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Author Topic:   Is everything made of the same material?
taylor_31
Member (Idle past 4088 days)
Posts: 86
From: Oklahoma!
Joined: 05-14-2007


Message 1 of 45 (401047)
05-18-2007 1:36 AM


Hello everybody, this is my first post! I’m a little nervous! :)

I have a question about evolution and how it occurs. Having had very little biological education in the past – my biology class consisted of reading a textbook, filling out a worksheet, and then discussing football and movies – I hope I can educate myself at this site. I’ll try to take the position as a student.

Let’s start at the beginning of life, with an organism called “X”. Theoretically, you can take the genetic material of X and mutate it, eventually forming a redwood tree, or a dog. This would take billions of years, and it would involve artificial selection instead of natural selection. It would also be improbable due to human constraints, but it's possible.

My question may sound stupid, but here it is: If you start out with X, and you end with a redwood tree, where did all that material come from? How can you go from X to bark and leaves and branches, etc.? Surely trees and bacteria aren’t made of the same material?

I think I have an explanation: Even the bark and the leaves are “planned” by DNA strands, and these strands can order the organism to gather materials. So DNA may be like the boss telling his employees to gather the buns and meat and fry a hamburger. He doesn’t contain the materials, but he gives orders to gather them. Is this on the right track?

Thanks for any help!!


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Message 2 of 45 (401050)
05-18-2007 1:45 AM


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Modulous
Member (Idle past 269 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 3 of 45 (401054)
05-18-2007 2:18 AM
Reply to: Message 1 by taylor_31
05-18-2007 1:36 AM


Even the bark and the leaves are “planned” by DNA strands, and these strands can order the organism to gather materials. So DNA may be like the boss telling his employees to gather the buns and meat and fry a hamburger. He doesn’t contain the materials, but he gives orders to gather them. Is this on the right track?

Essentially yes. Also, remember that life is built out of proteins, which are basically made in the same way (by chaining approximately 20 amino acids together in various different ways). The DNA contains the recipe for which amino acids are combined together and thus which proteins are made, when and how much.


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Doddy
Member (Idle past 4074 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 4 of 45 (401058)
05-18-2007 3:26 AM
Reply to: Message 1 by taylor_31
05-18-2007 1:36 AM


taylor_31 writes:

If you start out with X, and you end with a redwood tree, where did all that material come from?


Mostly, as you mention later in your post, from 'gathering' from the environment. This can be somewhat passive, like what trees do, or can be very active, like what we do when we hunt for a hamburger in the concrete jungle. :p
taylor_31 writes:

Surely trees and bacteria aren’t made of the same material?


Mostly, the answer is yes. We, plants and bacteria are all carbon-based lifeforms, meaning we are all made of chemical compounds comprised mostly of carbon, (with significant amounts of nitrogen, oxygen and hydrogen). All life as we know it uses DNA, RNA, fatty lipids, carbohydrates and mostly the same set of amino acids (exceptions exist of course). These nucleic acids (DNA and RNA) and the amino acids of the proteins aren't arranged in the same order, or present in the same amount, and aren't in the same spot within the cell, but mostly they are the same. These variations are, as you have pointed out, controlled by the DNA.

This is a good analogy, especially for the eukaryotes (like plants). The boss (DNA) stays in his office (the cell nucleus), and sends his managers (the RNA) to the employees (the rest of the cell) to gather the materials (from the environment). Bacterial are prokaryotes, so their DNA boss actually doesn't have an office, but walks around with the employees.


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taylor_31
Member (Idle past 4088 days)
Posts: 86
From: Oklahoma!
Joined: 05-14-2007


Message 5 of 45 (401368)
05-19-2007 12:33 PM
Reply to: Message 3 by Modulous
05-18-2007 2:18 AM


Thanks for your reply, it was very helpful!

Modulous writes:

Also, remember that life is built out of proteins, which are basically made in the same way (by chaining approximately 20 amino acids together in various different ways).

If life is made of roughly twenty proteins, then the chain holding them together should be very long, correct? So if each "link" in the chain has twenty possibilities, then the total number of possibilities grows very high. (20 x 20 x 20 x 20 etc.) This would account for the diversity in life, wouldn't it?

Modulous writes:

The DNA contains the recipe for which amino acids are combined together and thus which proteins are made

I read in The Blind Watchmaker that DNA is translated into RNA and then into amino acids. So DNA is made of nucleotides, and when they are transcribed, they "order" the amino acids in their places. These acids make up proteins, the basis of life. Is this right?

It's mind-boggling (for me) to think that proteins can have that much effect on life. Once the proteins are there, what happens? How do they directly effect the life process? If they are "instructions" of some sort, then what is reading them?

Again, thanks for any help!


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taylor_31
Member (Idle past 4088 days)
Posts: 86
From: Oklahoma!
Joined: 05-14-2007


Message 6 of 45 (401370)
05-19-2007 1:01 PM
Reply to: Message 4 by Doddy
05-18-2007 3:26 AM


Thanks for the good post, it was very helpful!

Doddy writes:

Mostly, as you mention later in your post, from 'gathering' from the environment.

That makes sense. I didn't think that mutation could generate that much "new" material on its own.

So gathering material must have been beneficial to the DNA in some way. Could this have been from food consumption? Or possibly protection?

Doddy writes:

We, plants and bacteria are all carbon-based lifeforms, meaning we are all made of chemical compounds comprised mostly of carbon, (with significant amounts of nitrogen, oxygen and hydrogen).

So even the nucleotides of DNA are formed of carbon, nitrogen, and oxygen, and hydrogen, right? A broader question is, is everything in the known universe made of elements from the periodic table?

Sorry if I seem twisted in knots. Biology has always had that effect on me. :)


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crashfrog
Inactive Member


Message 7 of 45 (401371)
05-19-2007 1:09 PM
Reply to: Message 5 by taylor_31
05-19-2007 12:33 PM


If life is made of roughly twenty proteins, then the chain holding them together should be very long, correct?

Er, that's not quite it. There are 20 different amino acids, and proteins are made out of these aminos chained together.

It's like having a box with 20 different kinds of Legos in it, and you can make whatever you want by hooking the Legos together, and you basically have as many of each kind of Lego that you need.

And when you put a certain number of Legos together in a specific order, that's a specific protein with a specific function in the body. DNA is basically a set of instructions a cell uses to put the Legos together to get the proteins that it needs.

So if each "link" in the chain has twenty possibilities, then the total number of possibilities grows very high. (20 x 20 x 20 x 20 etc.)

Yes, that's true. Theoretically there's a very large number of possible polypeptides (which is a way of describing what proteins are, referring to the chemical bonds between each amino acid, called "peptide bonds.") In reality, living things employ only a very small number of all the possible proteins, because the majority of "random" proteins have no chemical function at all.

It's mind-boggling (for me) to think that proteins can have that much effect on life.

They are life, basically. Or rather - life is your body doing chemistry in response to environment, and proteins are how that chemistry is done.

Once the proteins are there, what happens? How do they directly effect the life process?

Once a chain of amino acids is formed, it "folds up" based on electrical charges. That folding creates a specific shape, and it's the shape of the protein that determines its chemical properties. Some proteins become structural elements - building blocks, if you will, out of which your body is constructed - but many others form enzymes, which are catalysts (chemicals that cause other chemicals to react with each other without consuming or changing the catalyst in the process). Enzymes govern the chemical reactions your body is doing to stay alive. For instance, when your body breaks down food into usable materials and energy, enzymes are at work doing that.


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Coragyps
Member
Posts: 5391
From: Snyder, Texas, USA
Joined: 11-12-2002
Member Rating: 3.9


Message 8 of 45 (401372)
05-19-2007 1:15 PM
Reply to: Message 6 by taylor_31
05-19-2007 1:01 PM


So even the nucleotides of DNA are formed of carbon, nitrogen, and oxygen, and hydrogen, right?

And phosphorus, too.

A broader question is, is everything in the known universe made of elements from the periodic table?

Everything we can actually see may well be. The insides of neutron stars and white dwarfs were once periodic table residents but have been squashed to something else - but we don't see it directly.
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crashfrog
Inactive Member


Message 9 of 45 (401373)
05-19-2007 1:23 PM
Reply to: Message 6 by taylor_31
05-19-2007 1:01 PM


So even the nucleotides of DNA are formed of carbon, nitrogen, and oxygen, and hydrogen, right?

Plus phosphorus, but basically, yeah. Those four elements you named constitute the majority of a living thing, they're the heavy lifters if you will, but most of the other elements have uses in living things. For instance, iron is important to your blood (and why it's red), calcium is important to your bones, sodium and chloride are important for nerves, etc.

A broader question is, is everything in the known universe made of elements from the periodic table?

Without getting into astrophysics - nobody knows what "dark matter" is made of, but aside from that, everything we know about is made of atoms (unless we're talking about what atoms are made of) and every different "kind" of atom is an element on the Periodic table. When we discover a new kind of atom, the lucky SOB who discovered it gets to name it, and we add it to the table.

All atoms are made of the same three kinds of particles - protons, neutrons, and electrons, and then protons and neutrons are made up of even more elementary particles, and we think that's as far down as it goes. It's kind of a mess.


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taylor_31
Member (Idle past 4088 days)
Posts: 86
From: Oklahoma!
Joined: 05-14-2007


Message 10 of 45 (401449)
05-20-2007 1:42 AM
Reply to: Message 7 by crashfrog
05-19-2007 1:09 PM


Thank you for the helpful post, it was very interesting.

crashfrog writes:

It's like having a box with 20 different kinds of Legos in it, and you can make whatever you want by hooking the Legos together, and you basically have as many of each kind of Lego that you need.

Okay, so each protein is made of twenty different kinds of amino acids. The exact number making up the protein, however, doesn't have to be exactly twenty. There could be scores of amino acids, but each one is one of the twenty kinds, correct?

crashfrog writes:

In reality, living things employ only a very small number of all the possible proteins, because the majority of "random" proteins have no chemical function at all.

So should we find useless proteins in our bodies? Or is DNA so precise that there are none? I suppose that natural selection may have ruled out the DNA that gave instructions for useless proteins.

To draw back to my point in the OP, you could manipulate the DNA instructions to build a multitude of proteins. These proteins are the building blocks of all life, whether for bacteria or a redwood tree. The difference between the two is that the proteins for each species do different functions, correct? So the proteins for the redwood tree perform different functions from the bacteria proteins. Furthermore, every transitional from the bacteria to the redwood is a result of random mutation in the DNA instructions and natural selection, and each transitional is a fully functional species. Is this correct?

Also, theoretically, if we had the transitional "steps" from the two species, could we see a slight, successive change in the DNA instructions?


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Nuggin
Member (Idle past 658 days)
Posts: 2965
From: Los Angeles, CA USA
Joined: 08-09-2005


Message 11 of 45 (401453)
05-20-2007 1:58 AM
Reply to: Message 10 by taylor_31
05-20-2007 1:42 AM


Junk in the trunk
So should we find useless proteins in our bodies? Or is DNA so precise that there are none? I suppose that natural selection may have ruled out the DNA that gave instructions for useless proteins.

There's lots of useless stuff clunking around in our bodies. From bunches of "junk dna" which codes for nothing (that we know of), to redundant coding where more than one gene does the exact same thing.

And at a macro level - look at the appendix, the ticking timebomb of useless left over body parts. It's like it's there just to need to be removed.

As for natural selection ruling out the DNA which codes for useless proteins - natural selection is very good at selecting for something beneficial or against something harmful, but it's not very good at weeding out something which is neutral.

If you have a bit of junk DNA which has no real effect on your ability to reproduce (either for or against), chances are natural selection is gonna let that one slip on by.


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Doddy
Member (Idle past 4074 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 12 of 45 (401460)
05-20-2007 2:31 AM
Reply to: Message 10 by taylor_31
05-20-2007 1:42 AM


taylor_31 writes:

Okay, so each protein is made of twenty different kinds of amino acids. The exact number making up the protein, however, doesn't have to be exactly twenty. There could be scores of amino acids, but each one is one of the twenty kinds, correct?


Pretty much.

I may also note here, that the number is actually quite a bit higher than 20, due to what is called "post-translational modifications". Basically, using the Lego analogy, this is like breaking the Lego blocks to fit them into the construction properly. In much the same way, the amino acid called Proline can get a hydroxy (oxygen plus a hydrogen) group attached to form Hydroxyproline to fit them better into the common protein (that you may have heard of) called 'collagen ' (it's also found in elastin).

Sorry for confusing you additionally, but just have to point out that there are many exceptions to 'rules' in biology.

taylor_31 writes:

So should we find useless proteins in our bodies? Or is DNA so precise that there are none? I suppose that natural selection may have ruled out the DNA that gave instructions for useless proteins.

Oh, there are certainly useless proteins. For example, as crashfrog said, the proteins have to fold into the right conformation, but over time (or with stress, like high temperatures), they unfold and break. Mutations can also create useless (misfolded) proteins. Organisms of course have evolved to live with this, so they have structures (also proteins) we call 'chaperones' to refold the proteins, and 'proteasomes' to break up those damaged beyond repair, so they can be recycled.

taylor_31 writes:

To draw back to my point in the OP, you could manipulate the DNA instructions to build a multitude of proteins. These proteins are the building blocks of all life, whether for bacteria or a redwood tree. The difference between the two is that the proteins for each species do different functions, correct? So the proteins for the redwood tree perform different functions from the bacteria proteins.

Very much so. Of course, there are things that both bacteria and plants need to do, like gain energy, replicate their DNA and divide their cells, so the proteins that do these jobs are very similar in both organisms.

taylor_31 writes:

Furthermore, every transitional from the bacteria to the redwood is a result of random mutation in the DNA instructions and natural selection, and each transitional is a fully functional species. Is this correct?

Yes, although mutations aren't always the only thing that can lead to evolution, but we'll save that for another topic.

taylor_31 writes:

Also, theoretically, if we had the transitional "steps" from the two species, could we see a slight, successive change in the DNA instructions?

Certainly. In fact, much of evolutionary biology has moved away from looking at skeletons and organs, and towards looking at the DNA of species in order to determine the relationship between living species. The fact that both methods gave much the same results is a good evidence for evolution, in my opinion.

Edited by Doddy, : formatting of quote boxes

Edited by Doddy, : slight spelling error


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crashfrog
Inactive Member


Message 13 of 45 (401511)
05-20-2007 12:59 PM
Reply to: Message 10 by taylor_31
05-20-2007 1:42 AM


I just wanted to pop in with an example of what you were talking about.

Okay, so each protein is made of twenty different kinds of amino acids. The exact number making up the protein, however, doesn't have to be exactly twenty.

Yes, exactly. For instance, the protein hemoglobin, which you may recognize as the protein responsible for the oxygen-carrying capacity (and red color) of blood, is comprised of four protein subgroups, each containing about 145 amino acids.

Furthermore, every transitional from the bacteria to the redwood is a result of random mutation in the DNA instructions and natural selection, and each transitional is a fully functional species. Is this correct?

Basically. There was one big change, about a billion years ago, that led to a big difference between the cells of bacteria and the cells of plants and animals. While plant and animal cells have membrane-bound organelles, like the nucleus of the cell where DNA is located:

bacterial cells don't. Their DNA and cellular processes just happen "out in the open" within the cell:

The reason for the development of membrane-bound, "organized" cells (which we call "eukaryotic") from cells that had no internal membrane-bound organelles (which we call "prokaryotic") was something called "endosymbiosis."

What happened was, in the distant past, an organism like a bacteria literally absorbed a smaller, different organism into its cell, but instead of digesting it, they because dependent on each other. We believe this happened twice - first, an organism was absorbed that became known as mitochondria, which act as little "batteries" inside cells, using and storing power; then, one of the descendants of these composite-organisms absorbed a second endosymbiote that was able to generate power from sunlight. These were the ancestors of chloroplasts, and the cells that had absorbed chloroplasts became the ancestors of green plants.

We know this happened because, while plant and animal cells keep their DNA - the DNA that describes your body, the color of your hair and eyes, etc - in the cell nucleus, mitochondria (which both plants and animals have) and chloroplasts (which animals don't have) have their own DNA. Other cell organelles don't. This tells us that mitochondria and chloroplasts were once free-roaming individual organisms in their own right before they found a new home within our cells.

Sorry that was so complicated, and it's really beyond the scope of your question, but I wanted to show you that, while random mutation and natural selection are the primary forces of evolutionary change, sometimes big changes happen that aren't specifically about mutation and selection. If you don't feel like you "got it", don't worry too much about it.


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taylor_31
Member (Idle past 4088 days)
Posts: 86
From: Oklahoma!
Joined: 05-14-2007


Message 14 of 45 (401534)
05-20-2007 2:37 PM
Reply to: Message 11 by Nuggin
05-20-2007 1:58 AM


Re: Junk in the trunk
Nuggin writes:

If you have a bit of junk DNA which has no real effect on your ability to reproduce (either for or against), chances are natural selection is gonna let that one slip on by.

Okay, that makes sense. But you said only "a bit" of junk DNA. Would large pieces of junk DNA be selected against? I would think so because competing DNA strands might be more efficient by having less "junk".

Thanks for your help!


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taylor_31
Member (Idle past 4088 days)
Posts: 86
From: Oklahoma!
Joined: 05-14-2007


Message 15 of 45 (401539)
05-20-2007 2:48 PM
Reply to: Message 12 by Doddy
05-20-2007 2:31 AM


Thanks for the great post, it was very educational!

Doddy writes:

Organisms of course have evolved to live with this, so they have structures (also proteins) we call 'chaperones' to refold the proteins, and 'proteasomes' to break up those damaged beyond repair, so they can be recycled.

That's really amazing. It seems that the microbiological world is similar to the world we live in (plants, animals, etc.) but on a much smaller level. Natural selection must be equally potent in that world if it's so complex.

Did this "micro" complexity arise like our ecosystem did, which was through random mutation (with exceptions, like you and crashfrog pointed out) and natural selection? (This might be a poorly worded question because that "micro" world is part of our ecosystem, but I'm talking about the "big" world. It seems that the "micro" world has its own ecosystem, with predators and the like.)


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