Evolution question - how does complexity arise?

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Agrajag619
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Evolution question - how does complexity arise?

Postby Agrajag619 » Thu May 02, 2013 6:52 pm UTC

I currently consider myself a creationist, but I am open to the idea of evolution and am interested in learning more about it. One question I have is how complexity arises in evolution.

A human being is much more complex than a single-celled organism. However, the primary mechanism for evolution is mutation, and I don't see how mutation can make an organism more complex. So, how could a single-celled organism evolve into a human through mutation?

Defining complexity is tricky, but I propose Francis Heylighen's definition: "Intuitively then, a system would be more complex if more parts could be distinguished, and if more connections between them existed." (http://pespmc1.vub.ac.be/papers/ComplexityGrowth.html). Does anyone else have a better definition?

Mutation can add new parts, such as through gene duplication. I don't, however, see how it can produce new connections between them.

Of course some mutations are beneficial; this is not, however, the same as adding complexity, and complexity must increase for evolution to be true.

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Re: Evolution question - how does complexity arise?

Postby screen317 » Thu May 02, 2013 7:16 pm UTC

Agrajag619 wrote:A human being is much more complex than a single-celled organism. However, the primary mechanism for evolution is mutation, and I don't see how mutation can make an organism more complex. So, how could a single-celled organism evolve into a human through mutation?
Before talking about complexity between microbes and humans, I suggest thinking instead about how complexity arises within microbial communities.

Mutation can add new parts, such as through gene duplication. I don't, however, see how it can produce new connections between them.
As DNA mutates, the structure of the coded proteins (or noncoding RNAs) therein can change, affecting protein-protein interactions which can result in previously nonexisting "connections" between them (metabolic pathways, etc.)..

Of course some mutations are beneficial; this is not, however, the same as adding complexity, and complexity must increase for evolution to be true.
This is definitely not necessarily true. Plenty of "simpler" organisms continue to exist and thrive; their simplicity has provided an advantage that allowed them to reproduce and survive.

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Re: Evolution question - how does complexity arise?

Postby Agrajag619 » Thu May 02, 2013 8:01 pm UTC

As DNA mutates, the structure of the coded proteins (or noncoding RNAs) therein can change, affecting protein-protein interactions which can result in previously nonexisting "connections" between them (metabolic pathways, etc.)..


My knowledge of biochemistry is quite superficial, but as far as I can tell new metabolic pathways arise through substrate ambiguity, not mutation. Could you please explain more?

Source: http://books.google.com/books?id=K-Pj-6X3n1kC&pg=PA347&dq=substrate+ambiguity&hl=en&sa=X&ei=z8KCUZ-xI6nf0gH8o4GwDw&ved=0CDEQ6AEwAA#v=onepage&q=substrate%20ambiguity&f=false

My understanding of mutation is that it leads to a loss of function, though this may have adaptive value. An example is sickle-cell disease, where mutation causes loss of function in the hemoglobin gene, but confers malaria resistance. What am I missing?

This is definitely not necessarily true. Plenty of "simpler" organisms continue to exist and thrive; their simplicity has provided an advantage that allowed them to reproduce and survive.


Indeed, but evolution posits that at one point there were only simple organisms and now there are also complex organisms. How did the complex organisms arise except by descent from simple organisms, with an increase in complexity?

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Re: Evolution question - how does complexity arise?

Postby ahammel » Thu May 02, 2013 8:08 pm UTC

Agrajag619 wrote:My understanding of mutation is that it leads to a loss of function, though this may have adaptive value.
That is incorrect.
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Re: Evolution question - how does complexity arise?

Postby LaserGuy » Thu May 02, 2013 8:12 pm UTC

Well, complexity can arise quite naturally from simple systems all the time. Patterns with simple rules iterated indefinitely can create extremely complex structures. See, for example fractals or Conway's game of life. In these sorts of systems, the effects of a point mutation can in fact be very dramatic--the mutated structure may end up being completely different from the structure absent the mutation.

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Re: Evolution question - how does complexity arise?

Postby scarecrovv » Thu May 02, 2013 8:18 pm UTC

I've reordered the chunks of your post a bit, to aid the flow of my response. I trust you won't mind.

Agrajag619 wrote:Defining complexity is tricky, but I propose Francis Heylighen's definition: "Intuitively then, a system would be more complex if more parts could be distinguished, and if more connections between them existed." (http://pespmc1.vub.ac.be/papers/ComplexityGrowth.html). Does anyone else have a better definition?

Agrajag619 wrote:Mutation can add new parts, such as through gene duplication. I don't, however, see how it can produce new connections between them.


That seems like a reasonable stab at a definition. However, the dichotomy between parts and connections seems a little arbitrary. As an example, the brain might be one part, and an arm muscle another. A nerve going from one to the other could be considered a connection, or it could be considered a part in it's own right. If you considered the nerve a seperate part, then the synapses could be considered connections from the nerve to it's end points, or they could be considered parts. You could carry this on as long as you like.

While it has some disadvantages, I like to consider the well defined concept of information (as formalized by Claude Shannon) as a proxy for the poorly defined concept of "complexity". I'm a computer scientist though, not a biologist, so take my opinion on this matter with a grain of salt. I don't think I have a terribly good grasp on what "complexity" is, but I'll try to help you with the rest of your concerns as best I can.

Agrajag619 wrote:A human being is much more complex than a single-celled organism. However, the primary mechanism for evolution is mutation, and I don't see how mutation can make an organism more complex. So, how could a single-celled organism evolve into a human through mutation?


Mutation is not the only mechanism. There's also crossover in species that reproduce sexually. In species that reproduce asexually, including many bacteria, there are also mechanisms for genetic material to move between organisms. This is called "horizontal gene transfer", and can happen when bacteria exchange chunks of material with eachother. I think I've heard that viruses can sometimes screw up and transfer genetic material from place to place too. Transposons are another mechanism that can shuffle DNA around (even in complex multicellular organisms). While many of these effects may be lumped into the umbrella term "mutation", it's far from the simplistic image I once had (and suspect you may have) of mutation being just random bits of radiation changing a base pair here and there.

Agrajag619 wrote:Of course some mutations are beneficial; this is not, however, the same as adding complexity, and complexity must increase for evolution to be true.


As I've described above, there are mechanisms that can shuffle and duplicate sequences of DNA. For exmaple, copying a chunk of DNA from one place to another might not break the function of the original piece, and might induce a new behavior. If a plant had a gene for a pesticide that was turned on in one circumstance (detecting a competing plant nearby), and that gene got copied to a DNA location that was turned on in a different circumstance (insects are eating the leaves) then that is unarguably an increase in complexity, and would be beneficial to the plant if the pesticide was harmful to insects.

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Re: Evolution question - how does complexity arise?

Postby screen317 » Thu May 02, 2013 8:41 pm UTC

Agrajag619 wrote:
As DNA mutates, the structure of the coded proteins (or noncoding RNAs) therein can change, affecting protein-protein interactions which can result in previously nonexisting "connections" between them (metabolic pathways, etc.)..


My knowledge of biochemistry is quite superficial, but as far as I can tell new metabolic pathways arise through substrate ambiguity, not mutation. Could you please explain more?

Source: http://books.google.com/books?id=K-Pj-6X3n1kC&pg=PA347&dq=substrate+ambiguity&hl=en&sa=X&ei=z8KCUZ-xI6nf0gH8o4GwDw&ved=0CDEQ6AEwAA#v=onepage&q=substrate%20ambiguity&f=false
I think part of the issue here is that you're taking potential sources of changes as the only source of changes.

Sure, the ideas behind substrate ambiguity are valid, but mutations in the enzymes that bind to substrates lead to diversity in the binding specificity of enzymes to substrates. This plus gene duplication events, transposition events, etc. all lead (but aren't the only things that do!) to complexity.

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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Thu May 02, 2013 9:11 pm UTC

Your question 'how does complexity arise' is superficially easily answered; via mutations. Mutations change existing proteins, which change living systems. This can lead to more complexity through a variety of methods, which simplified may be summed as 'by changing a part of the way things currently work'.

For a more detailed answer, I humbly suggest you may need more education, particularly around taxonomy, biochemistry, and molecular biology. By all means though, continue asking questions, but please be aware that answers will often go beyond a laymans understanding. For example, your point that mutation leads to a loss of function is only part of the fact; mutation CAN lead to a loss of function, but it can also lead to a gain of function. It can also lead to a CHANGE of function; making a, say, slightly different binding interaction.

Also, out of curiosity, as a Creationist, are you asking this because you want to learn more, or are you asking this because you want an argument?
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Re: Evolution question - how does complexity arise?

Postby Agrajag619 » Thu May 02, 2013 10:00 pm UTC

Thank you all for your responses!

Izawwlgood: My purpose in making this thread is to figure out if my ideas are true or not by testing them in a hostile environment. If I see an objection that I can't answer, I'll know I'm wrong; if not, I'll continue to assume I'm right. So, I am asking because I want to learn more, and also because I want an argument. I appreciate everyone's willingness to humor me so far, and I apologize if I was misleading in my opening post.

To your other point, most random change does not lead to complexity, but rather to disorder, so I am trying to determine how in this case it could lead to complexity.

ahammel: In the example of sickle-cell disease, there is a gain of function on the one hand (malaria resistance) but a loss of function on the other hand (hemoglobin functionality), so there is a net decrease in functional complexity. Are there other mutations which provide a net increase?

LaserGuy: Wow, that is interesting! I wonder, though, how good the analogy is - other simple systems do not tend towards complexity, so how can we determine which category biological systems fall into?

scarecrovv: I think your concern about complexity is valid, and information may very well be a good alternative.

I like your examples of alternate mechanisms, I'll try to investigate those more. I'm not sure how they can increase complexity/information though - I understand that sexual reproduction can produce variation, but does the offspring really have more genetic information than its parents? Intuitively, it seems like the genetic code should degrade through successive generations, as errors accumulate. I suppose the same considerations could apply to asexual organisms.

As for the other processes you mentioned, I'll have to study them more, but it's not immediately clear to me that shuffling DNA around makes the system more complex. In your plant example, it seems likely copying the DNA would break the function of the original piece. The wikipedia article on transposons says that they damage their host genomes and that multiple copies of the same sequence can "hinder precise chromosomal pairing during mitosis and meiosis" - isn't that a decrease in complexity?

screen317: If an enzyme is coded to bind to a specific substrate, and it then loses its specificity and begins binding with a greater variety of substrates, it seems that it is now less complex than it was before - its ability to distinguish between substrates has been lost.

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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Thu May 02, 2013 10:12 pm UTC

Agrajag619 wrote:To your other point, most random change does not lead to complexity, but rather to disorder, so I am trying to determine how in this case it could lead to complexity.
Well, lets be clear here; disorder/order/simplicity/complexity is not interchangable the way you're using it. A mutation may make a protein 'more complex' in it's function, which translates to a protein interacting with a variety of binding partners, which results in the organism being unable to survive, and die. Is that an example of 'more complexity', 'less complexity', 'order' or 'disorder'?

Agrajag619 wrote: In the example of sickle-cell disease, there is a gain of function on the one hand (malaria resistance) but a loss of function on the other hand (hemoglobin functionality), so there is a net decrease in functional complexity. Are there other mutations which provide a net increase?
Being recessive for sickle-cell imparts malaria resistance as a feature, not as the function of the mutation. This is one reason we see the disease both persisting, and so prevalent in some places; it was not entirely selected against, indeed, was in some cases, selected for. Again, you cannot apply 'complexity' here the way you seem to be.

Yeah... looking over your responses, I think you're going to run into a lot of problems with your poorly defined and understood definitions of the words 'simple' and 'complex'. It's going to be hard to tackle this discussion until we hammer down a better understanding of why you seem to be applying those words the way you are.
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Re: Evolution question - how does complexity arise?

Postby ahammel » Thu May 02, 2013 10:15 pm UTC

Agrajag619 wrote:ahammel: In the example of sickle-cell disease, there is a gain of function on the one hand (malaria resistance) but a loss of function on the other hand (hemoglobin functionality), so there is a net decrease in functional complexity.
How do you figure that? That doesn't square with your definition of complexity at all.

Are there other mutations which provide a net increase?
Yes. The GoF mutation(s) that resulted in citric acid metabolism in the E. coli long-term experimental evolution experiment is a particularly famous example.
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Re: Evolution question - how does complexity arise?

Postby Agrajag619 » Thu May 02, 2013 10:20 pm UTC

Agrajag619 wrote:Yeah... looking over your responses, I think you're going to run into a lot of problems with your poorly defined and understood definitions of the words 'simple' and 'complex'. It's going to be hard to tackle this discussion until we hammer down a better understanding of why you seem to be applying those words the way you are.


I think you're right, but I've been unable to find a clear definition - this article discusses the problem, but doesn't seem to settle on anything definite. What would you say is a good definition? Perhaps information is a better concept, as scarecrovv suggests.

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Re: Evolution question - how does complexity arise?

Postby douglasm » Thu May 02, 2013 11:22 pm UTC

Consider a scientist. This scientist has a rock solid clear and unambiguous definition of 'complexity'. This scientist also has tools for manipulating DNA in the seeds of a plant. He can copy genes, move genes, insert or remove small (really small) fragments of DNA, and so on. He wants to increase the complexity of the plant's offspring. Assume he has perfect knowledge of how the plant works and what consequences (to the plant's offspring) his changes will have.

Now, with that hypothetical scenario in mind and before you open the spoiler, would you accept that the scientist is capable of increasing the plant's complexity?

Spoiler:
Anything that scientist can do, mutation can do too. Mutation just won't be reliable about it. Sooner or later, a random mutation will coincidentally happen to match one of the things the scientist might do, resulting in increased complexity.

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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Thu May 02, 2013 11:35 pm UTC

I admit I didn't read the entire paper, but I'll tell you what I did do;
When entering these conversations, I'm usually very skeptical of the sources people provide. I've never heard of this guy, so after perusing the abstract, I googled him. Lo! He's a professor at Duke, and has a couple books that are for sale on Amazon.

You may find the book most associated with his name to be somewhat interesting.

But my impressions from reading the abstract; he makes the same point we did. 'Complexity' is a difficult thing to define. He even points out that it's a bit culturally influenced. You may find a beetle to be a really simple organism, but hoooooo boy, have you SEEN those mouthparts?

Agrajag619 wrote:What would you say is a good definition? Perhaps information is a better concept, as scarecrovv suggests.
Yeah, I think scarecrovv's suggestion is a reasonable first pass at it truthfully. I guess one way to think of it is to imagine the internet; the amount of complexity that increased over time is based on the increasing needs of the present, and is influenced by the past. But really, I don't think complexity is a good descriptor of what's happening to life over time.

Over time, life is just perpetually attempting to adapt to the environment it finds itself in. This is rendered more... complicated? by the fact that a lot of life has already been, so the adapting species finds itself drawing on a kind of genetic history that naturally includes 'more moving parts' to change for adaptation.

Your question is how does NEW stuff arise; via mutations. Mutations will make protein x do 'something different', which will result in 'new stuff'. If you're having trouble imaging how an organism goes from worm to ape, you need to learn more about evolutionary biology/taxonomy.
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Re: Evolution question - how does complexity arise?

Postby gmalivuk » Thu May 02, 2013 11:52 pm UTC

Agrajag619 wrote:To your other point, most random change does not lead to complexity, but rather to disorder, so I am trying to determine how in this case it could lead to complexity.
As Izawwlgood already mentioned, whatever might be meant by simplicity/complexity, it is quite simply not the same dimension as order/disorder. You could add both complexity and order, or you could add complexity and disorder, or you could remove complexity and add disorder, or you could reduce complexity and add order.
---
Even if we ignore complexity for the moment (which we should do until you give a precise definition the rest of us can work from when discussing this), I've bolded an extremely important word there.

Most random changes, but not all of them, increase entropy (i.e. disorder). Some of them, by chance alone, will inevitably decrease entropy (i.e. add more order), unless you started out with minimum entropy. Which is absolute zero. Which you didn't start out at.

Natural selection could work to gradually increase order over time by simply throwing out all the mutations that add too much disorder, though in practice it's much messier than this. The sheer number of reproducing organisms provide enough trials that every generation is extremely likely to include some mutations that increase order rather than decreasing it.
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And now we can throw "complexity" back into the mix, even without defining it more rigorously. If we simply assume that the level of complexity is a quantitative property all organisms have, then by chance alone some random mutations will increase it, even if the vast majority of mutations decrease it. If there is any advantage to being more complex in a particular environment, organisms which are more complex will outcompete those which are less complex, and have more offspring which tend to carry whatever complexity-giving traits their parents have. Some of these offspring in turn will almost certainly be even *more* complex, and if increased complexity continues to be advantageous, they will in turn outcompete their neighbors and continue the process.
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Re: Evolution question - how does complexity arise?

Postby Agrajag619 » Fri May 03, 2013 12:41 am UTC

ahammel wrote: The GoF mutation(s) that resulted in citric acid metabolism in the E. coli long-term experimental evolution experiment is a particularly famous example.


Thank you all again for your responses! ahammel's example here is a solid counter to my arguments - complexity seems intuitively to increase here, however it is defined. This is a serious objection to my views, and indicates that they are flawed in some way, possibly even fatally so. Everyone else, too, has brought up excellent points.

If I cannot find answers to these objections, then of course I will accept evolution. I hope you will understand, however, if I delay a little bit - I'm not ready to make such an important judgment solely on the basis of a brief internet conversation, so I am going to respectfully withdraw from this discussion in order to do further research. I'll make another post here in one year, hopefully with some conclusions. Thank you.

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Re: Evolution question - how does complexity arise?

Postby ahammel » Fri May 03, 2013 1:53 am UTC

I read that when I was an undergrad. It is somewhat interesting. They make a decent argument, but I haven't seen their math and I wouldn't be qualified to judge it.

Agrajag619 wrote:Thank you all again for your responses! ahammel's example here is a solid counter to my arguments - complexity seems intuitively to increase here, however it is defined. This is a serious objection to my views, and indicates that they are flawed in some way, possibly even fatally so. Everyone else, too, has brought up excellent points.

If I cannot find answers to these objections, then of course I will accept evolution.
Well I...didn't see that coming. Good luck!
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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Fri May 03, 2013 2:17 am UTC

Agrajag619 wrote:If I cannot find answers to these objections, then of course I will accept evolution. I hope you will understand, however, if I delay a little bit - I'm not ready to make such an important judgment solely on the basis of a brief internet conversation, so I am going to respectfully withdraw from this discussion in order to do further research. I'll make another post here in one year, hopefully with some conclusions. Thank you.
I cannot tell you how refreshing it is to hear that. Good luck in your studies, and of course, feel free to pop here with any questions along the way.
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Re: Evolution question - how does complexity arise?

Postby scarecrovv » Fri May 03, 2013 2:29 am UTC

Agrajag619 wrote:If I cannot find answers to these objections, then of course I will accept evolution. I hope you will understand, however, if I delay a little bit - I'm not ready to make such an important judgment solely on the basis of a brief internet conversation, so I am going to respectfully withdraw from this discussion in order to do further research. I'll make another post here in one year, hopefully with some conclusions. Thank you.

You are one of the most intellectually honest creationists I have ever interacted with. I congratulate you. If you continue to think in this manner you'll go far.

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Re: Evolution question - how does complexity arise?

Postby ThirdParty » Fri May 03, 2013 5:32 am UTC

I think I'm late to the party, but I'm going to go ahead and post anyway:

Agrajag619 wrote:Are there other mutations which provide a net increase?
My favorite example of complexity arising, because it's relatively easy to wrap my mind around, is the speculated origin of trichromatic vision in primates.

There are these two types of cells in the eye which we'll call "green-sensitive cones" and "red-sensitive cones". Green-sensitive cones send a signal to the brain in the presence of green light. Red-sensitive cones send a signal to the brain in the presence of red light. The signals are identical in structure--they don't say "I see green!" or "I see red!"; they just say "I see light!". One of the things a newborn baby has to do is sort out which cone sees which color, based on the theory that same-color cones are more likely to fire simultaneously than different-color cones. There's no reason in principle why a newborn couldn't sort out extra colors if they were present.

We've found the genes that code for the color-sensitive pigments in the cones. They're located on the X chromosome. First is the gene for red-sensitive pigment. Then, immediately following it, are a bunch of copies of the gene for green-sensitive pigment. The two genes are suspiciously similar. Immediately following the gene for green-sensitive pigment are some non-functional copies of the gene for green-sensitive pigment. (Think of the chromosome as reading "Yabba-yabba-dabba! Yabba-dabba! Do! Yabba-dabba! Yabba-dabba!" where "Yabba-yabba-dabba!" is the recipe for red-sensitive pigment, "yabba-dabba!" is the recipe for green-sensitive pigment, and the transcriber stops cooking after it hits the "Do!".)

The number of non-functional copies of the green-sensitive pigment gene varies but doesn't seem to matter--it's a mutation in a part of the genome that doesn't do anything. (So some people's chromosomes, instead of reading "Yabba-yabba-dabba! Yabba-dabba! Do! Yabba-dabba! Yabba-dabba!", read "Yabba-yabba-dabba! Yabba-dabba! Do! Yabba-dabba!" or "Yabba-yabba-dabba! Yabba-dabba! Do! Yabba-dabba! Yabba-dabba! Yabba-dabba!") A mutation that does matter--it's the most common form of color-blindness--causes a man to have twice as many red-sensitive cones as he should, but no green-sensitive cones. (His chromosome reads "Yabba-yabba-dabba! Yabba-yabba-dabba! Do! Yabba-dabba! Yabba-dabba!".)

Other catarrhini--old world monkeys and apes--have the same kind of color vision that humans do. However, non-catarrhini mammals can't see red. (Their X chromosomes just read "Yabba-dabba! Do! Yabba-dabba! Yabba-dabba! Yabba-dabba!".)

All of the above is stuff we know. What we don't know is how it got that way. Our guess is that in the common ancestor of the catarrhini, one of the extra genes for green-sensitive pigment accidentally landed in the functional part of the chromosome, and then one of the two functional green-sensitive pigment genes got mutated into a red-sensitive pigment gene. This would explain all the data, and we've got a fairly good idea of how the duplications and mutation would have happened--the chromosome copying and shuffling mechanisms tend to lose their place, for well-understood reasons, when sequences are too repetitive, and this section of the X chromosome qualifies as "too repetitive". At the very least it seems that it would be possible for a new-world-monkey-like animal to suffer a duplication of its green-sensitive pigment gene followed by a mutation of that gene into red-sensitive pigment, and for this to result in increased function. We can't be sure that this has happened, but if it did happen--as certainly appears to have been the case--it would be a mutation that resulted in increased function.

In contrast, creationism doesn't handle this case very well. Why would an intelligent designer give mammals a bunch of extra non-functioning copies of the green-sensitive pigment recipe? Why would an intelligent designer decide that macaques, orangutans, and humans ought to have a gene for red-sensitive pigment too, but that capuchins and bears oughtn't? Maybe there's some purpose beyond our ken, but at first glance this looks a lot more like accident than like anybody's got a plan.

Agrajag619 wrote:My understanding of mutation is that it leads to a loss of function, though this may have adaptive value.
Mutations are just changes. Some chemical receptor ends up more or less sensitive than usual. Some body part ends up bigger or smaller than usual. Or, in the above case, some pigment changes color slightly.

Since there are a lot more ways to be non-functional than ways to be functional, and since we may already have most of the functions that beings like us are capable of having, loss of functions is much more common than gains of functions. But there's no reason in principle why mutations can't occasionally create new functions.

Agrajag619 wrote:Mutation can add new parts, such as through gene duplication. I don't, however, see how it can produce new connections between them.
Connections turn out to be easy. "Cancer" gets its name because as tumors--any tumors--grow they start forming connections, new blood vessels and stuff, to nearby structures, acquiring a crab-like shape. And that happens in an adult body. In a fetal body, heck, almost anything's possible. The other day I was reading about an experiment where they grafted eyeballs onto tadpoles' tails without changing their genes at all, and then watched as optic nerves grew in the tails (which is not supposed to happen) to connect the eyeballs to the spinal cords (which is not supposed to happen), after which the tadpoles learned to see with the grafted eyeballs.

Apparently our nerves, blood vessels, etc., follow a "connect to whatever parts happen to be available" algorithm rather than having a hard-coded list of what connections they should form where. Probably a good idea anyway since some individuals are shaped differently from others due to accidents of growth and of nutrition, but a side-effect is that it makes evolution easier.

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Re: Evolution question - how does complexity arise?

Postby ahammel » Fri May 03, 2013 2:22 pm UTC

ThirdParty wrote:
Agrajag619 wrote:Mutation can add new parts, such as through gene duplication. I don't, however, see how it can produce new connections between them.
Connections turn out to be easy. "Cancer" gets its name because as tumors--any tumors--grow they start forming connections, new blood vessels and stuff, to nearby structures, acquiring a crab-like shape in an adult body.
Most cancer mutations are knockouts, AFAIK. Izzy might know of some counterexamples.
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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Fri May 03, 2013 2:41 pm UTC

You mean loss of function, not knockout, I think. Knock out means the whole gene is gone, which would, of course, result in a loss of function, but is a bit less likely to happen than a simple point mutation which may still render the protein non-functional.

The p53 oncogene is mutated in, like, a lot (half? 3/4th?) of all cancers, and is a tumor suppressor gene. When mutated, it no longer functions as intended.

As for gain of function oncogenesis... I imagine mutations to pro-proliferation, pro-growth signals that result in them being constitutively active will serve that purpose nicely? I don't know of any specifically, but I wager Angua does. PTEN signals through PI3K and Akt, and over activation of any of those probably leads to cancer-like cells.
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Re: Evolution question - how does complexity arise?

Postby Angua » Fri May 03, 2013 2:51 pm UTC

The braf? Vraf? One in malignant melanoma might count. That's left on. They are just trialling a drug that intereferes with it.

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Re: Evolution question - how does complexity arise?

Postby ahammel » Fri May 03, 2013 2:52 pm UTC

Izawwlgood wrote:You mean loss of function, not knockout, I think.
Oh, probably. It's been a long time since I've taken genetics.

EDIT: Acording to a highly reliable source, BRAF V600E mutants are resistant to having their activity down-regulated. So I suppose YMMV as to whether you want to call that a gain-of-function or a loss-of-function (the 'function' in question being the ability to not phosphorylate MEK).
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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Fri May 03, 2013 3:13 pm UTC

Angua wrote:Vraf?

VEGF? It's tumerogenic when over expressed or activated, so that could be a GoF example.
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Re: Evolution question - how does complexity arise?

Postby Angua » Fri May 03, 2013 3:17 pm UTC

No. Definitely a raf of some sort.

Found it http://en.m.wikipedia.org/wiki/BRAF_(gene)
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Re: Evolution question - how does complexity arise?

Postby Technical Ben » Fri May 03, 2013 4:34 pm UTC

douglasm wrote:Consider a scientist. This scientist has a rock solid clear and unambiguous definition of 'complexity'. This scientist also has tools for manipulating DNA in the seeds of a plant. He can copy genes, move genes, insert or remove small (really small) fragments of DNA, and so on. He wants to increase the complexity of the plant's offspring. Assume he has perfect knowledge of how the plant works and what consequences (to the plant's offspring) his changes will have.

Now, with that hypothetical scenario in mind and before you open the spoiler, would you accept that the scientist is capable of increasing the plant's complexity?

Spoiler:
Anything that scientist can do, mutation can do too. Mutation just won't be reliable about it. Sooner or later, a random mutation will coincidentally happen to match one of the things the scientist might do, resulting in increased complexity.


Imagine hypothetically I have 2 samples of DNA. One is constructed through mutations and iterations with inheritance and selection from the environment. One is selected for by said scientist in the example. How do we differentiate between the samples so as to match each one to the respective mechanism?

This is assuming the two samples are not identical. If they are identical, we could look at the subsequent history of the DNA sequence and what was required to get it up to our current sample.
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Re: Evolution question - how does complexity arise?

Postby ahammel » Fri May 03, 2013 4:45 pm UTC

Technical Ben wrote:Imagine hypothetically I have 2 samples of DNA. One is constructed through mutations and iterations with inheritance and selection from the environment. One is selected for by said scientist in the example. How do we differentiate between the samples so as to match each one to the respective mechanism?
We can't. That's rather the point of that thought experiment.
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Re: Evolution question - how does complexity arise?

Postby screen317 » Fri May 03, 2013 5:17 pm UTC

Izawwlgood wrote:As for gain of function oncogenesis... I imagine mutations to pro-proliferation, pro-growth signals that result in them being constitutively active will serve that purpose nicely? I don't know of any specifically, but I wager Angua does. PTEN signals through PI3K and Akt, and over activation of any of those probably leads to cancer-like cells.
A little off topic, but since my research involves these, I thought I'd point out that PTEN doesn't really signal through PI3K.. PI3K phosphorylates PIP2 into PIP3 and PTEN does the opposite.

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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Fri May 03, 2013 5:18 pm UTC

Yeah, your question is basically;
Assume a plasmid of DNA with the sequence ATGCCGT in bacteria. How do we differenciate between a subsequent plasmid that reads ATCCCGT caused by an error on the part of the bacteria's replication process, or a subsequent plasmid that reads ATCCCGT caused by SDM on the part of a scientists molecular biology.

As ahammel said, you can't, and that's the point of the experiment.

That said, there are some quircks that scientists use for identifying differences in otherwise identical sequences. For example, if you perform SDM, and the resulting DNA is unmethylated. It will thus be in a pool of DNA that is methylated and unmethylated (the methylated DNA coming from the bacterially generated plasmid pool, the unmethylated DNA coming from the SDM replication process). Some enzymes will cut methylated DNA. Viola! You now have a pool of unmethylated DNA, which incidentally, is the pool of DNA that is mutagenized.

screen317 wrote:I thought I'd point out that PTEN doesn't really signal through PI3K.. PI3K phosphorylates PIP2 into PIP3 and PTEN does the opposite.
Ah, my bad. Opposite acting. Thanks!
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Re: Evolution question - how does complexity arise?

Postby stianhat » Fri May 03, 2013 5:25 pm UTC

If complexity alone is supposed to be the compelling argument I hereby invite you to the sensible side of this discussion.

You can easily create the most vivid and complex (and furthermore; completely unpredictable) patterns on a video screen by three small steps.

1. Connect a camera to the tv so the tv shows output from the camera'
2. Point the camera at the TV
3. Wait, and be surprised.

Feedback loops combined with the fractal nature of the world will produce complexity, unpredictable complexity.

http://www.youtube.com/watch?v=UFnIcpgC14A

Does nature have feeback loops? Yes, all over the place. Thus, complexity is a certainity, given time. No need to give up religion just to accept this fact. God made the laws of nature, afterwards nature made itself. If that isnt more likely the actions of a perfect and omnipotent being, I don't know what is. At least a lot more probable than just jimmyfixing everything to fit after the fact. That would not be very perfect, now would it.

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Re: Evolution question - how does complexity arise?

Postby qetzal » Fri May 03, 2013 5:36 pm UTC

This page talks about some classic gain-of-function mutations that can cause cancer, including activation of the c-myc proto-oncogene, and the bcr-abl translocation that causes most cases of chronic myelogenous leukemia.

As for Technical Ben's hypothetical, if all we have is the two samples, we can't differentiate, as ahammel and Izaawlgood said. That's why we don't try to infer sequence origin only by looking at a single sequence in isolation. Instead, we look for similar sequences. If we do that, we'll find that one has homologs in various living organisms, and that the pattern of similarity between those sequences fits a descent-with-modification model that's consistent with other DNA sequences in those same organisms (as well as phenotypic characters, fossil data, etc.).

In contrast, the closest relatives for the other sequence will be in the scientist's lab, and the changes that the scientist introduced won't show the above patterns in living organisms.

Of course, one might claim that the entire Earth could be some "Super-Scientist's" lab. And it's true that we can't absolutely rule that out. But if life on Earth is the result of some Super-Scientist's activities, then for some reason He went to a lot of trouble to make it look like a natural process of descent with modification that took place over several billion years, and not at all like how things would look if some super version of a human scientist were responsible.

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Re: Evolution question - how does complexity arise?

Postby Technical Ben » Fri May 03, 2013 5:40 pm UTC

As said. If we cannot tell by looking at the sequence, then we cannot make a claim by looking at the sequence then. If both methods apply to being able to create the sequence, we have to state some other measurable difference.

So, assuming the scientist stands in as any mechanism that is not "random mutations", how do I distinguish between a sample from a scientist and a sample from random mutations? (Basically to exhaust all possible alternatives)

If I cannot look at just the DNA sequence alone, what else should I be looking at? I'm sure there are other things we can look at to find such differences. Like the history of the sequence, the specific mechanism and it's limits, compared to a scientist only applying an end result?

PS, qetzal. If I have a set of DNA sequences, how do I tell if one set if from a lab made artificially and the other is from "random iterations" made in nature? If that helps put the hypothetical in the right scope of consideration.

Yeah, I don't see how, for example, Dog breeds look anything unlike "natural processes of decent", yet are they a natural breed? It's an honest question. We have one thing made by "people", and one by "nature". So if a DNA sequence or a dog at a breed show, how do I tell the artificial from the "natural"?

stianhat, we get complexity, but we do not get "Star Wars the Phantom Menace" via that method, do we? We have to blame George Lucas for that one. ;)
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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Fri May 03, 2013 5:47 pm UTC

Technical Ben wrote:So, assuming the scientist stands in as any mechanism that is not "random mutations", how do I distinguish between a sample from a scientist and a sample from random mutations? (Basically to exhaust all possible alternatives)
I don't understand what your issue here is; is the DNA being handed to you by a scientist who says "I performed SDM on this"? Yes? It's been mutagenized by a scientist. Is the DNA being handed to you by a scientist who says "This is a genomic prep from wild [critter]"? Any mutations are due to replication errors in the wild.

Technical Ben wrote:f I cannot look at just the DNA sequence alone, what else should I be looking at? I'm sure there are other things we can look at to find such differences. Like the history of the sequence, the specific mechanism and it's limits, compared to a scientist only applying an end result?
Look at... for what? What are you asking?

Technical Ben wrote:Yeah, I don't see how, for example, Dog breeds look anything unlike "natural processes of decent", yet are they a natural breed? It's an honest question. We have one thing made by "people", and one by "nature". So if a DNA sequence or a dog at a breed show, how do I tell the artificial from the "natural"?
Now you're mistaking 'generated in a lab' with 'selectively bred by humans' with 'selectively bred by nature'.

Can you please back up and restate your question directly, instead of just raising a contention against something no one claimed?
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Re: Evolution question - how does complexity arise?

Postby DaBigCheez » Fri May 03, 2013 5:54 pm UTC

Some of my personal favorite examples of interesting - and in some cases, unnecessary - "complexity" (loosely defined) generated by evolution are in the development of the mammalian eye, and in the laryngeal nerve (most notably in giraffes). These are somewhat well-known pseudo-pop-cultural examples, so my apologies if my understanding is somewhat oversimplified. I think they both do a fairly good job of demonstrating how complex structures can arise through random drift and gradual changes, filtered through the mesh of natural selection, while at the same time resulting in final structures that no designer would ever even consider.

The eye has often been a favorite example for creationists of a structure with "irreducible complexity" - where if you take away one part, the whole stops functioning, and this has been used as an argument against evolution, for how could such a structure develop from nothing without a coherent design? The Wikipedia article gives a good outline - it probably arose as a series of much more gradual steps, from a photosensitive patch of skin ("can tell whether there is light"), to a curved patch ("get a crude sense of direction of the light"), to a curved patch with a pinhole opening ("start to see blurry images"), then one filled with fluid, then a lens, and so on. This does lead to several design flaws, such as the "blind spot" where the optic nerve attaches and the possibility of retinal detachment, among others; there are a few more somewhat-ridiculous problems with the design of the eye that I cannot recall right now; the "evolutionary baggage" section of the article provides a limited selection.

The laryngeal nerve is another fun one - the nerve connecting the voice box to the brain, which traverses from the larynx, loops under the heart, and then travels back up towards the brain. This is a bit of a detour compared to the few inches it would have to go with a direct path, and is even more pronounced in giraffes, with laryngeal nerves of up to fifteen feet to bridge a six-inch gap; this is theorized to be a hold-over from the nerve's placement in fish, where it quite sensibly goes from the brain past the heart and to the gills, and as animals developed and the "gills" ceased to function in the same way, well...

I realize neither of these *directly* answers your question, being more examples of "why should we believe this complex thing evolved rather than was designed" as opposed to "how does complexity evolve in the first place", but I believe they still provide examples of complexity increasing through evolution, if not direct proof of the mechanism.
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Re: Evolution question - how does complexity arise?

Postby qetzal » Fri May 03, 2013 6:05 pm UTC

Technical Ben wrote:PS, qetzal. If I have a set of DNA sequences, how do I tell if one set if from a lab made artificially and the other is from "random iterations" made in nature? If that helps put the hypothetical in the right scope of consideration.


Like I said: compare each set to additional sequences in diverse living organisms. Look at the patterns of similarity between the sequences in each set, and any additional similar sequences you can find in other organisms. Look for patterns suggestive of a single ancestral sequence that changed step-wise and gradually over time, versus patterns where the sequences show little similarity to one another or to other natural sequences. If a sequence set does show a descent with modification pattern in living organisms, then other sequences from that same set of organisms should show a similar descent with modification pattern. E.g., if one set of sequences are quite similar in species A & B, but not nearly as similar in species C, then other sequences from those same species should show a similar pattern: A & B more alike than C. (There won't be perfect agreement, since evolution is a stochastic process, but the overall pattern will be reproducible across most sequences in those organisms.)

You can also look for fossil relatives of A, B & C, and try to trace them back to a common ancestor, using fossil morphology along with dating methods. You expect to find that A & B shared a relatively recent common ancestor, whereas the common ancestor of A, B & C is older.

What you don't generally expect is to find sequences that are really similar between, say, lizards and dogs, but not at all similar in snakes.

Once again, the 'artificial' sequences could also show the patterns predicted above. If they did, we'd have no way to distinguish them. The difference is that evolution predicts explains why such patterns should be present, and successfully predicts what else we should see. There's no obvious reason why such patterns would result from a super-powerful genetic engineer.

Edit: Dog breeds are actually an excellent example of evolution! There was reproduction with heritable variation, and selection that allowed some variants to reproduce more than others. Sure, humans imposed the selection, but the basic mechanisms are the same as natural evolution.

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Re: Evolution question - how does complexity arise?

Postby gmalivuk » Fri May 03, 2013 6:29 pm UTC

Technical Ben wrote:As said. If we cannot tell by looking at the sequence, then we cannot make a claim by looking at the sequence then. If both methods apply to being able to create the sequence, we have to state some other measurable difference.

So, assuming the scientist stands in as any mechanism that is not "random mutations", how do I distinguish between a sample from a scientist and a sample from random mutations? (Basically to exhaust all possible alternatives)
If you want to know how we can tell the difference between a genetic sequence that arose through natural mutation and selection and one that was intelligently designed by your god, just come out and say so. Cut it out with your continued vague questioning and backstepping and refusal to use words the same way everyone who knows what they're talking about uses them.
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Re: Evolution question - how does complexity arise?

Postby gmalivuk » Fri May 03, 2013 6:36 pm UTC

And the answer to that implied question, of course, is that ultimately we couldn't, because God (or the scientist you're using as a rhetorical stand-in for God so it doesn't look so much like that's what you're talking about) could in principle choose any desired sequence at all, including ones that are indistinguishable from naturally evolved ones.

However, except through a desire to trick us into believing falsehoods, I have yet to see any good explanation for why any deity would choose to design things as messily and roundabout-ly as evolution has. Our backwards eye, the laryngeal nerve, the multiple useless copies of a gene for seeing green, the slight mutation in one such copy to allow people to see red, and on and on and on, are all things which make perfect sense in the context of a long process of mutation and selection and drift and everything else that goes into evolution. What they don't do is make any damn sense at all in the context of an omnipotent creator God who could have made things any way he liked and chose to make them this way.
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Re: Evolution question - how does complexity arise?

Postby Technical Ben » Sat May 04, 2013 5:54 am UTC

gmalivuk, with all due respect it has nothing to do with a "deity" and everything to do with how I would falsify (thus "sicence!") a theory, or in this case show the alternative to be falsified so we can say "yes evolution is the closest correct theory". Really, it's down to the fact that if I cannot confirm the difference between "natural" and "lab" that I have a specific problem with a theory. If we confirm fusion is possible in a lab, but observe no stars, then we could not say "we have a strong inference of fusion else where than the lab". I see mutations in the lab and in nature. Do I see the same results in both?

For example, if talking about SDM, I see that it happens in both the lab and in nature. I see no "trick" there, it's a plain observation. Is a scientist "tricking" people when he applies SDM? No. Is nature "tricking" people? No. However, in nature there will be differences to in the lab. Why? Because we are not replicating the natural system 1) Completely and 2) perfectly.

So, I would either expect someone to honestly say "but in nature there are more mutations/steps/generations/trials needed" because we have less time/people to replicate it in the lab. Or "but in nature it is undirected so takes the least efficient (or less than most efficient) route" because in the lab the scientist will select for something other than the environment usually does. Those things I can test for.

Why is this important? Random systems look different than systems with mechanisms of action. I could even look for Gaussian distributions, right? If I was looking at the stars and ask an astronomer "well, the motion of the stars look like they follow some rules, do they?" and the answer was "oh, it's all random motion", I'd be rather concerned about such an astronomer. But yet it's suggested mutations are random. So, I am looking to see where in the system of evolution the "rules" are applied. I can't apply rules to the mutations, yet we can agree there are specific rules in evolution.

And the answer to that implied question, of course, is that ultimately we couldn't, because God (or the scientist you're using as a rhetorical stand-in for God so it doesn't look so much like that's what you're talking about) could in principle choose any desired sequence at all, including ones that are indistinguishable from naturally evolved ones.

So no, I don't want to know the difference between nature and a deity. I want to know the difference between "a person in a lab making these things" and "nature making these things". Does the scientist select randomly, or for a specific mutation? Does nature select randomly or for specific mutations?

For example, if I had a hypothetical planet with very high rate of new life appearing. How do I tell the difference between two samples independently appearing and both being selected for the same environment, versus one ancestor appearing and evolving into two samples? Or two samples converging into one phenotype/genotype verses one sample having double the population? Hopefully such an example removes the "complexity" problem and the "deity" problem, as I am honestly looking at how the theory of evolution gives different, specific and observation matching predictions. So that I know it's both "better" than other theories and "predicting" observation. Just like the LHC, if I cannot confirm the histories of my observation, I can confirm if there is no other route to the current observation, or if the strongest "match" of observations fits the theory. Thanks. :)
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Re: Evolution question - how does complexity arise?

Postby PossibleSloth » Sat May 04, 2013 7:07 am UTC

Technical Ben wrote:gmalivuk, with all due respect it has nothing to do with a "deity" and everything to do with how I would falsify (thus "sicence!") a theory, or in this case show the alternative to be falsified so we can say "yes evolution is the closest correct theory". Really, it's down to the fact that if I cannot confirm the difference between "natural" and "lab" that I have a specific problem with a theory.

That isn't how science works. The theory of evolution by natural selection is a straightforward theory which explains most, if not all, the observed data and has made numerous verifiable predictions. We don't need to falsify every possible alternative, especially when the alternative is that all life on Earth was made by a "scientist" in a "lab".

This is one of those burden of proof situations. You don't replace an old theory with a new, less specific theory unless you find a case where the old theory is incorrect. You need to provide a case where your "mystical lab in the sky" theory fits the observations better than the "organisms evolve through natural selection" theory.


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