The tree of life, what is it and what does it tell us?

[ReluctantProphet]

So what is the tree of life? Basically, it is a way of grouping things. We want to divide creatures into groups to meaningfully categorize them. ..

Although I would agree that the Biblical tree of life has nothing at all to do with evolution. I have to object a bit to the notion that it is a categorization tree for animals.

The tree of life is a display of how the concerns or issues of life branch out to reach upwards from a more primary concern which is rooted in the Earthy matters.

It is very related to the tree of knowledge. The tree of knowledge is catagorizing information about things (including animals) but the tree of life is categorizing why anything cares.

In effect, it is showing that this kind of life effort branches out into those kind of life efforts. Or the longing for security eventually leads to the longing for control issues and dictatorships.

 

[Tomk80]

Although I would agree that the Biblical tree of life has nothing at all to do with evolution. I have to object a bit to the notion that it is a categorization tree for animals.

The tree of life is a display of how the concerns or issues of life branch out to reach upwards from a more primary concern which is rooted in the Earthy matters.

It is very related to the tree of knowledge. The tree of knowledge is catagorizing information about things (including animals) but the tree of life is categorizing why anything cares.

In effect, it is showing that this kind of life effort branches out into those kind of life efforts. Or the longing for security eventually leads to the longing for control issues and dictatorships.

Are we talking about the same thing here? I'm not talking about the 'garden of Eden tree of life' here, I'm talking about the name we give to the result of us categorizing animals.

I have a hard time following you here.

 

[ReluctantProphet]

Are we talking about the same thing here? I'm not talking about the 'garden of Eden tree of life' here, I'm talking about the name we give to the result of us categorizing animals.

I have a hard time following you here.

Well, maybe I misunderstood your intentions.

Its okay, it has just occured to me that discussing spiritual matters on this forum is not likely to get anywhere anyway.

My mistake, sorry.

 

[Edial]

Moving on, one more concept that is important to learn is that of homologie and analogie. It ties right in with using characteristics of the animal itself as a basis for classification. The creationist sir Richard Owen came up with these terms. Owen described this as: "the same organ in different animals under every variety of form and function." The opposite is analogy, which is the same function, but stemming from a different organ.

What did he mean by this? Let's first take homology. Examine the skeletal structures of the limbs below (klick the link for a larger picture):

The flipper of a whale, the wing of a bat, the arm of a human and the paw of a cat all have the same basic structure. Sure, the different bones have a different length, but all the bones it is made up of are the same bones, only modified. This is what we call homology.

Analogy is the opposite. Take a look at this picture. The wings of an insect, pterodactyl (flying reptile), bird and bat all have approximately the same shape. However, with insects, no skeleton is present. In birds, bats and pterodactyles, the same homologuous structure becomes apparant again, although all modified in different ways.

So, the first separation is skeletal from non-skeletal. And then the "limbs" of the skeletal types.

Question: why skeletal from non-skeletal?

Thanks,
Ed

 

[Tomk80]

So, the first separation is skeletal from non-skeletal. And then the "limbs" of the skeletal types.

Question: why skeletal from non-skeletal?

Thanks,
Ed

Basically, although we can be more specific than that. It's not skeletal or not skeletal, it's origin of the structure that is important. In all the wings and paws shown, the basic structure is build up of the bones that would make the front paws/feet, the limbs closest to the head. The same organ (front feet) gives rise to different structures. In the butterfly wing, the front paw did not give rise to the wing, but an entirely different organ. The front paws of butterflies are still firmly in place. So butterflies and birds have comparable features, wings. However, the structure is different. In birds, the wings come from the organs that, in other animals, form front paws. In butterflies, the wings come from a different organ.,

Another structure that can be considered analogous are the torns in the picture on this lin'k. I hope you forgive me for not knowing the names of the plant, but the important thing is the thorns. They look exactly alike. However, they have a different origin. In the top plant, the thorn is a result of a 'modified leaf', where the rest of the leaf is not produced, but only the midrif of the leaf. In the bottom flower, the thorn forms from an auxillary bud, which usually would form another branch instead of a leaf. So the organ looks the same, but their origin is different.

 

[Edial]

Basically, although we can be more specific than that. It's not skeletal or not skeletal, it's origin of the structure that is important. In all the wings and paws shown, the basic structure is build up of the bones that would make the front paws/feet, the limbs closest to the head. The same organ (front feet) gives rise to different structures. In the butterfly wing, the front paw did not give rise to the wing, but an entirely different organ. The front paws of butterflies are still firmly in place. So butterflies and birds have comparable features, wings. However, the structure is different. In birds, the wings come from the organs that, in other animals, form front paws. In butterflies, the wings come from a different organ.,

Another structure that can be considered analogous are the torns in the picture on this lin'k. I hope you forgive me for not knowing the names of the plant, but the important thing is the thorns. They look exactly alike. However, they have a different origin. In the top plant, the thorn is a result of a 'modified leaf', where the rest of the leaf is not produced, but only the midrif of the leaf. In the bottom flower, the thorn forms from an auxillary bud, which usually would form another branch instead of a leaf. So the organ looks the same, but their origin is different.

OK.
But let's stick to the tree of life.

 

[Tomk80]

OK.
But let's stick to the tree of life.

Well, we should first know how to construct it, and this is where analogy and homology are important concepts. So to go to the 'tree of life' we first have to treat these concepts.

 

[Edial]

Well, we should first know how to construct it, and this is where analogy and homology are important concepts. So to go to the 'tree of life' we first have to treat these concepts.

OK.

 

[Tomk80]

Okay, after a short away, let's start with our categorization. I've decided to start at the top and work the way down. So we'll start by grouping different species of animals together and then see how far we come with that and what kind of a result we get if we do that. Since recent discussions on this board were so much about foxes, let's examine them first.


Now we have determined how we are going to categorize animals, let's go to the categorization itself. Let's start with categorizing foxes. Let's look at a number of foxes and categorize a number of their characteristics. This is necessarily going to be somewhat basic, as extremely detailed knowledge is hard to come by and basically, makes the story a bit too complicated. Of course, I also may forget certain things and make errors, so if you have any questions, point them out.


First off, at their most basic, the cells that make up foxes are eukaryotic cells. This means that the DNA of their cells is collected in a special part of the cell, the core.


Second, all foxes are heterotrophs. This means that they cannot produce their own organic substrates. In other words, they'll need to eat other organisms. This as opposed some other organisms, like plants, that can build up their cells from minerals, CO2, water and sunlight.


Going further, all foxes have a bilateral build. This means that they are symmetrical, their left side is symmetrical with their right side.


Foxes also have a head, middle and tail, a spine and a body plan with four limbs. They are also mammals, meaning that they suck their young. Furthermore, their young develop in a uterus before they are born alive.


Going a little more specific, they all have a skull with large canines, three pairs of incisors in each jaw and specialized molars for chewing meat. Furthermore, they have bushy tails and pointed muzzles.


Now, of course there are different kinds of foxes. For example, the well-known red fox is characterized by it's red coat. It's habitat are fields and forrests. The pale fox, on the other hand, has a pale coat and longer slender legs. It it more adapted to living in the desert (among it's known range is the Sahel desert). On the other hand, the Cape fox has a more silvery drawing and always has a black tipped tail. But no matter the differences, all these foxes share the same characteristics pointed out above. So we should categorize them all in the same group. In Linnean nomenclature, their genus name is Vulpes.


(red fox)

Pale fox

Cape fox

 

[mark kennedy]

There are also prions that turn genes on and off and a number of regulatory genes that also facilitate adaptation.


i have never seen this claim for prions before.


but no evidence that the prion is ever a regulatory protein.

What I said was that prions turn genes on and off:

"Prions that switch genes on and off in one cell, say, could be passed onto another, Lindquist suggests - a form of inheritance that bypasses DNA. "I think it's an aspect of protein biology that has probably existed since the beginning of time," she says."

http://www.bioedonline.org/news/news.cfm?art=702

I also said that there are regulatory genes that facilitate adaptation.

"Regulatory loci, which may encode both transacting proteins as well as cis acting promoter regions, are crucial components of an organism’s genetic architecture. Although evolution of these regulatory loci is believed to underlie the evolution of numerous adaptive traits, there is little information on natural variation of these genes. Recent molecular population genetic studies, however, have provided insights into the extent of natural variation at regulatory genes, the evolutionary forces that shape them and the phenotypic effects of molecular regulatory variants. These recent analyses suggest that it may be possible to study the molecular evolutionary ecology of regulatory diversification by examining both the extent and patterning of regulatory gene diversity, the phenotypic effects of molecular variation at these loci and their ecological consequences."

http://www4.ncsu.edu/~michaelp/publ....pdf#search="regulatory genes and adaptation"

does anyone know where this claim comes from?
or is it just a simple error?

It comes from confusion on your part, I never said that prions were used as a regulatory protein.

 

[mark kennedy]

By the way, you guys let me know when you get to the classification of primates. I will want to participate in the one.

 

[Edial]

By the way, you guys let me know when you get to the classification of primates. I will want to participate in the one.

I would also be interested to see what is what.

I just do not grasp why there MUST be one tree and not MANY, say a tree of foxes, tree of cats ...

The only explanation I hear so far is that it is theoretically impossible to have many trees in a context of evolution.
The odds of this hapenning do not allow for that.

But in my personal view it is also theoretically impossible for all to come out of one tree in a context of evolution.

Bible does make more sense concerning the creation.

It is an "unbelievable" book, true.
But it claims to be true, and it makes more sense than a single tree evolution.

But, we'll see what this leads to.
How single tree makes sense and why it makes sense outside of having many trees.

Ed

 

[Edial]

Ok.

 

[Mincus]

But in my personal view it is also theoretically impossible for all to come out of one tree in a context of evolution.

Bible does make more sense concerning the creation.

It is an "unbelievable" book, true.
But it claims to be true, and it makes more sense than a single tree evolution.

But, we'll see what this leads to.
How single tree makes sense and why it makes sense outside of having many trees.

Ed

I guess this is a personal view... I can't grasp the mentality that allows people to believe the bible to this extent. But, that's a topic for another thread, don't want to derail this one, it's an interesting topic.

 

[JohnR7]

I just do not grasp why there MUST be one tree and not MANY, say a tree of foxes, tree of cats ...

They can not get the concept of a tree to work anymore. For one thing there is to much data and it is to difficult to get it to fit. They use the software designed to set up various networks. That seems to be working a lot better for them.

 

[Chronohistorian]

There are many misconceptions about the twin nested hierarchy, what it shows and how it is arrived at. This thread is an attempt to clear some of these up. The main point of this thread will be to show that we can draw up such a tree without using evolution as reason for it. Rather, evolution is a conclusion from the tree instead of vice versa. I've created this thread because of the comments made by Edial in this thread, so I do hope he will participate himself.

So what is the tree of life? Basically, it is a way of grouping things. We want to divide creatures into groups to meaningfully categorize them. So the first thing to do is to see what is a meaningful way of grouping organisms, when we are talking about biology.

Now, the way we categorize organisms is essentially thought up by the creationist Linnaeus (1707-1778. Before Linneaus, there were many different ways of classification, giving rise to many different names, some more then 10 words long. Linnaeus got the idea of grouping organisms in larger groups, based on characteristics intrinsic to the organism itself. The groups are drawn up according to the similarities. This results in a hierarchy, where only two words were necessary to name an organism. This largely simplified name-giving. His system was refined by many others, for example John Ray and Richard Owen, but the basic idea stayed the same.

So the first question to ask is what we should use as characteristics to group animals meaningfully. Many characteristics can, and have been used in the past. For example, animals were grouped according to whether they could fly, swim or walk, or based on whether they can be eaten or not. But these characteristics do not tell us much. Both chickens, austriches and hawks are grouped in the same group, and all would agree. But autriches cannot fly and hawks aren't used as food. So we need something better, more specific.

Using a combination of all morphological and genetic traits of an organism to group organisms gives the most meaningful results, it is the most justified. This has two main reasons:
1. They are intrinsic to the organism; whether an organism can be used by us, for example, tells us more about us and what we can use (or can think of to use) than it tells us about the organism itself. Using the morphology and genetics of an organism, gives us meaninful groupings when talking about them in a biological context.

2. It is detailed; Referring to whether an organism can fly or not, tells us something about the organism, but not much. Looking at the wings is preferable, because it is more precise, more detailed.

So we have determined which characteristics to use. After comments have been given regarding this first post, I will move on to how we group things using these characteristics.

Wasn't the Tree Of Life the one God protected with an angel with a burning sword?

Anybody know why the Tree Of Knowledge wasn't also guarded as well??? Of course there'd be no wheel or cars or microwave ovens or internet if that had happened but at least we could all still be walking in the Garden with Our Lord and some docile T-Rex's.

 

[Tomk80]

I would also be interested to see what is what.

I just do not grasp why there MUST be one tree and not MANY, say a tree of foxes, tree of cats ...

We'll get to that. First, do you agree with the above. Do you agree that putting all foxes in one group together makes sense, since they all share the same characteristics?

And I would like you to really think about it. I would like you to think about whether it makes more sense to place them all together in one group or do not do that. I also want you to keep anything like evolution or such things out of it. Just think on whether, if we want to group animals together, for whatever reason, it makes more sense to put them together than not too. Would you put them together with cats, for example? Why or why not? Or would you put all in a different category (pale fox, cape fox, red fox) instead of in a single group ('foxes'). Why or why not?

The only explanation I hear so far is that it is theoretically impossible to have many trees in a context of evolution.

I'm wondering why? The only one who I have seen make that suggestion, at least on this forum, is you. But I may be mistaken in that of course.

The odds of this hapenning do not allow for that.

I mean this very sincerely. If you don't know how to handle probabilities, please don't make statements abou them.

But in my personal view it is also theoretically impossible for all to come out of one tree in a context of evolution.

Bible does make more sense concerning the creation.

It is an "unbelievable" book, true.
But it claims to be true, and it makes more sense than a single tree evolution.

But, we'll see what this leads to.
How single tree makes sense and why it makes sense outside of having many trees.

Ed

Okay, that is all I ask. Please look at it from the sense of categorizing animals, not one which theory you connect to that.

I must stress here again, that the single tree of life is a product of creationism, not evolution. The interpretation of what this tree means may differ, but not the basic idea behind constructing it.

 

[Edial]

We'll get to that. First, do you agree with the above. Do you agree that putting all foxes in one group together makes sense, since they all share the same characteristics?

And I would like you to really think about it. I would like you to think about whether it makes more sense to place them all together in one group or do not do that. I also want you to keep anything like evolution or such things out of it. Just think on whether, if we want to group animals together, for whatever reason, it makes more sense to put them together than not too. Would you put them together with cats, for example? Why or why not? Or would you put all in a different category (pale fox, cape fox, red fox) instead of in a single group ('foxes'). Why or why not?



I'm wondering why? The only one who I have seen make that suggestion, at least on this forum, is you. But I may be mistaken in that of course.


I mean this very sincerely. If you don't know how to handle probabilities, please don't make statements abou them.


Okay, that is all I ask. Please look at it from the sense of categorizing animals, not one which theory you connect to that.

I must stress here again, that the single tree of life is a product of creationism, not evolution. The interpretation of what this tree means may differ, but not the basic idea behind constructing it.

OK. Go on.

Responses to other points -

1. I heard at these forums from a non-theist that for many trees to "come up" the odds of this happening are practically impossible.

2. I understand what the concept of probabilities is from basic perspective. Is there more to it than that in order to see the impossibility of a single tree coming out from a single element?
The probability of a single tree (via non-intelligent design) would certainly be a curious thing to see once you present it.

3. OK. Let's group them as foxes and cats. I do not know much about foxes, and since you specifically picked that animal certainly suggests that there might be some things that I do not know about them ... but from a perspective of grouping - OK.

Thanks,
Ed

 

[Tomk80]

OK. Go on.

Responses to other points -

1. I heard at these forums from a non-theist that for many trees to "come up" the odds of this happening are practically impossible.

Hmmm, I would need to look at the quote for that to see specifically what he meant. There are some probability properties that come up with constructing trees, but I think it is best to put that off. I'll keep this in mind though, so I can touch on it at the end.

2. I understand what the concept of probabilities is from basic perspective. Is there more to it than that in order to see the impossibility of a single tree coming out from a single element?
The probability of a single tree (via non-intelligent design) would certainly be a curious thing to see once you present it.

Well, there is a lot more to it then just 'probabilities'. Unfortunately, 'odds', 'statistics' and 'probabilities' are used in these discussions way to often without any of the people (from both sides of the debate) having a good enough grip on the subject. I'll note this down too for later in the thread.

3. OK. Let's group them as foxes and cats. I do not know much about foxes, and since you specifically picked that animal certainly suggests that there might be some things that I do not know about them ... but from a perspective of grouping - OK.

Thanks,
Ed

Okay, then I'll try to continue soon with the posts. Note first that I'm not an expert on this either. I don't know much more on foxes then what I presented here, so if you have anything that would contest what I assert in my posts, please point it out with some sources, I'll definitely read them and comment on them.

Unfortunately, I'm quite busy this week with finishing up a lot of work before I go on a week's holiday on Monday (yay France, here I come!). I'll try to do one more post before I leave, but this might not be possible due to time constraints.

 

[Edial]

Have a good vacation.