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Ask me anything you want about biology!

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belle
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7/1/2012 1:27:33 PM
Posted: 11 months ago
At 6/29/2012 6:00:55 PM, Lasagna wrote:
A classmate and I had a question for my Bio 1 teacher, which he failed miserably to answer. I'm interested to see if you can do better.

Mitochondria and chloroplasts are said to have evolved from foreign cells that invaded the cells of plants and animals and then evolved into them (I believe this is called endosymbiosis). I cannot make logical sense of this. Evolution is attained through changes in DNA, so how could an organism just evolve into another like this? It seems as implausible as a mother with breast implants giving birth to a child with them as well :P

so basically, you start with two bacterial cells. one engulfs the other and it doesn't die. call them A (the outside cell) and B (the inside cell). then both cells continue to divide. when B divides it makes 2 Bs inside of A. when A divides, the Bs may be split up between progeny, or they may end up clustered in one cell. it doesn't really matter. over generations these cells continue to divide and you end up with a bunch of As with a bunch of Bs inside of them. eventually, B starts to lose some of its genes through random mutation, but since its inside of A it makes no difference- it doesn't need those genes anymore. eventually B can't live except inside of A because its too genetically reduced to carry out all the functions necessary to life. part of the evidence we have for this is that mitochondria and chloroplasts still contain genes of their own and divide semi-independently inside the host cell.
evidently i only come to ddo to avoid doing homework...
The_Fool_on_the_hill
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7/1/2012 2:31:09 PM
Posted: 11 months ago
At 7/1/2012 6:50:38 AM, Sidewalker wrote:
At 6/24/2012 6:35:32 PM, Microsuck wrote:
Hey guys,

I'm opening this thread to hopefully be able to learn a bit more about biology myself and teach it to members of the forum.

This is an open Q&A session where you can ask me any question you want about biology and evolution. I am going to major in biology and thought this would be a good "precursor" to my college lab studies.

I have several questions that are all one question really, proposed as a fruitful line of investigation for your studies.

How did the components for the first cell come together within a membrane, and by what mechanism did this come to self replicate as a unified whole?

The Fool: whatever it is it doesn't entail GOD, it at best entials I don't know. we didnt' see it develop but we do know there were there.

What caused the various prokaryotes to assemble into a symbiotic whole to become the first eukaryotic cells?

The Fool: whatever it is it doesn't entail GOD, it at best entails I don't know. we didnt' see it develop but we do know there were there. God is not a default answer!

When the single cell paramecium came into existence, how and why did cilia attach and why did this amalgam of independent organisms become a single self replicating entity? What mental state can there be in a single celled creature with no brain that causes the protozoa to be able to "will" the attached cilia to work in such harmony to make the unified whole such a great swimmer? Is the paramecium sentient, is it conscious?

The Fool: whatever it is it doesn't entail GOD, it at best entails I don't know. we didnt' see it develop but we do know there were there. God is not a default answer!

At what point in the evolution of inanimate to life complex living beings did sentience come into existence, how about consciousness, how did a complex arrangement of inanimate matter become living, sentient, and conscious?

The Fool: whatever it is it doesn't entail GOD, it at best entails I don't know. we didnt' see it develop but we do know there were there. God is not a default answer!

There is some unexplained principle involved that certainly appears to manifest itself in self organizing wholes. Is the principle that caused the first self replicating cell to become a single unified whole the same principle that caused single celled creatures to form colonies that became multi-cellular creatures, and become unified into single sentient entities at some point? Is the same principle at work in ant and termite colonies, social organization, culture and civilization, and if so, what's next?

The Fool: whatever it is it doesn't entail GOD, it at best entails I don't know. we didnt' see it develop but we do know there were there. God is not a default answer!

I'm not suggesting that you look outside of science for answers, ‘God did it" isn't an answer, it just begs questions, and the word emergent is descriptive rather than explanatory, it isn't an answer either, in effect it says "something from nothing", which also begs questions.

The Fool: whatever it is it doesn't entail GOD, it at best entails I don't know. we didnt' see it develop but we do know there were there. God is not a default answer!

Knowledge is learned over time the next generation will know more then we do. that is how knowledge works. We don't have to know NOW!
"All the same, it could be that I am mistaken, and what I take for Gold and Diamonds is perhaps nothing but a bit of copper and glass."
"I know how much we are prone to err in what affects us, and also how much the Judgments made by our friends should be distrusted when these Judgments in our favor." Rene Descartes
The_Fool_on_the_hill
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7/1/2012 3:56:29 PM
Posted: 11 months ago
At 7/1/2012 1:27:33 PM, belle wrote:
At 6/29/2012 6:00:55 PM, Lasagna wrote:
A classmate and I had a question for my Bio 1 teacher, which he failed miserably to answer. I'm interested to see if you can do better.

Mitochondria and chloroplasts are said to have evolved from foreign cells that invaded the cells of plants and animals and then evolved into them (I believe this is called endosymbiosis). I cannot make logical sense of this. Evolution is attained through changes in DNA, so how could an organism just evolve into another like this? It seems as implausible as a mother with breast implants giving birth to a child with them as well :P

so basically, you start with two bacterial cells. one engulfs the other and it doesn't die. call them A (the outside cell) and B (the inside cell). then both cells continue to divide. when B divides it makes 2 Bs inside of A. when A divides, the Bs may be split up between progeny, or they may end up clustered in one cell. it doesn't really matter. over generations these cells continue to divide and you end up with a bunch of As with a bunch of Bs inside of them. eventually, B starts to lose some of its genes through random mutation, but since its inside of A it makes no difference- it doesn't need those genes anymore. eventually B can't live except inside of A because its too genetically reduced to carry out all the functions necessary to life. part of the evidence we have for this is that mitochondria and chloroplasts still contain genes of their own and divide semi-independently inside the host cell.

The Fool: We don't know how it all happened its a hypothysis.,
"All the same, it could be that I am mistaken, and what I take for Gold and Diamonds is perhaps nothing but a bit of copper and glass."
"I know how much we are prone to err in what affects us, and also how much the Judgments made by our friends should be distrusted when these Judgments in our favor." Rene Descartes
Lasagna
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7/1/2012 8:29:52 PM
Posted: 11 months ago
At 7/1/2012 1:27:33 PM, belle wrote:
At 6/29/2012 6:00:55 PM, Lasagna wrote:
A classmate and I had a question for my Bio 1 teacher, which he failed miserably to answer. I'm interested to see if you can do better.

Mitochondria and chloroplasts are said to have evolved from foreign cells that invaded the cells of plants and animals and then evolved into them (I believe this is called endosymbiosis). I cannot make logical sense of this. Evolution is attained through changes in DNA, so how could an organism just evolve into another like this? It seems as implausible as a mother with breast implants giving birth to a child with them as well :P

so basically, you start with two bacterial cells. one engulfs the other and it doesn't die. call them A (the outside cell) and B (the inside cell). then both cells continue to divide. when B divides it makes 2 Bs inside of A. when A divides, the Bs may be split up between progeny, or they may end up clustered in one cell. it doesn't really matter. over generations these cells continue to divide and you end up with a bunch of As with a bunch of Bs inside of them. eventually, B starts to lose some of its genes through random mutation, but since its inside of A it makes no difference- it doesn't need those genes anymore. eventually B can't live except inside of A because its too genetically reduced to carry out all the functions necessary to life. part of the evidence we have for this is that mitochondria and chloroplasts still contain genes of their own and divide semi-independently inside the host cell.

So these B cells are in sperm and eggs and continue to live and divide inside cells and somehow the new B cell always makes it into the new A cell?
Rob
belle
Posts: 4,113
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7/2/2012 12:22:32 PM
Posted: 11 months ago
At 7/1/2012 8:29:52 PM, Lasagna wrote:
At 7/1/2012 1:27:33 PM, belle wrote:
At 6/29/2012 6:00:55 PM, Lasagna wrote:
A classmate and I had a question for my Bio 1 teacher, which he failed miserably to answer. I'm interested to see if you can do better.

Mitochondria and chloroplasts are said to have evolved from foreign cells that invaded the cells of plants and animals and then evolved into them (I believe this is called endosymbiosis). I cannot make logical sense of this. Evolution is attained through changes in DNA, so how could an organism just evolve into another like this? It seems as implausible as a mother with breast implants giving birth to a child with them as well :P

so basically, you start with two bacterial cells. one engulfs the other and it doesn't die. call them A (the outside cell) and B (the inside cell). then both cells continue to divide. when B divides it makes 2 Bs inside of A. when A divides, the Bs may be split up between progeny, or they may end up clustered in one cell. it doesn't really matter. over generations these cells continue to divide and you end up with a bunch of As with a bunch of Bs inside of them. eventually, B starts to lose some of its genes through random mutation, but since its inside of A it makes no difference- it doesn't need those genes anymore. eventually B can't live except inside of A because its too genetically reduced to carry out all the functions necessary to life. part of the evidence we have for this is that mitochondria and chloroplasts still contain genes of their own and divide semi-independently inside the host cell.

So these B cells are in sperm and eggs and continue to live and divide inside cells and somehow the new B cell always makes it into the new A cell?

well at first it was kind of messy like that, but now theres nuclear genes that control how the mitochondria and chloroplasts get divided up every time the cell divides. those genes developed later though, as a useful adaptation to having these cells living inside you since they benefited the parent cell by being there.
evidently i only come to ddo to avoid doing homework...
Sidewalker
Posts: 2,068
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7/3/2012 9:53:07 AM
Posted: 11 months ago
At 7/1/2012 2:31:09 PM, The_Fool_on_the_hill wrote:
At 7/1/2012 6:50:38 AM, Sidewalker wrote:
At 6/24/2012 6:35:32 PM, Microsuck wrote:
Hey guys,

I'm opening this thread to hopefully be able to learn a bit more about biology myself and teach it to members of the forum.

This is an open Q&A session where you can ask me any question you want about biology and evolution. I am going to major in biology and thought this would be a good "precursor" to my college lab studies.

I have several questions that are all one question really, proposed as a fruitful line of investigation for your studies.

How did the components for the first cell come together within a membrane, and by what mechanism did this come to self replicate as a unified whole?

The Fool: whatever it is it doesn't entail GOD, it at best entials I don't know. we didnt' see it develop but we do know there were there.

Then perhaps I should have said something like "I'm not suggesting that you look outside of science for answers, ‘God did it" isn't an answer, it just begs questions"…oh wait, that's exactly what I did say, I guess you were just being pointless again.

What caused the various prokaryotes to assemble into a symbiotic whole to become the first eukaryotic cells?

The Fool: whatever it is it doesn't entail GOD, it at best entails I don't know. we didnt' see it develop but we do know there were there. God is not a default answer!

Pointless , the sequel.

When the single cell paramecium came into existence, how and why did cilia attach and why did this amalgam of independent organisms become a single self replicating entity? What mental state can there be in a single celled creature with no brain that causes the protozoa to be able to "will" the attached cilia to work in such harmony to make the unified whole such a great swimmer? Is the paramecium sentient, is it conscious?

The Fool: whatever it is it doesn't entail GOD, it at best entails I don't know. we didnt' see it develop but we do know there were there. God is not a default answer!

The Return of Pointless.

At what point in the evolution of inanimate to life complex living beings did sentience come into existence, how about consciousness, how did a complex arrangement of inanimate matter become living, sentient, and conscious?

The Fool: whatever it is it doesn't entail GOD, it at best entails I don't know. we didnt' see it develop but we do know there were there. God is not a default answer!

Son of Pointless.

There is some unexplained principle involved that certainly appears to manifest itself in self organizing wholes. Is the principle that caused the first self replicating cell to become a single unified whole the same principle that caused single celled creatures to form colonies that became multi-cellular creatures, and become unified into single sentient entities at some point? Is the same principle at work in ant and termite colonies, social organization, culture and civilization, and if so, what's next?

The Fool: whatever it is it doesn't entail GOD, it at best entails I don't know. we didnt' see it develop but we do know there were there. God is not a default answer!

Beneath the Planet of Pointless.

I'm not suggesting that you look outside of science for answers, ‘God did it" isn't an answer, it just begs questions, and the word emergent is descriptive rather than explanatory, it isn't an answer either, in effect it says "something from nothing", which also begs questions.

The Fool: whatever it is it doesn't entail GOD, it at best entails I don't know. we didnt' see it develop but we do know there were there. God is not a default answer!

Pointless, Episode Six.

Knowledge is learned over time the next generation will know more then we do. that is how knowledge works. We don't have to know NOW!

Pointless…and incredibly uninteresting…you are a master of the mundane.

Be careful kiddie, I'm sure the terms of service expressly forbid threatening people's lives here…and it sure looks like you are trying bore us all to death.
Sidewalker
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7/3/2012 10:16:11 AM
Posted: 11 months ago
At 7/1/2012 10:59:26 AM, Thaumaturgy wrote:
At 7/1/2012 6:50:38 AM, Sidewalker wrote:

How did the components for the first cell come together within a membrane, and by what mechanism did this come to self replicate as a unified whole?

When you put soap into water at sufficient concentration it forms what are called "micelles". Micelles form because the hydrophobic tails of the soal molecule orient away to a place that is free of water and the hydrophilic heads of the soap molecule orient outward into a water-environment. The interior of these micelles is proper for the hydrophobic side and the exterior is comfortable to the hydrophilic side.

This technique happens spontaneously at certain concentrations of a SURFACTANT.

Cell walls are similar except they are made up of two layers of amphiphilic compounds. A polar (hydrophillic) head and a non-polar (hydrophobic) tail. The layers form similarly to provide a condition comfortable to the hydrophobic tails and exterior that is comfrotabe in an aqueous surrounding.

So now you have a first step that explains a great deal of the process.

Yeah, I'm familiar with that step of the process, and it looks like the raw materials were delivered via meteorites and comets, when we were in school who'd have thought the abiogenesis process was going to be explicated by a field called Astrobiology? But we are a long way from understanding the process by which the protocell came to self replicate as a unified whole, and I think there is a principle there that runs across a large scale and broad range of phenomena that needs to be researched, which is why I'm recommending it as a "fruitful line of investigation" for this kid's studies. There's a method to my madness and a reason that Niels Bohr is my favorite physicist, its these young kids that walk into the labs and shake the foundations of science to deliver something really new, and I try to challenge them every chance I get.

When the single cell paramecium came into existence, how and why did cilia attach

I doubt they 'attached' but rather formed from the cell itself. Do you have a citation that they are colonial or exogenous to the paramecium?

Yeah, but I can't recall where I read it, it was a long time ago, perhaps something from Lewis Thomas, and it may have been refuted by now, quite possible it formed from the cell itself as you say, but it used to be the leading hypothesis and how the cilia attached was a vexing problem. Even if the paramecium example isn't particularly accurate, the point is still valid. The study of the membranes of cellular organelles make it pretty clear that primitive eukarotes originated as symbiotic relationships among prokariotes, and something is operating in nature that makes these collections of matter of increasing complexity become self organizing wholes in direct violation of the second law. Single celled organisms with nothing even resembling a rudimentary brain or nervous system show themselves to be sensate beings with complex behavior, certainly beyond the capabilities of complex "chemical factories". Bacteria can respond to a broad range of stimuli, demonstrate rudimentary forms of "memory", and engage in purposeful activities. They shown themselves to be extraordinarily perceptive, demonstrating elaborate behavioural responses and adaptations to a wide range of attractants and repellants and other environmental stimuli such as light. They have complex signaling capabilities, show the ability to communicate, and change their behavior based on population size, which implies some kind of quorum sensing ability and clearly demonstrates social behavior on at least a rudimentary level. They been proven to have some form of memory and a rudimentary ability to learn, and the discriminatory ability to "choose" among alternatives, regarding among other things, gene expression. They clearly integrate these capabilities into a self organized and sensate being that in at least an extremely attenuated way if perceiving, discriminating, remembering, and even "thinking", on some level it is conscious.

And please don't try to tell me what a thermostat does, I know what a thermostat does and it isn't even in the ballpark of being explanatory regarding these phenomena.

To be continued in the next post...
Sidewalker
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7/3/2012 10:22:48 AM
Posted: 11 months ago
At 7/1/2012 10:59:26 AM, Thaumaturgy wrote:
At 7/1/2012 6:50:38 AM, Sidewalker wrote:

and why did this amalgam of independent organisms become a single self replicating entity?

DNA and RNA work quite well to direct (bias) the selection of compounds. It is a base structure that selectively binds with component compounds and the formation of a copy of itself (through, albeit, rather complex chemistry. But plain old chemistry nonetheless).

Perhaps it's plain old chemistry if you ascribe consciousness to plain old matter in some kind of extremely attenuated way, but I'll presume you don't do so. And there isn't even a speculative theory as to how DNA relates to outward form. We know it's always there and we can associate changes in outward form with corresponding changes in DNA, but it is a complete mystery as to what the mechanism is. We are going to have to go beyond plain old chemistry to find some kind of explanatory principle that connects DNA molecules to their expression of outward form.

In a sense the formation of a mineral crystal is a simple form of "replication". The crystal face that is growing provides a template upon which only certain atoms and in only certain configurations will be allowed to bind and so the crystal grows.

Not always without defect either, so in a very real sense it can "evolve". A cubic crystal can have defects which induce the shape of the crystal to change direction somewhat.

Well there you go, we aren't always going to have to be adversarial  Your comments play very well into the point I'm getting at here. With the broad scale perspective that evolution demands, it becomes pretty clear that we don't have to reconsider life, we have to reconsider matter itself to understand what is happening here, especially as it relates to abiogenesis, where physics and biology converge. Granted, religious fundamentalists crap all over the second law with uninformed zeal, but nevertheless, The universe taken as a whole is a closed system, so the second law of thermodynamics does in fact apply. When we take an honest look on the broad scales of evolutionary theory it becomes self-evident that the evolution of life shows itself to involve a creative force rather than the adaptive force represented by Darwinism's model. We see that life reveals itself to be self-transcendent, constantly reaching out beyond the systems boundaries, and there is some explanatory principle involved that isn't going to be reductionistic in nature. And I'm not saying it will be supernatural either, I love my Constitution almost as much as I love science and I defend both.
I'm merely saying that your materialistic determinism is going to need to be supplemented by at least a new principle to make some kind of adequate explanatory progress. The only reality we know directly is experiential, and David Chalmers' hard problem of consciousness simply cannot be reduced to physical and chemical processes in the brain, especially when single celled creatures with no brain or nervous system are demonstrating an attenuated form of consciousness. The observed data just doesn't fit the mechanistic conceptual scheme of plain old chemistry.

What mental state can there be in a single celled creature with no brain that causes the protozoa to be able to "will" the attached cilia to work in such harmony to make the unified whole such a great swimmer?

There need be no "mental state" or even "will". Many protozoa are essentially "chemical detectors". They will go in directions that are not "disfavored".

Again the idea of the appearance of motivation and will are deceptive anthropomorphisms.

I know that, it's why I put the word "will" in quotation marks, but as I have explained above, there is something going on that transcends the level of mechanistic explanation. To deny that you pretty much have to deny observations, facts and evidence, and that isn't science, it's something else. You are no longer doing science when you have to use an intellectual hammer to pound round facts into square holes in order to fit the theory, that is when it's time to become open minded and creative in the spirit of true science. By the way, the very existence of "creativity" is another slap in the face of the materialistic determinism model but we can save that for another discussion.

To be continued in the next post...
Sidewalker
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7/3/2012 10:27:35 AM
Posted: 11 months ago
At 7/1/2012 10:59:26 AM, Thaumaturgy wrote:
At 7/1/2012 6:50:38 AM, Sidewalker wrote:

At what point in the evolution of inanimate to life complex living beings did sentience come into existence, how about consciousness, how did a complex arrangement of inanimate matter become living, sentient, and conscious?

There are many examples of the development of the "brain". Everything from the development of nerve cells to anterior ganglia to simple up to more complex brains.

The concept of "sentience" is probably so fraught with nebulous ideals that one would have to have a specific question around this. Overall something as difficult ot nail down as "sentience" is probably a function of the complexity of the system. A secondary trait of a neural network.

No way, the hard problem of consciousness will never reduce down to a mechanistic explanation, like the aforementioned problem with DNA, the mere association of corresponding physical changes does not constitute an explanatory mechanism, and as also previously mentioned, "emergent" is not an explanatory term, it's a descriptive term. In my business there is a widely used saying that "Any sufficiently advanced technology is indistinguishable from magic", but that it just something we say for comic relief. You don't just get to say "sufficiently complex" and viola, something "emerges" as if by magic, scientifically speaking, it needs to include an effective causal sequence if you are going to call something explanatory, and we both know "magic" doesn't cut it.

There is some unexplained principle involved that certainly appears to manifest itself in self organizing wholes.

Actually not necessarily so. In the case of your first questions the "driving mechanism" is little more than basic chemistry, albeit complex, but still underlain by standard chemical concepts. There is little to really break down "life" from "non-life". They both use the same chemistry.

The higher order questions are probably still manifestly underlain by purely natural processes.

I'm not advocating "unnatural" processes as explanations, I'm saying that there are natural principles that need to be researched, discovered, and applied to explain the higher order questions, evolutionary theory's requisite abiogenesis problem has brought physics and biology together with an interdisciplinary problem that is exciting, let's recall that I'm simply trying to suggest a fruitful line of investigation for this kid so perhaps he can make a difference.

Is the principle that caused the first self replicating cell to become a single unified whole the same principle that caused single celled creatures to form colonies that became multi-cellular creatures, and become unified into single sentient entities at some point?

Sponges are a great example of a "living thing" which may actually be a colony. No one would probably call it "sentient" but it shows a stepping stone from individuals in a colonial setting (such as a coral) up to a colony of specialized cells and so forth. The fact that ultimately we wind up with animals like us is not an indication of any sort of guidance or causative principal. It could have just happened. We all use the same chemistry and the same elements largely.

You reductionists just love to say "it could have just happened" but no, it couldn't, we don't get to invoke "magic" in science. You can't make randomness a principle, randomness is not a principle, it's the absence of a principle, and when you really think it through, the increasing complexity of the observed universe cannot be explained as fortuitous randomness, there is something more than meets the mechanistic eye happening here.

I'm not suggesting that you look outside of science for answers, ‘God did it" isn't an answer, it just begs questions, and the word emergent is descriptive rather than explanatory, it isn't an answer either, in effect it says "something from nothing", which also begs questions.

The "something from nothing" in this case doesn't really apply. The "nothing" in this case is actually just plain old chemistry. The rules that drive reactions in the sink when you put some soap in the water are at their heart electrostatic interactions. Polar-nonpolar, chemical affinity, quantum mechanical interactions, electron affinity, electronegativity, size/charge ratios, etc. etc.

No, it isn't just plain old chemistry, its plain old chemistry with a twist added, something else needs to be happening here. Much like Einstein's Relativity theory was just plain old Classical Physics with the twist of the constant speed of light from all frames of reference added to it, and look how fruitful that was, all kinds of value dropped out of the formulas when he worked through the mathematics.
The rules that drive reactions in the sink when you put some soap in the water are at their heart electrostatic interactions. Polar-nonpolar, chemical affinity, quantum mechanical interactions, electron affinity, electronegativity, size/charge ratios, etc. etc.
It's interesting that you added "quantum mechanical interactions" to your description of "plain old" chemistry, quantum mechanics isn't just plain old physics by any stretch of the imagination, and it all really started in 1905 with those three papers young Einstein wrote. He didn't like where that went any more than you want to like where this chain of reasoning might go, and I think Thomas Kuhn explained that pretty well. But the fact remains that something is going on here that is very hard to take a picture of, something is missing from our current models and it's clearly going to transcend the analytical and mechanistic paradyme to include the more synthetic approach of top down system's thinking..and the point here is that it's a fruitful line of investigation.
I'm posing questions rather than proclaiming to have answers here, but let me be more explicit about where I think this quest for explanations needs to go. The world is certainly receiving energy from the sun, the differences in temperature provides motive power to the Earth, so spontaneous changes on Earth are accompanied by an increase in randomness of the energy distributed in the system. That's certainly your point, "in theory", when you rely on increasing complexity to account for the "magical" emergence of completely new things, but the law of cause and effect doesn't really allow now things to just "emerge", as if by magic, there needs to be an explanatory principle and it has yet to be developed or discovered, depending on your point of view. Einstein showed us that matter and energy are different forms of the same thing. So Kelvin's first law necessarily needs to be modified into a broader conceptual scheme regarding the conservation of energy/matter. We aren't just talking about the distribution of heat and random motion anymore and we have to redefine the definition of disorder and in the process, I think we will necessarily achieve some progress along the lines of new explanatory principles when we do. The second law does not take into account the observed fact that natural form building activities are occurring over time. Self-integrated units of matter are in fact observed opposing the predicted statistical trend toward randomness. Manmade systems impose shape and order from outside, and they break down, classical entropy applies there. But there are naturally forming units of matter, the hydrogen atom, ice crystals, protein molecules, and the biggie, life, are units whose form is organized within. They all show a tendency to protect themselves from dissolution and repair themselves from within when they have been disturbed or damaged. We need not think of it as imposed from outside by the way, but we are observing a universe in which entities of matter are increasing form and complexity in space and time, and they are clearly defying the second law.
Sidewalker
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7/3/2012 10:29:30 AM
Posted: 11 months ago
At 7/1/2012 6:50:38 AM, Sidewalker wrote:

Final piece...

Let's take a simple example; it's true that heat is dissipating from the sun, so we can postulate the increase in order and complexity on earth results from the net increase in energy. But there is also a corresponding increase in order occurring in the sun by the very process that generates the heat. In the sun, we have a spontaneous reaction, four hydrogen atoms combine to create one helium atom, add up the total matter and it's slightly less, the excess matter was released in the form of heat, that's where the heat coming from the sun came from. But the resultant helium atom is a much more complex assembly, it is a whole that is more than the sum of its parts, it's more stable, it will in fact recover its form when damaged, and it possesses new "potentials". This potential resulting from the increase in order also begins a chain of events of further increasing order and form, resulting in oxygen, carbon, iron, amino acids, nucleoproteins, and biological systems, life, and man. At the end of the chain, biological systems certainly appear to operate under a different set of laws; life pretty much has to be considered a special case. The second law just does not take into consideration the increase in order that occurs at the bottom of the sun's dissipation of heat to the earth equation. It doesn't assign any value to the corresponding increase in order or the higher levels of complexity achieved, and Einstein's theory necessitates that it must. The second law is incomplete if it is seen in the terms of mere heat exchange any longer. In the universe's field aspect of energy, heat is released or dissipated from the sun, in it's aspect of matter, and there is a corresponding process of synthesis, four atoms of hydrogen becoming one atom of helium, and it is an increase in complexity that the second law does not recognize. The analytic mode of thought applied in this regard is incomplete; there is also the synthetic mode of thought to consider if we are going to consider the whole in both its spatial and temporal aspects, which by its very nature, the study of evolution requires..

What is this polar opposite, this inherent principle that results in an apparent progressive increase in complexity culminating in sentience, consciousness, and to date, self consciousness in Man. and directedness of the universe? We can see a natural tendency for the creation of self-organizing wholes to form. And I tend to question what other processes are explained by this underlying principle in order to force the requisite synthetic thought processes which will ultimately lead to an answer. Let's first take a look at its manifestations so we can at least see it in operation. We certainly won't be able to define it until we first recognize its characteristics.

Because of its remarkable progress, current scientific theory has become conceptually inconsistent, for it to hold together we need to postulate something else, as always, new principles need to be added to explain new discoveries, and in the end, its going to be something that brings things together to form larger, self organizing wholes, and I firmly believe it's going to be something that transcends the reductive and materialistic frame of reference of science, something that creates "unity", and in the end, leads to consciousness.

And that my adversarial friend, is going to be a very fruitful line of investigation.

Postscript:

I was careful to avoid associating your rigidly structured thinking with religious fundamentalism because I know how much that upsets you and despite it's validity, I will admit I took it too far to make a point before. But let me tell you why I come by this "poke you with a stick" tendency honestly. My field is physics, and I don't know where I went wrong as a parent, but I actually have a chemist in my own family  One of my sons is a biochemist that has taken the vow of poverty to dedicate his life to cancer research. As a proud father I can tell you that the consensus opinion in his field is that he is on the front end of a world class research career, unfortunately his mother gets most of the credit, at least for his passion by dying of cancer while he was an undergrad senior, but and I firmly believe that I've played a significant role in his success by constantly pushing him to go beyond structured thoughts of the current paradyme to think outside the box. So in the spirit of an apology for taking it too far before, I'll explain that I come by this irritating tendency to push your buttons quite honestly. Trust me, he hates it when I associate rigid scientific thinking with religious fundamentalism even more than you do, with both of you I do it for shock value and out of respect for your intellect, I think it works and it's a lot of fun, so you should probably just get used to it :)
Thaumaturgy
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7/3/2012 2:49:59 PM
Posted: 11 months ago
At 7/3/2012 10:16:11 AM, Sidewalker wrote:
I think there is a principle there that runs across a large scale and broad range of phenomena that needs to be researched, which is why I'm recommending it as a "fruitful line of investigation" for this kid's studies. There's a method to my madness and a reason that Niels Bohr is my favorite physicist, its these young kids that walk into the labs and shake the foundations of science to deliver something really new, and I try to challenge them every chance I get.

Oh I totally agree! No problem there. I think, however that the answer will lie in the prosaic drudgery of detailed and complex application of basic chemistry. Very little to do with any major "breakthrough". Now that being said, the wondrousness of it will be in the application of basic chemistry to making something like life.
Thaumaturgy
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7/3/2012 3:03:35 PM
Posted: 11 months ago
At 7/3/2012 10:22:48 AM, Sidewalker wrote:
Perhaps it's plain old chemistry if you ascribe consciousness to plain old matter in some kind of extremely attenuated way

"Consciousness" is probably something more like "emergent complexity" from the system.

We are going to have to go beyond plain old chemistry to find some kind of explanatory principle that connects DNA molecules to their expression of outward form.

Why? Just because something is complex does not mean it is some hugely unrelated concept? It could just be very complex.

When we take an honest look on the broad scales of evolutionary theory it becomes self-evident that the evolution of life shows itself to involve a creative force rather than the adaptive force

Hmmm, I don't see that as a necessity. In fact it kind of works very well. It's a simple system at it's core:

1. Take a self-replicating item which can have changes in the "replication code"
2. Put it in a system where DISADVANTAGES are selected AGAINST (ie "don't survive to reproduction age)
3. Repeat a lot of times
4. Wind up with an item that seems to have been "created" for its environment when in reality it only responded to the "passive filter" of survival

(I'm not saying that is all there is to evolution, but at its core that's a good way to explain how a well-fit organism could be the product just of passive selection against maladaptive features.)

represented by Darwinism's model. We see that life reveals itself to be self-transcendent, constantly reaching out beyond the systems boundaries, and there is some explanatory principle involved that isn't going to be reductionistic in nature.

I don't know what any of that means. Sorry.

I'm merely saying that your materialistic determinism is going to need to be
supplemented by at least a new principle to make some kind of adequate explanatory progress.

That is not necessarily so. Again, putting the "unknown" into a reservoir of some "new principle" may not be necessary when most of the pieces/parts are lying around already. They just need to be properly put together.

The only reality we know directly is experiential, and David Chalmers' hard problem of consciousness simply cannot be reduced to physical and chemical processes in the brain

I am always fascinated by cases where the brain "breaks". A phsyical effect that can bring about dramatic changes in someone's personality, the ability to remember things, etc. etc.

Watching my dad go from one of the smartest guys I knew to someone barely able to construct a coherent sentence longer than 3 words, visiting him in a nursing home populated with people who were little more than babbling blobs but used to be the hearty and hale farmers around town indicated to me that the physical brain can be affected to EFFECT dramatic changes in what we call our "essence".

I see no reason to add in something "other" to the equation. If it can be broken by physical build of plaques or by small strokes (the latter was my dad's thing) or just injury to the brain indicates that it is likely sourced in the physical structure of the brain.

, especially when single celled creatures with no brain or nervous system are demonstrating an attenuated form of consciousness.

How "attenuated" is it? I am extremely skeptical that what you may be calling anything like "consciousness" could even remotely be attributed to a single-celled organism. That seems to be stretching the defintion to extremes.

I know that, it's why I put the word "will" in quotation marks, but as I have explained above, there is something going on that transcends the level of mechanistic explanation. To deny that you pretty much have to deny observations, facts and evidence

Or willfully anthropomorphize chemical reactions.

Perhaps you can limit this to one single example with a citation. I would be interested in reading about this.
Thaumaturgy
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7/3/2012 3:23:56 PM
Posted: 11 months ago
At 7/3/2012 10:27:35 AM, Sidewalker wrote:
No way, the hard problem of consciousness will never reduce down to a mechanistic explanation

Universal negatives? That's a logical minefield.

In my business there is a widely used saying that "Any sufficiently advanced technology is indistinguishable from magic",

So you're an editor for Arthur C. Clarke?

but that it just something we say for comic relief. You don't just get to say "sufficiently complex" and viola, something "emerges" as if by magic, scientifically speaking, it needs to include an effective causal sequence if you are going to call something explanatory, and we both know "magic" doesn't cut it.

Oh I don't expect it to be an explanation. I do, however, expect that the final answers will, if they are ever known, be all physical in nature.

evolutionary theory's requisite abiogenesis problem

Pedantic Clarifiaction: Evolution has nothing to do with abiogenesis. Just an FYI. They are to separate topics.

You reductionists just love to say "it could have just happened" but no, it couldn't, we don't get to invoke "magic" in science.

I pointed out sponges as an example of a transition. Nothing more.

You can't make randomness a principle, randomness is not a principle,

Well, in many ways it is. Chemical reactions, while quite deterministic, often come down to random interactions which define things like rates and yields etc.

Gases are stochastic. Thermodynamics is stochastic. So randomness can be important in science.

it's the absence of a principle,

Not really. As I said: chemical reactions are quite deterministic based on a wide variety of quantum mechanical and stearic factors, but what can make a reaction not happen or happen at a given rate can also relate to the propensity of random interactions.

Remember that a given reaction doesn't just happen if two chemicals bash into each other. They have to bash into each other with the proper orientation and the proper energy. Those things are often the function of "distributions" of energy and orientation.

and when you really think it through, the increasing complexity of the observed universe cannot be explained as fortuitous randomness

Nor would I explain it as such.

No, it isn't just plain old chemistry, its plain old chemistry with a twist added, something else needs to be happening here.

Why?

It's interesting that you added "quantum mechanical interactions" to your description of "plain old" chemistry, quantum mechanics isn't just plain old physics by any stretch of the imagination, and it all really started in 1905 with those three papers young Einstein wrote.

I will quibble with that assessment just a bit. Actually one could go back to Planck's work in 1900 wherein he proposed the first idea of the "quantization" of energy from his work on blackbody radiation. Einstein's later work on the photoelectric effect was also very important. But it could hardly be simply pinned on this one paper. It was much more than just that and it came from a wide variety of sources.

But I digress.



The world is certainly receiving energy from the sun, the differences in temperature provides motive power to the Earth, so spontaneous changes on Earth are accompanied by an increase in randomness of the energy distributed in the system. That's certainly your point, "in theory", when you rely on increasing complexity to account for the "magical" emergence of completely new things

Ummm, not really. I'm not just making an entropy argument here.

, but the law of cause and effect doesn't really allow now things to just "emerge", as if by magic

Nor did I say that. But emergent complexity actually exists.

Here's Goldstein's definition:
Every resultant is either a sum or a difference of the co-operant forces; their sum, when their directions are the same -- their difference, when their directions are contrary. Further, every resultant is clearly traceable in its components, because these are homogeneous and commensurable. It is otherwise with emergents, when, instead of adding measurable motion to measurable motion, or things of one kind to other individuals of their kind, there is a co-operation of things of unlike kinds. The emergent is unlike its components insofar as these are incommensurable, and it cannot be reduced to their sum or their difference. (Lewes 1875, p. 412),

The second law does not take into account the observed fact that natural form building activities are occurring over time. Self-integrated units of matter are in fact observed opposing the predicted statistical trend toward randomness.

Well this may be a fundamental misunderstanding of entropy. Entropy can actually decrease locally, so long as universally it increases. That's how my freezer works. It lowers the entropy in the water molecules as they form ice crystals but in so doing it exhausts heat into the atmosphere thus providing for a net drop in entropy universally. (That's why the closed system part you mentioned earlier is important).

No one said entropy cannot decrease locally.

Manmade systems impose shape and order from outside, and they break down, classical entropy applies there.

Well that's incorrect. When someone "makes something" ('imposes shape and order') I bet every single time you can find that they expended energy in a way such that overall, universally, entropy increased.

In fact I am about as sure of that as I am of just about anything else.
Lasagna
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7/3/2012 4:15:59 PM
Posted: 11 months ago
At 7/2/2012 12:22:32 PM, belle wrote:
At 7/1/2012 8:29:52 PM, Lasagna wrote:
At 7/1/2012 1:27:33 PM, belle wrote:
At 6/29/2012 6:00:55 PM, Lasagna wrote:
A classmate and I had a question for my Bio 1 teacher, which he failed miserably to answer. I'm interested to see if you can do better.

Mitochondria and chloroplasts are said to have evolved from foreign cells that invaded the cells of plants and animals and then evolved into them (I believe this is called endosymbiosis). I cannot make logical sense of this. Evolution is attained through changes in DNA, so how could an organism just evolve into another like this? It seems as implausible as a mother with breast implants giving birth to a child with them as well :P

so basically, you start with two bacterial cells. one engulfs the other and it doesn't die. call them A (the outside cell) and B (the inside cell). then both cells continue to divide. when B divides it makes 2 Bs inside of A. when A divides, the Bs may be split up between progeny, or they may end up clustered in one cell. it doesn't really matter. over generations these cells continue to divide and you end up with a bunch of As with a bunch of Bs inside of them. eventually, B starts to lose some of its genes through random mutation, but since its inside of A it makes no difference- it doesn't need those genes anymore. eventually B can't live except inside of A because its too genetically reduced to carry out all the functions necessary to life. part of the evidence we have for this is that mitochondria and chloroplasts still contain genes of their own and divide semi-independently inside the host cell.

So these B cells are in sperm and eggs and continue to live and divide inside cells and somehow the new B cell always makes it into the new A cell?

well at first it was kind of messy like that, but now theres nuclear genes that control how the mitochondria and chloroplasts get divided up every time the cell divides. those genes developed later though, as a useful adaptation to having these cells living inside you since they benefited the parent cell by being there.

I think I get it now... If I think really hard I can envision it from start to finish :P Thanks for explaining that to me, I always wondered how that possibly could have happened.
Rob
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