Evolution?

[juvenissun]

For the same reason that we call all eukaryotes eukaryotes. What's so hard to understand about this? It's just a name that we give to a certain group of organisms that share certain characteristics.

Yes they did. The populations diversified into organisms with different genetic characteristics. Evolution.

Then why do you keep ignoring the definition of evolution?

I am NOT ignoring it. You should admit that it is becoming a problem in the biological field. It is not as well defined as it was before.

 

[Naraoia]

This is a good question.

While I was saying the life tree does not appear to be random, I also asked myself, what would be the shape which shows the status of random? Earlier, someone presented a tree arranged in a radial pattern.

Was it this one or something similar? This tree isn't radial, it's just a standard bifurcating tree bent around so it takes up less space.

I will think about this. When I get something, I will post it.

Glad I've got you thinking.

 

[Naraoia]

I am NOT ignoring it. You should admit that it is becoming a problem in the biological field. It is not as well defined as it was before.

In what sense is it not as well defined? I'm not aware that it's changed since the invention of the allele frequency-based definition...

 

[juvenissun]

It is. At least random with respect to the environment organisms live in. This has been shown extensively in lab experiments.

Nit pick: organisms (life) either have a mutation or don't. Acceptance has nothing to do with it.

Whether an organism with a certain mutation survives or not is not deterministic, but stochastic. Meaning that it can increase or decrease survival, but does not guarantee it.


How would you know, you've never studied it. No, sub-stable environment is not good enough for life to maintain the same trait. Otherwise, we wouldn't see populations evolve anymore at all, but we do.


You did no such thing. At best you did so on a misunderstanding of that knowledge.

Then tell me how did [bless and do not curse][bless and do not curse][bless and do not curse][bless and do not curse] roaches remain the same through millions of years? They might evolve into new species. But they are still there. Why didn't they disappear due to environmental change? The common-ancestor concept does not quite fit with your mutation idea.

 

[TheGnome]

Thanks, Gnome.

Maximum likelihood was basically the first more advanced statistical concept used in tree-building that came to my mind As I've said to Blayz, at this point I'm interested in the whole thing because I want to have a better idea of how much I can trust trees others made.

Do you know about the Neighbor Joining method? It's great in that you can actually do it by hand, and my professor found a tutorial online that allows you to walk through it by hand. http://www.icp.be/~opperd/private/neighbor.html is a really good tutorial, and I believe it uses the Jukes-Cantor substitution model if I remember right. It doesn't teach you about testing the node, like bootstrapping--one of the most basic. You could do bootstrapping by hand, but I wouldn't recommend it considering you'd probably do at least 500 bootstrap replicates per node. Just know how to do one, then use MEGA do all of the calculations for you.

The best way to learn phylogenetics is by just doing. Download MEGA and MrBayes, do the tutorials, and get the trees. I'm sure you've heard of GenBank by now. Develop your own miniproject by grabbing sequences off of GenBank and use the various tree building methods in MEGA and use MrBayes to build trees. See where they're similar and we're they're the same, look at the values of the nodes, when should you more comfortable with the nodes? Does a high value mean a correct node? In distance trees, what is long branch attraction?

Know what Maximum Likelihood, Bayesian Inference, and Bootstrapping are supposed to do, but not the math behind it. Know what Markov Chain Monte Carlo does, but not the math behind it. Know the various substitution models, and know the math on the ones that aren't so parameter heavy.

Most importantly, know that if you see a tree in the literature, realize that it may be wrong only because of poor alignment, and it may be something that is out of their control, and it may be an issue that can be solved by knowing a little more about the organisms and how they got to where they are and such.

Hope that helps.

 

[Tomk80]

This is a good question.

While I was saying the life tree does not appear to be random, I also asked myself, what would be the shape which shows the status of random? Earlier, someone presented a tree arranged in a radial pattern. But that is not random either. I have an idea on what a random pattern is in crystalline structure. But I never thought how to apply that to live evolution.

I will think about this. When I get something, I will post it.

Apparantly you are missing a point here. Even the tree in the radial pattern shows in essence the same. You start in one point and then every node contains a split, where the line continues as two or more lines. Regardless of whether you arrange this as a tree, with the first single line at the bottom and the rest above it, or in a radial shape, the concept behind it is exactly the same. In other words this:

is in essence the same as this:

Or this:

The shape of these mathematically have nothing to do with randomness or non-randomness. They have to do with one group splitting into two or more new groups, where there is no cross-over between the different groups. You could perform that exercise with a group diversifying randomly or a group developing through some deterministic mechanism, the tree-shape would stay the same.

 

[[serious]]

Then tell me how did [bless and do not curse][bless and do not curse][bless and do not curse][bless and do not curse] roaches remain the same through millions of years? They might evolve into new species. But they are still there. Why didn't they disappear due to environmental change? The common-ancestor concept does not quite fit with your mutation idea.

Which of the 4000 evolved species of roaches is the one that hasn't evolved?

Roaches are remarkably effective survivors as they are so they aren't changing rapidly, but they do still evolve.

 

[Tomk80]

I am NOT ignoring it. You should admit that it is becoming a problem in the biological field. It is not as well defined as it was before.

It has been defined this way ever since we know what genes are, which means for the past 50 years at the least. And no, it is not becoming a problem in the biological field.

 

[Tomk80]

Another fun way of displaying a cladogram.

 

[Tomk80]

Then tell me how did [bless and do not curse][bless and do not curse][bless and do not curse][bless and do not curse] roaches remain the same through millions of years? They might evolve into new species. But they are still there. Why didn't they disappear due to environmental change? The common-ancestor concept does not quite fit with your mutation idea.

Because the niche they occupy is still there. It is a shape that works. Nowhere in the common-ancestor model is it required for succesful species to go extinct (edited to add: better to say similar shapes, since there have been different cockroach species over time). That is neither observed nor logical.

edited to add: what is more, both cockroaches and humans are eukaryotes.

 

[Naraoia]

Do you know about the Neighbor Joining method?

Yeah, did something similar in a practical last year. I take it Neighbour Joining is good for little more than getting basic ideas.

It doesn't teach you about testing the node, like bootstrapping--one of the most basic.

And the only one I actually know how to do (in principle ).

The best way to learn phylogenetics is by just doing.

I figured that, that's why I'm planning to arrange some related experience.

Download MEGA and MrBayes, do the tutorials, and get the trees. I'm sure you've heard of GenBank by now. Develop your own miniproject by grabbing sequences off of GenBank and use the various tree building methods in MEGA and use MrBayes to build trees.

That's kind of what I was told today by the person I approached (although he recommended PHYLIP). I would prefer playing under the guidance of someone who knows their treebuilding, but just playing seems like a good way to start.

Hope that helps.

It does indeed It's always good to see things from the insider's viewpoint.

 

[Bombila]

Then tell me how did [bless and do not curse][bless and do not curse][bless and do not curse][bless and do not curse] roaches remain the same through millions of years? They might evolve into new species. But they are still there. Why didn't they disappear due to environmental change? The common-ancestor concept does not quite fit with your mutation idea.

There are more than 4000 known cockroach species. They differ in size, shape, wings, environment/habitat, food sources, etc. They are not 'the same'. Also, you've been told that lifeforms that are not subject to external pressures very much don't change much because any mutation is diluted by the fact of the entire population not having the mutation being able to successfully reproduce without it.

Does it never occur to you, juvenissun, that the reason most of the world, including the great majority of Christians, think evolution is a fact-based rational theory that predicts and explains a great deal of biological reality is because it is the truth?

Look back at all your posting here, all your arguments. Do you not see how much twisting of concepts, nitpicking at semantics, denial of facts, you have had to engage in without any success in refuting anything scientists present?

Granting, for the moment, that your version of God exists, do you really think he would approve of your methods, which rely on the thinnest and most credulous surmisings? Have you not noticed that creationists themselves have multiple disagreeing ideas about how to interpret the evidence the earth divulges, that most of their notions depend on a deceptive god who tries to fool humans about the age of the earth, and that almost all of these creationists have very little background in the very sciences they pretend to find wrong?

How can you reconcile these facts with honesty?

 

[TheGnome]

Yeah, did something similar in a practical last year. I take it Neighbour Joining is good for little more than getting basic ideas.

And the only one I actually know how to do (in principle ).

I figured that, that's why I'm planning to arrange some related experience. That's kind of what I was told today by the person I approached (although he recommended PHYLIP). I would prefer playing under the guidance of someone who knows their treebuilding, but just playing seems like a good way to start.

It does indeed It's always good to see things from the insider's viewpoint.

The Neighbor Joining Method (NJ) is still used. It would be silly to only use Maximum Likelihood (ML) to construct trees, what would you have to compare them with other than trees constructed using morphological data? Maximum Likelihood and Bayesian Inference (BI) typically give the same tree, and any differences may result would be what the prior was defined as in BI. BI may give the more correct topology depending on how reliable the informative prior is, and frequentists seem to be uncomfortable with using priors, therefore they put more emphasis on ML.

NJ is quick and dirty. It gets the job done much faster than ML and BI, and it's pretty good at determining the right topology. I see it in the literature, usually contrasting it with another method. I believe Maximum Parsimony is still used, and is probably decent for very related organisms. This is where all my basic knowledge breaks down. I don't really know which is good in which situations, and the experts are probably still figuring that out. Typically, the different methods produce very similar trees.

I doubt I'll learn phylogenetics any deeper than this until I have my own lab, or maybe when I go for my PhD, depending on my opportunities.

 

[juvenissun]

Juvenissun, at this point your assertions become increasingly dishonest. It has already been explained to you that "bacteria" is a grouping, the same way the "eukaryotes" is a grouping. Why do you pretend that this hasn't been explained to you?

Same with evolution. It has already been explained to you that in biology evolution is defined as "the change of allele frequencies in a population over time". This is the definition used by biologists everywhere in the world, as has been explained to you multiple times in this thread. It is not a "borrowed" or "abused" term in this sense, it is applying the term according to the definition. The correct thing to do in this case, is for you to use the actual terms you mean, not to arrogantly hold to your own debunked points like a five year old sticking his fingers in his ear and going "LALALA, I can't hear you!".

Show some honesty, please?

Disagreement is not dishonest. You should know that.

First, I don't think a group of cells is the same as multi-cellular.
Second, I argued that your definition of evolution might be a newer one, but is not a traditional one. I may not agree with it.

 

[Tomk80]

Disagreement is not dishonest. You should know that.

What you portray here is not disagreement. It is ignoring whatever has been explained to you.

First, I don't think a group of cells is the same as multi-cellular.

Then your problem is not with "bacteria", but with all single-celled organisms. You keep referring to "bacteria" as if the fact that we call them the same is an argument. It is not. We also call all eukaryotes the same.

Second, I argued that your definition of evolution might be a newer one, but is not a traditional one. I may not agree with it.

It is a traditional one. It is older than you are. And whether you agree with it or not is completely irrelevant, unless you give an actual argument why that definition would not be referring to would not be valid. You have not given any semblance of an argument in that direction.

 

[juvenissun]

Abused. Please. Evolution, as applied to living organisms, is a technical term of the biological sciences. Biologists gave it a rigorous definition, so they sort of have the right to use that definition when talking about biology. If anyone "borrows" or "abuses" the word in this thread that's you.

Oh yes. Whatever living things do, it is still done by "living things".

So living things don't evolve?

Hmm... would you say mitochondria and chloroplasts are still bacteria?

OK, since the beginning of this thread, it was always you people asked me what does evolution mean. It was like you know it and I don't. Somehow I was only trying to answer the question and forgot to ask back.

Now, I am going to ask you (people): WHAT IS EVOLUTION? You people better give me a consistent answer, which is biologically meaningful and not ambiguous. What I want is a definition, not content or explanation. So, go for it and make my day.

Tomk80 already gave me one:

biology evolution is defined as "the change of allele frequencies in a population over time"

. May be someone likes to modify it and makes it agreeable to everyone.

 

[Tomk80]

OK, since the beginning of this thread, it was always you people asked me what does evolution mean. It was like you know it and I don't. Somehow I was only trying to answer the question and forgot to ask back.

Now, I am going to ask you (people): WHAT IS EVOLUTION? You people better give me a consistent answer, which is biologically meaningful and not ambiguous.


What I want is a definition, not content or explanation. So, go for it and make my day.

A change of allele frequencies in a population over time.

This is what, the fourth time this definition is given in this thread?

And don't pretend I haven't given this answer earlier in this thread and others have not given answers that say exactly the same. Because that definition has been provided in this thread multiple times by multiple people already.

 

[juvenissun]

There are more than 4000 known cockroach species. They differ in size, shape, wings, environment/habitat, food sources, etc. They are not 'the same'. Also, you've been told that lifeforms that are not subject to external pressures very much don't change much because any mutation is diluted by the fact of the entire population not having the mutation being able to successfully reproduce without it.

Does it never occur to you, juvenissun, that the reason most of the world, including the great majority of Christians, think evolution is a fact-based rational theory that predicts and explains a great deal of biological reality is because it is the truth?

Look back at all your posting here, all your arguments. Do you not see how much twisting of concepts, nitpicking at semantics, denial of facts, you have had to engage in without any success in refuting anything scientists present?

Granting, for the moment, that your version of God exists, do you really think he would approve of your methods, which rely on the thinnest and most credulous surmisings? Have you not noticed that creationists themselves have multiple disagreeing ideas about how to interpret the evidence the earth divulges, that most of their notions depend on a deceptive god who tries to fool humans about the age of the earth, and that almost all of these creationists have very little background in the very sciences they pretend to find wrong?

How can you reconcile these facts with honesty?

I don't care who else said what. In science, I think my way.

And, I don't agree with what you said (highlighted). Evolution is fact based. That is fine with me. But evolution predicts little and does not explain well. So it is certainly not a truth. So, why don't you join others and trying to give a definition to the term "evolution"?

 

[juvenissun]

A change of allele frequencies in a population over time.

This is what, the fourth time this definition is given in this thread?
[/COLOR]
And don't pretend I haven't given this answer earlier in this thread and others have not given answers that say exactly the same. Because that definition has been provided in this thread multiple times by multiple people already.

Fine. I have no problem if you want to define it that way.

Before others give their opinion, I want to ask you, based on your definition:

How do you provide any evidence to show that ape did "evolve" to human according to your definition? In fact, if you use your definition, you can not give a single evidence to any evolutional features presented in paleontology.

 

[Tomk80]

And the original definition of evolution was descent with modification, it has since been refined to change in allele frequencies over successive generations. Notice that I said refined, change in allele frequences is still descent with modification.

In fact, the difference between "descent with modification" and "change in allele frequencies is over time" is that the latter defines what changes in the former.