Evolution?

[Naraoia]

IIRC it was by identifying the number of organs, or some similar measure. What was especially interesting was that in most lineages, some kind of parasitism would often evolve.

Hmm... I think I will be more interested in his examples where decreasing complexity doesn't accompany becoming a parasite.

You'll get interested as soon as you do your own research.

Well, I kind of hope I can spend my next summer doing something involving molecular phylogenetics. Seems like a good area to learn what the hell Maximum Likelihood is.

 

[Naraoia]

I am a profession in academic field. Having fun in my way is pretty heavy in brain activity. To me, think about anything outside my field of geology is having fun. Sorry if this way of description offended you.

And I'm sorry if I was rude. It's just that the "having fun", taken together with your explanation of your expectations, sounded too much like "laughing at people".

 

[Naraoia]

The development described by the live tree. Do you suggest it is a product of random evolution?

Yes, with the warning that the natural selection part of that "random evolution" throws heavily biased dice.

The geometry does not look like one.

You keep telling me that, but you haven't told me why you think a bifurcating tree is a sign of non-random processes. I thought it was only a sign that lineages once separated don't usually mix again.

 

[Tomk80]

Sorry, I misread your question.

They changed from this bacterium to that bacterium and so on. But we still call them bacteria instead of other names. You tell me why.

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.

So, if they remained to be single-cell lives, they did not evolve.

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

Yes, the definition of evolution is important. Just like the definition of creationism is.

Then why do you keep ignoring the definition of evolution?

 

[Tomk80]

The mutation process could be random (not sure).

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

But which mutation is accepted by the life is not random.

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.

Biology is not chemistry. sub-stable environment is good enough for life to maintain the same trait (and to suppress all mutations).

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.

I said the above based on the knowledge passed to me by evolutionist. I don't really like it.

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

 

[Tomk80]

Then Gould echoed my OP. Bacteria does not evolve.

That in no way follows from what I wrote. Read it again and respond to what I actually wrote.

 

[Tomk80]

Hmm... I think I will be more interested in his examples where decreasing complexity doesn't accompany becoming a parasite.

I can understand. I knew I should have bought the book instead of borrowing it the moment I read it

Well, I kind of hope I can spend my next summer doing something involving molecular phylogenetics. Seems like a good area to learn what the hell Maximum Likelihood is.

Definitely.

 

[Blayz]

Well, I kind of hope I can spend my next summer doing something involving molecular phylogenetics. Seems like a good area to learn what the hell Maximum Likelihood is.

Which area? I worked in viral phylogentics for 4 years.

 

[Assyrian]

Sorry, I misread your question.

They changed from this bacterium to that bacterium and so on.

So?

But we still call them bacteria instead of other names. You tell me why.

Same reason lion and tigers and bears are called 'animals'. Does that mean animals didn't evolve either? It is actually evidence they did, you know nested hierarchies.

So, if they remained to be single-cell lives, they did not evolve.

By that reasoning since Tiktaalik crawled out of the mud only snakes, birds and humans have evolved because all the other tetrapods still walk around on four legs. It is a really bad arguement Juv. You are saying because one characteristic remained the same you can ignore all of the other changes and claim they didn't evolve.

Yes, the definition of evolution is important. Just like the definition of creationism is.

Except you had to made up your own definition of evolution to try to show bacteria don't evolve.

 

[TheGnome]

Hmm... I think I will be more interested in his examples where decreasing complexity doesn't accompany becoming a parasite.

Well, I kind of hope I can spend my next summer doing something involving molecular phylogenetics. Seems like a good area to learn what the hell Maximum Likelihood is.

If you're taking a class, or even being in a lab, you're not going to learn Maximum Likelihood (ML) in any appreciable detail. It's a statistical method of determining the likelihood of a given node, so that the ML value you got on the node gives you a certain amount of confidence in it being true. Unless you want to do research in mathematical biology, it won't be very useful for you to learn the actual math, and while it would be great to know the math behind the science, that philosophy won't take you very far once you try to figure out Bayesian Inference and Markov Chain Monte Carlo (MCMC).

Here's a quote from a handout authored by Dr. Bret Larget that I think clears up what Maximum Likelihood does:
A probability model contains parameters and possible values for the data. When the parameters are treated as being known, it tells the probability of observing each possible value, and may be thought of as a function over the possible values of the data.

The likelihood function is the same, except that the possible values are treated as fixed (by plugging in the actual observed data) and the parameters are allowed to vary. So the likelihood function is a function of the parameters. Maximizing the likelihood function is searching for the parameters that make the actual observed data most likely

For further knowledge, Bayesian Inference is the likelihood function times the prior, and the result is the posterior probability.

MCMC is just a really good mathematically way of shuffling up the data so that you could perform "resampling."

When I took Molecular Phylogenetics, all we got was a handout on Maximum Likelihood and we didn't get tested on it because it wasn't something we could do by hand. Knowing the generalize idea of Maximum Likelihood is important, but that's about it. You'll probably benefit best from learning the various tree building methods and substitution models. A lot of the problems in phylogenetics are generally due to a poor alignment.

 

[Naraoia]

Which area? I worked in viral phylogentics for 4 years.

Basically anything I can find, but preferably animals I'm mostly interested in the methods and models and assumptions that go into trees, mainly because I want to know what the trees I see in papers actually mean (and even more importantly, what they don't mean).

 

[Naraoia]

When I took Molecular Phylogenetics, all we got was a handout on Maximum Likelihood and we didn't get tested on it because it wasn't something we could do by hand. Knowing the generalize idea of Maximum Likelihood is important, but that's about it. You'll probably benefit best from learning the various tree building methods and substitution models. A lot of the problems in phylogenetics are generally due to a poor alignment.

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.

 

[Radagast]

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.

I've been wondering that myself. People tend to give the maximum-likelihood tree (or various approximations to it), but quite different-looking trees might have very similar likelihood.

Splits-networks are a way of retaining the uncertainties that might exist (see here for an introduction) and summarising the range of feasible trees. However, I haven't quite got my head around them yet.

 

[Naraoia]

I've been wondering that myself. People tend to give the maximum-likelihood tree (or various approximations to it), but quite different-looking trees might have very similar likelihood.

As to that, the only solution I've heard about so far is giving a consensus tree riddled with polytomies.

Splits-networks

are a way of retaining the uncertainties that might exist (see here for an introduction) and summarising the range of feasible trees. However, I haven't quite got my head around them yet.

Ugh, that's a bit too much for my maths engine right now

 

[juvenissun]

Evolution in Real Time: How Bacteria Beat Antibiotics

Bacteria make major evolutionary shift in the lab

Biologists may not agree with the use of "evolution" in this sense.

 

[Tomk80]

Biologists may not agree with the use of "evolution" in this sense.

Biologists do indeed not agree with the way you define evolution.

 

[juvenissun]

No, Gould was pretty adamant that all living things evolved. Maybe you should try reading some of his work.

Again, I present this as an example. I know you said you had problems opening it before, so you could always read the article in New Scientist instead of the peer-review article.

Yes, why bother. You should already know my argument. What's shown in the research is not evolution. The term is borrowed and in a sense is abused.

Whatever the bacteria can do, it is still done by "bacteria".

 

[Tomk80]

Yes, why bother. You should already know my argument. What's shown in the research is not evolution. The term is borrowed and in a sense is abused.

Whatever the bacteria can do, it is still done by "bacteria".

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?

 

[juvenissun]

Yes, with the warning that the natural selection part of that "random evolution" throws heavily biased dice.

You keep telling me that, but you haven't told me why you think a bifurcating tree is a sign of non-random processes. I thought it was only a sign that lineages once separated don't usually mix again.

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.

 

[Naraoia]

Yes, why bother. You should already know my argument. What's shown in the research is not evolution. The term is borrowed and in a sense is abused.

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.

Whatever the bacteria can do, it is still done by "bacteria".

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?