because you are the one that has the theory that they exist-the basis for all of life in fact. I was so naive to think that since they are the foundation of your theory, you knew what they looked like.

That is indeed biological naivety on a scale that surpasses the dreams of lesser creationists.

You might as well think that since I believe that some babies grow up to be brain surgeons, I should know what such a baby looks like. Well, in a sense, I do --- small, baldish, wrinkled, goes waaah! a lot. Just like all the others.

Well, how about some beneficial random mutations that COULD be starting points? Surely you at least can name a few of those right?

Yes. Pretty much all of them. Just as I could name lots of babies that COULD grow up to be brain surgeons.

In reurn, could you point out one thing poofing into existence by magic which COULD be the result of divine fiat?

Go read a biology book! Ouch, I am bleeding!!

The idea that you might one day learn something about biology seems to particularly distress you. Yes, it would put a crimp into your ability to be wrong. But as I can tell you from personal experience, being right has its pleasures too.

Edited by Dr Adequate, : No reason given.


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Meldinoor
Member (Idle past 3067 days)
Posts: 400
From: Colorado, USA
Joined: 02-16-2009


Message 95 of 134 (548994)
03-03-2010 2:27 AM
Reply to: Message 94 by Dr Adequate
03-03-2010 1:56 AM


Re: unreal expectations based on false information
Dr Adequate writes:

You might as well think that since I believe that some babies grow up to be brain surgeons, I should know what such a baby looks like. Well, in a sense, I do --- small, baldish, wrinkled, goes waaah! a lot. Just like all the others.

Hmm... that's odd. That's the exact analogy I thought of using before I settled for the temple analogy instead. Almost the exact wording I had intended too. A bit scary how that works out sometimes.

-Meldinoor

Edited by Meldinoor, : No reason given.


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Percy
Member
Posts: 18842
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


Message 96 of 134 (548998)
03-03-2010 3:37 AM
Reply to: Message 68 by Bolder-dash
03-02-2010 8:45 AM


Re: unreal expectations based on false information
Hi Bolderdash,

My reply in Message 28 wasn't intended as a defense of the existence of positive mutations. The very premise of this thread assumes the existence of positive mutations and asks whether they're random or guided. I at first thought you were claiming that evolutionary processes were insufficient to explain the history and diversity of life, and that's the position I was addressing.

But if you don't even accept the possibility of positive mutations, which is what I now understand your position to be, then you're in the wrong thread.

--Percy


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Percy
Member
Posts: 18842
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


Message 97 of 134 (549003)
03-03-2010 3:47 AM
Reply to: Message 77 by slevesque
03-02-2010 1:20 PM


Re: Neutral mutations
slevesque writes:

A beetle changing color isn't a near-neutral mutation, precisely because it gives a noticeable advantage to the beetle in a given environment.

Why do you think that a change in color must provide a "noticeable advantage?" Why must it be an advantage? Couldn't be a "noticeable disadvantage?"

And why must it be "noticeable?" Are you saying you can imagine no environment in which a change in color would be neutral? Perhaps an environment where the beetle's only predators operate by smell? And then a new predator enters the environment that operates by sight?

If you still don't like the "beetle color change" example then just invent one of your own where a mutation causes a detectable change that is neutral regarding reproductive success. Or are you operating under the misimpression that expressed mutations can never be neutral?

--Percy


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Taq
Member
Posts: 8011
Joined: 03-06-2009
Member Rating: 4.5


Message 98 of 134 (549031)
03-03-2010 10:23 AM
Reply to: Message 89 by Bolder-dash
03-02-2010 9:34 PM


Re: unreal expectations based on false information
Hmm, they show evolution, by random mutations (you do mean evolution by random mutations, correct? Because certainly YOU would never post something off topic) occurring? Interesting.

To better understand what biologists mean by "random mutations" you would be well served by studying the two classic examples.

First, the Luria-Delbruck fluctuation experiment. In this experiment they determined that mutations leading to phage resistance occurred prior to the bacteria being exposed to phage. IOW, the phage resistance (beneficial trait) occurred in an environment where it wasn't beneficial.

Wiki page on the experiment

The other experiment is the Lederbergs' plate replica experiment. In this experiment they demonstrated the same thing for antibiotic resistance using a plate replica system. They were able to purify for resistant bacteria without the bacteria ever seeing antibiotics. Again, they demonstrated that the mutations leading to antibiotic resistance occurred in the absence of antibiotic.

You can read the original Lederberg paper here.

When biologists state that mutations are random they are saying that mutations are random with respect to fitness. A mutation does not occur at a higher rate than background simply because it is beneficial in the current environment.


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Taq
Member
Posts: 8011
Joined: 03-06-2009
Member Rating: 4.5


Message 99 of 134 (549032)
03-03-2010 10:29 AM
Reply to: Message 91 by Bolder-dash
03-02-2010 10:59 PM


Re: unreal expectations based on false information
Let's see, there is the ongoing E. Coli experiments that demonstrate , they demonstrate hm, ...the ability of random mutations to develop, um, um.... how to say "nothing" in your school of verbal disemboweling?

Nothing?

quote:
BMC Evol Biol. 2009 Dec 29;9:302.

Identification and dynamics of a beneficial mutation in a long-term evolution experiment with Escherichia coli.
Stanek MT, Cooper TF, Lenski RE.

Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA. mstanek@ltu.edu

BACKGROUND: Twelve populations of E. coli were serially propagated for 20,000 generations in a glucose-supplemented minimal medium in order to study the dynamics of evolution. We sought to find and characterize one of the beneficial mutations responsible for the adaptation and other phenotypic changes, including increased cell size, in one of these populations. RESULTS: We used transposon-tagging followed by P1-transduction into the ancestor, screening for increased cell size and fitness, co-transduction analysis, and DNA sequencing. We identified a 1-bp insertion in the BoxG1 region located upstream of glmUS, an operon involved in cell-wall biosynthesis. When transduced into the ancestor, this mutation increased competitive fitness by about 5%. This mutation spread through its population of origin between 500 and 1500 generations. Mutations in this region were not found in the other 11 evolving populations, even after 20,000 generations. CONCLUSION: The 1-bp insertion in the BoxG1 region near glmUS was demonstrably beneficial in the environment in which it arose. The absence of similar mutations in the other evolved populations suggests that they substituted other mutations that rendered this particular mutation unimportant. These results show the unpredictability of adaptive evolution, whereas parallel substitutions at other loci in these same populations reveal the predictability.

PMID: 20040094 [PubMed - indexed for MEDLINE]


And that's just one of the mutations they studied.


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herebedragons
Member
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 100 of 134 (549037)
03-03-2010 11:21 AM


Help! my thread has been hyjacked
First of all, I didn’t want to reply to everyone individually, since there were so many issues I wanted to address. Since I’m fairly new on this forum and didn’t know a better way to do this, I just did a general reply. Is there a better way to do this? Maybe tag those involved that I want to know I was responding to them?

Let’s try to get this discussion back on topic. This thread has been hijacked by pointless arguing. No one benefits from this. I came to this forum seeking some scientific discussions on this debate between evolution and creation. If I wanted a pointless arguement, I would just talk to my wife . So let’s get back to the discussion, please.

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.

Note the bolded word “evidence”.

Zen Monkey wrote in message 3:

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?

Yes I do. Directed vs. random mutations is not a dead issue. If I were arguing that the Earth was flat, that would deserve such a response. However, I don’t feel this is anywhere near the same type of argument. (Also note that I am not necessarily arguing for directed mutations, but asking the question. But since this is a debate forum, I am taking the “side” of directed mutations).

I’m not sure how my religion came into this discussion. What verse in the Bible or any other religious material addresses the issue of mutations? I don’t know of any. So, if you want to spend time bashing me for my religious beliefs, we won’t do much science, will we?

I have also noticed that there has been a resurrection of Lamarkism in recent years. I don’t think I would go to that extreme, but perhaps a form of it. I have also seen some instances of adaptation that , at least for me, call into question the randomness of those adaptations. One of my problems is I don’t have access to scientific journals (they require a subscription). So when I have found some research in this area, I only have access to the abstract (if I’m lucky). So I was hoping those that had information from scientific writing could help me find such papers or point me in the right direction.

Taz wrote in message 17:

... you could have worded your OP a lot better. Try to understand it from my view. We get a hundred or so ignorant creationists a month declaring that evolution = 100% random. Hell, even our long time (years) resident creationists still insist that evolution = 100% random.

Sorry, my first thread. Hopefully I’ll get better at this. And hopefully I’ll be able to earn enough respect that even if I disagree, it’s not just because of religious dogma. I love science, isn’t that why your all here too?

Stagamancer wrote in message 23:

It doesn't "know". The processes of the cell occur spontaneously. All of the reactions that happen in the cell are either thermodynamically favorable (exergonic) or are fueled by an outside source of energy. Either way, they occur simply as a consortium of biochemical reactions without any conscious thought. Cognitive function is an emergent property of groups of cells. It cannot exist within a single cell.

This is the sort of hand waving dismissal of cellular complexity that prompted me to write my OP the way I did. It goes far beyond “simply biochemical reactions”. As a most basic example, put glucose and oxygen together and what happens? Nothing. The reaction requires an input of energy from the cell in the form of ATP. The complexity of these reactions, interactions and cellular controls increases exponentially from there. One of the key points here is the cell must be living for most of the processes to occur.

This may not constitute conscious thought, nor require it, but it deserves more recognition than calling them “simply biochemical reactions”. Without considering the issue of mutations or evolution, have I made my point about cellular complexity? Or do we need to continue discussing it?

Stagamancer also wrote in message 23:

Because, as I said, individual cells do not have knowledge, much less the creative capacity to guess at what they'll need. What you're implying is that a single cell has the ability not only to recognize that it needs to adapt, but has the knowledge of how a change in nucleotide sequence will alter the function of a protein.

Perhaps not knowledge in the traditional sense, but the cell does contain a vast amount of information. Each individual cell has all the information needed to construct an entire organism from a single cell. This is remarkable in itself - that from one cell all the tissues, organ and systems of an organism can develop. I would say that the cell “knows” how to develop in to the mature organism. It does not leave development to “chance” (although clearly there are instances where things go wrong or develop incorrectly, but the cell is extremely accurate and in the grand scheme makes very, very few mistakes).

I think the best Response so far is:

Bluegenes wrote in message 25:

The answer to the question in the O.P. title, "Are mutations truly random or are they guided" is that some mutations are partially guided by a combination of environmental factors and the history of the species involved (whether or not it has inherited the tendency to react positively to a specific kind of stress).

I do have some specific examples that have caused me to question the randomness of mutations, but I don’t have time right now to go into them. I will try to post some by the end of the week.

Defendez-vous bien!


Replies to this message:
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herebedragons
Member
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 101 of 134 (549040)
03-03-2010 11:27 AM
Reply to: Message 32 by Percy
03-01-2010 9:58 AM


creationist??
It does seem strange that the creationists in this thread seem to be arguing against the possibility of advantageous mutations when the thread's premise is that positive mutations happen and that they are "directed by the cell and by cellular processes." (see Message 1)

Who are the “creationists”? How can you recognize them, just because they disagree with neo-darwinism? I never argued against advantageous mutations, so am I a creationist or not? I only saw one person arguing against advantageous mutations and I’m not sure whether he is a creationist or not. He just seems to like to derail the discussion and get the evolutionists all worked up.

I personally want the opportunity to discuss science with intelligent, knowledgeable people. I tried to present my opening in such a way as to describe why I was asking the question and none of it involved religion. I realize your experience may be that 99% of creationists are ignorant and base their assumptions on “religious dogma”, but it’s really not fair to lump everyone that disagrees into that one category. If you think I am an “ignorant creationist” so be it. But please, don’t judge me by bolder-dash.

I came to this forum because I love science and want to explore and discover the world around me, not to defend my religion or to convince you that my religion is right. I think you are here for the same reason, because you love science, not because you want to defend your beliefs.

Defendez-vous bien!


This message is a reply to:
 Message 32 by Percy, posted 03-01-2010 9:58 AM Percy has responded

Replies to this message:
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Taq
Member
Posts: 8011
Joined: 03-06-2009
Member Rating: 4.5


Message 102 of 134 (549043)
03-03-2010 11:50 AM
Reply to: Message 100 by herebedragons
03-03-2010 11:21 AM


Re: Help! my thread has been hyjacked
Note the bolded word “evidence”.

Note the two experiments I discuss (Luria-Delbruck and Lederberg) above. Those are the classic experiments which demonstrated the randomness of mutations.

We can also discuss differences in the genomes of species. It is observed that there are more synonymous mutations than non-synonymous mutations when comparing genomes which strongly indicates random mutations filtered through selection.

As to directed v. random, you still need to address why humans are born with genetic diseases due to mutations. At least to me, this seems like a contradiction to the directed mutation argument. Also, in the two experiments above they actually calcuate the rate at which the beneficial mutations occur. They occur only once in every hundred million replications or so. Does that sound like a directed process to you, where the beneficial mutation only arises once in every 100 million divisions? Sure doesn't to me.

So, if you want to spend time bashing me for my religious beliefs, we won’t do much science, will we?

It's a two way street. I have presented the scientific evidence, but instead of focusing on that you have chosen to talk about how people have persecuted you. If you don't want to discuss your religious beliefs then don't. Discuss the science.

This is the sort of hand waving dismissal of cellular complexity that prompted me to write my OP the way I did. It goes far beyond “simply biochemical reactions”. As a most basic example, put glucose and oxygen together and what happens? Nothing.

Actually, I would strongly suspect that glucose is slowly oxidized in the presence of oxygen, just at a much slower rate than is seen in the cell. Also, anyone who has done any cooking has probably experienced the black aftermath of scorching sugar.

Also, pointing to complexity gets us nowhere. "Wow, that's complex" is an ok observation, but it is not an explanation. The problem is that you seem to be pushing this observation as an explanation. We have seen this too many times to count.


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 Message 100 by herebedragons, posted 03-03-2010 11:21 AM herebedragons has not yet responded

  
Percy
Member
Posts: 18842
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


Message 103 of 134 (549048)
03-03-2010 1:13 PM
Reply to: Message 101 by herebedragons
03-03-2010 11:27 AM


Re: creationist??
Hi Herebedragons,

My comment was directed at those who rejected the thread's premise as stated in your Message 1. I assume you don't reject your own premise, so I don't understand why you think the comment may also have been directed at you. Didn't I describe the premise of the thread correctly?

--Percy


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AZPaul3
Member
Posts: 4512
From: Phoenix
Joined: 11-06-2006
Member Rating: 4.2


Message 104 of 134 (549054)
03-03-2010 2:26 PM
Reply to: Message 100 by herebedragons
03-03-2010 11:21 AM


Re: Help! my thread has been hyjacked
Note the bolded word “evidence”.

Was there something wrong with the randomness studies cited by Taq and myself?

Did you even look at them?

In your view do thses not constitute "evidence?"


This message is a reply to:
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Stagamancer
Member (Idle past 3174 days)
Posts: 174
From: Oregon
Joined: 12-28-2008


Message 105 of 134 (549058)
03-03-2010 3:29 PM
Reply to: Message 100 by herebedragons
03-03-2010 11:21 AM


Re: Help! my thread has been hyjacked
As a most basic example, put glucose and oxygen together and what happens? Nothing. The reaction requires an input of energy from the cell in the form of ATP. The complexity of these reactions, interactions and cellular controls increases exponentially from there. One of the key points here is the cell must be living for most of the processes to occur.

True, which is why I originally said,

All of the reactions that happen in the cell are either thermodynamically favorable (exergonic) or are fueled by an outside source of energy.
A big component determining the difference between life and non-life (and, to be clear, I'm not saying it's the only difference) is controlled conversion and use of energy. The ATP used to fuel cellular reactions initially came from some outside source. But unless you're implying that there is some mysterious life-force, the reactions in a living cell are no different at the basic chemical level than they are in a test tube.
I'm not saying that cellular processes are not incredibly complex, because they are. They are also directed and regulated by cell proteins. But at the most fundamental level, the interactions between molecules, e.g. between enzymes and reagents, is random. An enzyme does not "seek" out it's target they same way we would. It floats around until it makes contact with it's reagents and then catalyzes a reaction. The probability of this chance meeting can be increased a number of ways, an example of which would be compartmentalization.

I would say that the cell “knows” how to develop in to the mature organism. It does not leave development to “chance” (although clearly there are instances where things go wrong or develop incorrectly, but the cell is extremely accurate and in the grand scheme makes very, very few mistakes).

The development of a cell is indeed deterministic, and most cells do it very well, with very few mistakes. But that doesn't mean a cell can direct itself to mutate in a particular way. As I stated before in reference to that paper on nonrandom mutation, the only way a cell can direct mutation is to change mutation rate or differ mutation rates in various regions of the genome. However, though a cell contains information, it does not have the ability to UNDERSTAND how everything works. A cell cannot know that changing A to C or G to T in a sequence will change the resulting peptide in a particular way. It's just not possible. So, a cell cannot pick and choose the mutations it will get. If they get a mutation that is lethal, the cell will die; if it's deleterious, it will be outcompeted. What's left will be the lucky cells that got beneficial or neutral mutations. That's evolution.


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

This message is a reply to:
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