Molecular movement in living matter

Evolution, Natural Selection, Medicine, Psychology & Neuroscience.

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Re: Molecular movement in living matter

#81  Postby CharlieM » May 01, 2012 11:52 pm

Rumraket wrote:
CharlieM wrote:
All anyone ever does when pondering on the very beginnings of physical life is to make assumptions.

Nah, you can add doing experiments to that.


And these usually add to the number of assumptions being made. They cannot set up their models without making assumptions.

Rumraket wrote:
CharlieM wrote:Its too remote to do anything else

The conditions extant on the early earth has left evidence in ancient rocks, or specifically the crystals contained in them, like Zircons. That makes it at least partially observational. These observations can then be used as starting points when doing experiments.


In a ScienceDaily news item, Setting the Stage for Life: Scientists Make Key Discovery About the Atmosphere of Early Earth, they have this to say:
For decades, scientists believed that the atmosphere of early Earth was highly reduced, meaning that oxygen was greatly limited. Such oxygen-poor conditions would have resulted in an atmosphere filled with noxious methane, carbon monoxide, hydrogen sulfide, and ammonia. To date, there remain widely held theories and studies of how life on Earth may have been built out of this deadly atmosphere cocktail.

Now, scientists at Rensselaer are turning these atmospheric assumptions on their heads with findings that prove the conditions on early Earth were simply not conducive to the formation of this type of atmosphere, but rather to an atmosphere dominated by the more oxygen-rich compounds found within our current atmosphere -- including water, carbon dioxide, and sulfur dioxide.


So scientists had made assumptions about the atmosphere on the early earth for decades. And they used these assumptions to set up their experiments. Now these assumptions have been turned on their heads. Until the next time when the new assumptions will no doubt be superceded.

Rumraket wrote:
CharlieM wrote:The proposed RNA molecules would be delicate things, how long would they be able to remain in a dormant state?

I see you're arguing from a position of an RNA-first hypothesis. Even if we just run with that, they're still not assumed to be free living, bare molecules. They're envisioned to be enclosed in fatty acid vesicles which live inside precipitated mineral structures near hydrothermal vents. They don't get to survive leaving these conditions until the molecular machinery that allows this has evolved.


I am going with the RNA-first hypothesis because I thought that was the most popular hypothesis at the moment. I'm sure conditions inside these mineral structures would be vastly different from conditions outside in the wide ocean. So the proto-organisms must have fortuitously developed the ability to survive in these external conditions before they actually ventured out into them. They would have had to be pretty sophisticated to be able to survive in both of these diverse environments. After leaving the comfort of their mineral homes they would need energy to build the molecules they needed for survival. Assuming this energy come from chemical reactions there are a few questions I have. How did they convert it into energy they could use? How did these early replicators distinguish between needed chemicals and harmful chemicals and to ingest just the beneficial ones? Were there enough of these required chemicals around away from the original specialized environment? These questions may or may not have been reasonably answered. Either way I'd like to know what the answers are.

Rumraket wrote:
Again you're infusing nature with teleology.


Nature is already infused with teleology. It is evident in such things as birds building nests, sperm and egg coming together, mason wasps building their little prisons.

Rumraket wrote:
It would be more correct to say that life managed to evolve the ability to spread out and thrive.


Yes the same way that a zygote manages to spread out and develop. It can do this because the environment that it moves into is fit for it to thrive.

Rumraket wrote:
CharlieM wrote:Okay so they could synthesize ribose, but you have to assume that in the wider environment there were ample amino acids and phosphates too.

Why do I have to assume that? Why can't they have evolved the ability to synthesize these compounds themselves from the bottom-up, like chemoautotrophs do today near hydrothermal vents and in the earth's crust?


So, while still in their original environment, did they also evolve the necessary mechanisms to use chemicals other than they were used to dealing with?

Rumraket wrote:
CharlieM wrote:Most of the phosphates on earth were locked in the rocks. A solution to the phosphate problem has been proposed. Meteorites seeded the earth with suitable amounts of phosphate before life got going. That was convenient.

Teleology all over again.


Yes it seems to be ubiquitous. :)

Rumraket wrote:
CharlieM wrote:And maybe the amino acids were delivered by comets.

No, they were first synthesized in atmospheric and geochemical reactions, then later a method of their synthesis evolved.


In other words your assumption trumps that of Jennifer G. Blank, Ph.D and her team as reported here
Rumraket wrote:
CharlieM wrote:Some people might think that the earth was being primed to assist in the arrival and spread of life.

And then the people who aren't nuts realise that we should only expect life to originate where it can.


And it could because conditions had been well prepared.

Rumraket wrote:
CharlieM wrote:And of course most people might assume that it was just another lucky accident :wink: :wink:

Your caricture doesn't mean it didn't happen, and the event itself isn't evidence that it was planned. It's a bit like the extremely improbable series of events required throughout the history of the planet that lead to the 2004 Indian Ocean earthquake and tsunami.

The only reason you happen to ascribe any meaning to the origin of life is because you supposedly resulted from it. It's a bit telling why you aren't all up in your arms about the very special conditions that, for example, produced the great red spot on jupiter. Was that intended too?


Speaking of Jupiter, here is someone who thinks its presence is necessary for life to develop on earth:
Solar systems that lack a Jupiter-sized object that can perturb mineral-rich asteroids inward toward terrestrial planets also have dim prospects for developing life, Lauretta added.


You continue:

Rumraket wrote:
I think you'd be even more surprised if we found we were the product of events that couldn't lead to us. The realization that conditions that favored the origin of life, were extant at the origin of life really shouldn't surprise anyone. Ever heard of Douglas Adams puddle?


Its no surprise that Douglas Adams puddle fits so well into its environment. What it should ask itself is, "Why have I been given the ability to ponder my own existance? After all I would fit in just as well whether I was aware of the fact or not. My existence does not depend on my awareness, so why do I have this ability?
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Re: Molecular movement in living matter

#82  Postby CharlieM » May 02, 2012 12:05 am

Sityl wrote:After reading this thread, I can say with cerainty that if I were still a creationist, I'd be hanging my head in shame at the lengths some go to keep confirmation bias alive. Ultimately, the problem is that if you're viewing something with a preconceived narrative of what the answer will be, you'll skew all evidence that you see. This is why it's so important to base worldviews on evidence, else we shape the evidence to our worldview, and fail at discovering reality.


I too think its important to base my worldview on evidence. Not the evidence gathered by doing lab experiments or making models of supposed reality, but the evidence gained from patiently studying nature directly.
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Re: Molecular movement in living matter

#83  Postby DavidMcC » May 02, 2012 8:49 am

CharlieM wrote:Not the evidence gathered by doing lab experiments or making models of supposed reality, but the evidence gained from patiently studying nature directly.

And you think that Darwin didn't gather evidence by direct study of nature during his Beagle voyage?
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Re: Molecular movement in living matter

#84  Postby DavidMcC » May 02, 2012 8:53 am

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Re: Molecular movement in living matter

#85  Postby CharlieM » May 02, 2012 2:26 pm

DavidMcC wrote:
CharlieM wrote:Not the evidence gathered by doing lab experiments or making models of supposed reality, but the evidence gained from patiently studying nature directly.

And you think that Darwin didn't gather evidence by direct study of nature during his Beagle voyage?


Darwin is a good example of a brilliant naturalist. By his observations it was demonstrated that species aren't immutable, that life evolves over time. David Attenborough is another good example of someone who brings to the general public their enthusiasm of the natural world.

So I think that through his writings Darwin furthered our understanding of the natural world by a tremendous amount, because he was such a good observer of nature.
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Re: Molecular movement in living matter

#86  Postby Rumraket » May 02, 2012 5:09 pm

CharlieM wrote:
Rumraket wrote:
CharlieM wrote:
All anyone ever does when pondering on the very beginnings of physical life is to make assumptions.

Nah, you can add doing experiments to that.

And these usually add to the number of assumptions being made.

No, they work from the assumptions made.

CharlieM wrote:
Rumraket wrote:
CharlieM wrote:Its too remote to do anything else

The conditions extant on the early earth has left evidence in ancient rocks, or specifically the crystals contained in them, like Zircons. That makes it at least partially observational. These observations can then be used as starting points when doing experiments.

In a ScienceDaily news item, Setting the Stage for Life: Scientists Make Key Discovery About the Atmosphere of Early Earth, they have this to say:
For decades, scientists believed that the atmosphere of early Earth was highly reduced, meaning that oxygen was greatly limited. Such oxygen-poor conditions would have resulted in an atmosphere filled with noxious methane, carbon monoxide, hydrogen sulfide, and ammonia. To date, there remain widely held theories and studies of how life on Earth may have been built out of this deadly atmosphere cocktail.

Now, scientists at Rensselaer are turning these atmospheric assumptions on their heads with findings that prove the conditions on early Earth were simply not conducive to the formation of this type of atmosphere, but rather to an atmosphere dominated by the more oxygen-rich compounds found within our current atmosphere -- including water, carbon dioxide, and sulfur dioxide.


So scientists had made assumptions about the atmosphere on the early earth for decades. And they used these assumptions to set up their experiments. Now these assumptions have been turned on their heads. Until the next time when the new assumptions will no doubt be superceded.

Why should they? The strange thing is you seem to think life did actually originate in some way which I gather you think was extremely fortuitous and therefore "planned/primed", though not strictly interventional. Whether that's correct or not, why can't these latest findings you link actually constitute some of the relevant conditions that were extant on the early earth? Do you think finding out is impossible?

CharlieM wrote:
Rumraket wrote:
CharlieM wrote:The proposed RNA molecules would be delicate things, how long would they be able to remain in a dormant state?

I see you're arguing from a position of an RNA-first hypothesis. Even if we just run with that, they're still not assumed to be free living, bare molecules. They're envisioned to be enclosed in fatty acid vesicles which live inside precipitated mineral structures near hydrothermal vents. They don't get to survive leaving these conditions until the molecular machinery that allows this has evolved.

I am going with the RNA-first hypothesis because I thought that was the most popular hypothesis at the moment. I'm sure conditions inside these mineral structures would be vastly different from conditions outside in the wide ocean. So the proto-organisms must have fortuitously developed the ability to survive in these external conditions before they actually ventured out into them. They would have had to be pretty sophisticated to be able to survive in both of these diverse environments. After leaving the comfort of their mineral homes they would need energy to build the molecules they needed for survival. Assuming this energy come from chemical reactions there are a few questions I have. How did they convert it into energy they could use?

One hypothesis is that photosynthesis evolved very early(before life left it's mineral habitats, see This and This. ), providing the necessary energy to fuel metabolism. Some of the earliest evidence for life is of photosynthesizing life at >3.7 Ga.
http://isites.harvard.edu/fs/docs/icb.topic463355.files/Readings%20for%20Discussion%20Sept%2022/Rosing%20and%20Frei%202004.pdf
U-rich Archaean sea-£oor sediments from Greenland ^ indications of 3700 Ma oxygenic photosynthesis
Abstract
s3700 Ma metamorphosed pelagic shale from West Greenland contains up to 0.4 wt% reduced carbon with N13C
values down to 325.6x [PDB, PeeDee Belemnite]. The isotopic signature and mode of occurrence suggest that the
carbon derived from planktonic organisms. The Pb isotopic composition shows that the shale had high primary U/Th.
This indicates that organic debris produced a local reducing environment which precipitated U transported to the site
of sedimentation by oxidized ocean water. The existence of highly productive plankton that fractionated C isotopes
strongly and set up oxidation contrast in the environment suggests that oxygenic photosynthesis evolved before 3700
Ma.

Interestingly this evidence of life is older than how far back we can go with phylogenetic reconstruction. This indicates photosynthesis evolved at least as early as DNA, and possible as far back as the RNA-world itself.

CharlieM wrote:How did these early replicators distinguish between needed chemicals and harmful chemicals and to ingest just the beneficial ones?

Maybe they didn't initially. Maybe those that didn't died out. That's normally how evolution works. The question is which/how many "harmful chemicals" were present?

CharlieM wrote:Were there enough of these required chemicals around away from the original specialized environment? These questions may or may not have been reasonably answered. Either way I'd like to know what the answers are.

I can't give you a complete picture here, I'm not that familiar with the subject. I can point you to litterature that attempts to answer some of these questions though. But as before, they're speculations of course, or "assumptions". The question is whether they're unreasonable. Most OOL scenarios to build on knowledge of extant processes on earth, like the existence of chemical and thermal gradients, geochemical processes etc. etc.

CharlieM wrote:
Rumraket wrote:
Again you're infusing nature with teleology.

Nature is already infused with teleology. It is evident in such things as birds building nests, sperm and egg coming together, mason wasps building their little prisons.

I'm afraid that teleology is either entirely in your own head, or evolved instinctual behavior. It seems to me there's a qualitative difference between stating that some given chemical reaction or physical process has been infused with intentions, or to say that a wasp intends to build a nest. The wasp may in some sense know what it's doing, perhaps at an extrely primitive level, but I can't see how sperm entering an egg could ever be said to contain the same level of intentions except in the most allegorical/metaphorical sense.

CharlieM wrote:
Rumraket wrote:
It would be more correct to say that life managed to evolve the ability to spread out and thrive.

Yes the same way that a zygote manages to spread out and develop. It can do this because the environment that it moves into is fit for it to thrive.

That's like saying a boulder intends to roll downhill. Both of them have evolved by fitting together. This process doesn't require some overarching design or planning.

CharlieM wrote:
Rumraket wrote:
CharlieM wrote:Okay so they could synthesize ribose, but you have to assume that in the wider environment there were ample amino acids and phosphates too.

Why do I have to assume that? Why can't they have evolved the ability to synthesize these compounds themselves from the bottom-up, like chemoautotrophs do today near hydrothermal vents and in the earth's crust?

So, while still in their original environment, did they also evolve the necessary mechanisms to use chemicals other than they were used to dealing with?

I think there's a gradient in contemporary models, where organisms at the "root" of the origin are dependent on organics supplied by geochemical sythesis, and as they get further away in the network of mineral structures, they're gradually exposed to greater concentrations of external compounds and inversely, a drop in the amount of the original compounds, providing a gradual shift in the extant selective pressures.

CharlieM wrote:
Rumraket wrote:
CharlieM wrote:Most of the phosphates on earth were locked in the rocks. A solution to the phosphate problem has been proposed. Meteorites seeded the earth with suitable amounts of phosphate before life got going. That was convenient.

Teleology all over again.

Yes it seems to be ubiquitous. :)

In your posts. Unfortunately, in nature the teleology you apparently see is of your own making.

CharlieM wrote:
Rumraket wrote:
CharlieM wrote:And maybe the amino acids were delivered by comets.

No, they were first synthesized in atmospheric and geochemical reactions, then later a method of their synthesis evolved.

In other words your assumption trumps that of Jennifer G. Blank, Ph.D and her team as reported here

Wow, a PhD and all.
Seriously, all they did was ask the question if amino acids could have been supplied from space and then proceed to do some experiments with high-energy impacts. They haven't got a model for the origin of life in there, which means they aren't making assumptions of relevance to the specific models I have alluded to. Whether amino acids could have been delivered from space or not doesn't change anything with respect to the scenarios I have described. There's nothing that would prevent both processes from taking place. So amino-acids could have been delivered from space and produced in atmospheric and geochemical reactions. Turns out life is even more plausible then. :roll:

CharlieM wrote:
Rumraket wrote:
CharlieM wrote:Some people might think that the earth was being primed to assist in the arrival and spread of life.

And then the people who aren't nuts realise that we should only expect life to originate where it can.

And it could because conditions had been well prepared.

Blind assertion again. There's no reason to assume they were planned, and the process itself isn't evidence that the process was planned. You seem to have a hard time grasping this elementary concept. I can throw a rock over a wall and hit someone in the head without it ever having been my intention. This demonstrates how an event cannot in itself serve as evidence of any intentions behind the event. This should settle this matter to any rational person.

The event itself cannot serve as evidence that the event was intended.

The event itself cannot serve as evidence that the event was intended.

The event itself cannot serve as evidence that the event was intended.

The event itself cannot serve as evidence that the event was intended.

The event itself cannot serve as evidence that the event was intended.

Seriously, I can't emphasize this enough, because it's the one fundamental mistake you keep making.

CharlieM wrote:
Rumraket wrote:
CharlieM wrote:And of course most people might assume that it was just another lucky accident :wink: :wink:

Your caricture doesn't mean it didn't happen, and the event itself isn't evidence that it was planned. It's a bit like the extremely improbable series of events required throughout the history of the planet that lead to the 2004 Indian Ocean earthquake and tsunami.

The only reason you happen to ascribe any meaning to the origin of life is because you supposedly resulted from it. It's a bit telling why you aren't all up in your arms about the very special conditions that, for example, produced the great red spot on jupiter. Was that intended too?


Speaking of Jupiter, here is someone who thinks its presence is necessary for life to develop on earth:
Solar systems that lack a Jupiter-sized object that can perturb mineral-rich asteroids inward toward terrestrial planets also have dim prospects for developing life, Lauretta added.

Yes and as it turns out, plenty solar systems have Jupiter sized (or actually bigger) gas-giants. Check the masses on those motherfuckers. :lol:

CharlieM wrote:
Rumraket wrote:
I think you'd be even more surprised if we found we were the product of events that couldn't lead to us. The realization that conditions that favored the origin of life, were extant at the origin of life really shouldn't surprise anyone. Ever heard of Douglas Adams puddle?


Its no surprise that Douglas Adams puddle fits so well into its environment. What it should ask itself is, "Why have I been given the ability to ponder my own existance?

No, because that would constitute an unwarranted loaded question. The first question should be "How did I come to ponder my own existence?". There's no reason to presuppose it was "given", or that it's a "why" question at all.

CharlieM wrote:After all I would fit in just as well whether I was aware of the fact or not. My existence does not depend on my awareness, so why do I have this ability?

And you would live equally well with a lot less sand under your toenails, yet there it is. That doesn't mean it was anythings intention.
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Re: Molecular movement in living matter

#87  Postby DavidMcC » May 03, 2012 10:11 am

Charlie, if you think that JG Blank's rail gun experiments was anything other than further evidence that abiogenesis could have happened on earth, you need to think again. The combination of comet collisions generating polypeptides from amino acids on the comets, adding to the "soup" generated by lightning strikes on sea water in an atmosphere very different from today's, further enhanced the chances of life forming on the earth. The ocean currents would eventually have brought the various molecules together on catalytic rock surfaces, and that's how the first life could have appeared.
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Re: Molecular movement in living matter

#88  Postby Spearthrower » May 12, 2012 6:07 am

CharlieM wrote:
DavidMcC wrote:... Furthermore, most of the gut flora and fauna are in a symbiotic relationship with us. The bad guys, like E. coli, are the exception, not the rule.
http://en.wikipedia.org/wiki/Intestinal_flora
Though people can survive without gut flora,[4] the microorganisms perform a host of useful functions, such as fermenting unused energy substrates, training the immune system, preventing growth of harmful, pathogenic bacteria,[2] regulating the development of the gut, producing vitamins for the host (such as biotin and vitamin K), and producing hormones to direct the host to store fats.


Furthermore, there is an evolutionary reason for this. Those gut bacteria that help their host would flourish better than those that harmed them.


Yes life can be viewed as a coordinated, symbiotic development. Seeing life as a struggle for existence is a narrow point of view that doesn't see the bigger picture.



A forest isn't a coordinated, symbiotic development - it's a vicious struggle for survival. Comforting notions do not intrinsically equate to reality.
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Re: Molecular movement in living matter

#89  Postby CharlieM » May 15, 2012 10:48 pm

Spearthrower wrote:
CharlieM wrote:
Yes life can be viewed as a coordinated, symbiotic development. Seeing life as a struggle for existence is a narrow point of view that doesn't see the bigger picture.


A forest isn't a coordinated, symbiotic development - it's a vicious struggle for survival. Comforting notions do not intrinsically equate to reality.


You're making my point for me. For a start 'vicious' is not an adjective I would use in connection with the plant life of a
forest. I wouldn't even use it for the animals. I would say that vice as a human failing and doesn't apply to the individuals of any other species. And why do you think that coordinated, symbiotic development is a comforting notion? The successful survival of wildebeest as a species involves the pain and suffering of individual animals. The coordinated death of countless bone cells go into the making of a vertebrate's skeleton.

Forests are regarded as ecosystems which sustain themselves despite and because of the fact that within the system individual organisms live and die. The ecosystem couldn't be sustained without the death of individual organisms.

And to bring this back on topic an average individual human cell is a community of molecules working together to ensure the coordinated function of the whole. Calculations indicate that each human cell contains roughly a billion protein molecules. This needs incredible organization.

Molecular Motors in Cells Work Together, Study Shows

February 13, 2009 — Even within cells, the left hand knows what the right hand is doing.

Molecular motors, the little engines that power cell mobility and the ability of cells to transport internal cargo, work together and in close coordination, according to a new finding by researchers at the University of Virginia. The work could have implications for the treatment of neurodegenerative disorders.

"We found that molecular motors operate in an amazingly coordinated manner when moving an algal cell one way or the other,"

said Jeneva Laib, the lead author and an undergraduate biomedical engineering student at the University of Virginia. "This provides a new understanding of the ways cells move."


Scientists Discover How Molecular Motors Go Into "Energy Save Mode"

PITTSBURGH—The transport system inside living cells is a well-oiled machine with tiny protein motors hauling chromosomes,

neurotransmitters and other vital cargo around the cell. These molecular motors are responsible for a variety of critical transport jobs, but they are not always on the go. They can put themselves into “energy save mode” to conserve cellular fuel and, as a consequence, control what gets moved around the cell, and when.
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Re: Molecular movement in living matter

#90  Postby Spearthrower » May 16, 2012 4:24 am

CharlieM wrote:
Spearthrower wrote:
CharlieM wrote:
Yes life can be viewed as a coordinated, symbiotic development. Seeing life as a struggle for existence is a narrow point of view that doesn't see the bigger picture.


A forest isn't a coordinated, symbiotic development - it's a vicious struggle for survival. Comforting notions do not intrinsically equate to reality.


You're making my point for me. For a start 'vicious' is not an adjective I would use in connection with the plant life of a
forest.


Precisely why you are mistaken - you are conceiving of things from the human perspective. Just because trees move slowly, doesn't mean that they're not cutthroat.

CharlieM wrote:I wouldn't even use it for the animals.


Haven't spent much time in the natural world then, have you? :)


CharlieM wrote: I would say that vice as a human failing and doesn't apply to the individuals of any other species.


That's some kind of mystical thinking, possibly connected to a religious narrative rather than drawn from observations of nature. Humans are far less vicious than the majority of animal species - we don't eat each others babies, attack on site, or murder in gangs very often. We're a very gentle social species for the most part - I'd guess you're putting an additional value on mindfulness - knowing that one is doing the act. That very element of knowing what is right and wrong for our society is the thing that keeps the majority of us in line.


CharlieM wrote: And why do you think that coordinated, symbiotic development is a comforting notion? The successful survival of wildebeest as a species involves the pain and suffering of individual animals. The coordinated death of countless bone cells go into the making of a vertebrate's skeleton.


Because it makes you believe its operating to a plan?


CharlieM wrote:Forests are regarded as ecosystems which sustain themselves despite and because of the fact that within the system individual organisms live and die. The ecosystem couldn't be sustained without the death of individual organisms.


There's a constant war for resources - it's a bit like if there was a limited amount of oxygen, so we strangled our neighbours to ensure our own survival.


CharlieM wrote:And to bring this back on topic an average individual human cell is a community of molecules working together to ensure the coordinated function of the whole. Calculations indicate that each human cell contains roughly a billion protein molecules. This needs incredible organization.


Yes, a body is a community of molecules - but they don't all work together, even detrimental rogue genes make a perfectly good living.

And yes, 'incredible organisation' like hydrogen and oxygen combining.


CharlieM wrote:
Molecular Motors in Cells Work Together, Study Shows

February 13, 2009 — Even within cells, the left hand knows what the right hand is doing.

Molecular motors, the little engines that power cell mobility and the ability of cells to transport internal cargo, work together and in close coordination, according to a new finding by researchers at the University of Virginia. The work could have implications for the treatment of neurodegenerative disorders.

"We found that molecular motors operate in an amazingly coordinated manner when moving an algal cell one way or the other,"

said Jeneva Laib, the lead author and an undergraduate biomedical engineering student at the University of Virginia. "This provides a new understanding of the ways cells move."


Scientists Discover How Molecular Motors Go Into "Energy Save Mode"

PITTSBURGH—The transport system inside living cells is a well-oiled machine with tiny protein motors hauling chromosomes,

neurotransmitters and other vital cargo around the cell. These molecular motors are responsible for a variety of critical transport jobs, but they are not always on the go. They can put themselves into “energy save mode” to conserve cellular fuel and, as a consequence, control what gets moved around the cell, and when.


Yes, but what's the point of sharing all this? Humans use metaphors to pass ideas between each other. A cell is not a machine, but a good way of communicating this so that others who have not witnessed it first hand, is to use a mechanism we know that mimics this: a machine. You can glean this with the 'energy saving mode' - clearly an analogy to promulgate a general understanding.
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Re: Molecular movement in living matter

#91  Postby Rumraket » May 16, 2012 7:37 am

CharlieM has this strange habit of linking some obscure article with a number of quotes about how wonderful and complex living systems are, then back it up with some bits of vague and arbitrary declarations like the need for "incredible" organization.

He seems to think this constitutes evidence for something, like his planning for perfection and love thingie or whatever it was. Somehow he just has this deep aversion to randomness. It just can't be probabilistic, it has to be planned. But as I've said before, the thing itself cannot be evidence of it having a planned/"primed" origin.
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Re: Molecular movement in living matter

#92  Postby DavidMcC » May 16, 2012 3:24 pm

Rumraket wrote:CharlieM has this strange habit of linking some obscure article with a number of quotes about how wonderful and complex living systems are, then back it up with some bits of vague and arbitrary declarations like the need for "incredible" organization.

He seems to think this constitutes evidence for something, like his planning for perfection and love thingie or whatever it was. Somehow he just has this deep aversion to randomness. It just can't be probabilistic, it has to be planned. But as I've said before, the thing itself cannot be evidence of it having a planned/"primed" origin.


Yeah! He should watch a flock of quelia finches and read how they do it without careful top-down co-ordination effort!
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Re: Molecular movement in living matter

#93  Postby CharlieM » May 16, 2012 4:52 pm

Rumraket wrote:CharlieM has this strange habit of linking some obscure article with a number of quotes about how wonderful and complex living systems are, then back it up with some bits of vague and arbitrary declarations like the need for "incredible" organization.

He seems to think this constitutes evidence for something, like his planning for perfection and love thingie or whatever it was. Somehow he just has this deep aversion to randomness. It just can't be probabilistic, it has to be planned. But as I've said before, the thing itself cannot be evidence of it having a planned/"primed" origin.


I have nothing against randomness, its a fact of life. What I am against is an unjustified assumption of randomness due to a prior belief in how things are supposed to operate. To give an example, here is quote from the book, Life Itself: Exploring the Realm of the Living Cell by Boyce Rensberger in 1998:

Whatever the source of the signal, its effect is to work within the nucleus, seeking out the regulatory portions of DNA
that govern the specific gene it "wants" to activate. The signal proteins must find and bind to the regulatory segments to cause a given gene's message to be "expressed" or, depending on the signal, to prevent expression. The sequence of DNA bases that constitute a gene's "on" switch is positioned next to the "go" signal at the beginning of the genetic sentence. Also taking part in the process are other regulatory sequences that are often situated some distance away from the gene. At one time it was assumed that the signal proteins wandered aimlessly within the nucleus until they chanced to bump into their target sequence. Now it is clear that they don't. They grab onto a DNA strand and "walk" along it, "looking" for the sequence - yet another example of the role of autonomous motion in life. Even though the molecule may have to walk a long way to find its gene (many miles in the living-room cell nucleus), the process is roughly 100 million times more efficient than simply bouncing around inside the nucleus.


Why did they automatically assume that the regulatory proteins just bounced around aimlessly? They could have said that they didn't yet know how these regulators found their target but they didn't; they assumed a blind unguided process at work. Their beliefs were found to be unjustified in light of the facts.

If we are not in possession of all the facts would it not be better to say that a certain process might turn out to be the result of random processes but on the other hand it might not.
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Re: Molecular movement in living matter

#94  Postby Spearthrower » May 16, 2012 4:59 pm

Rumraket wrote:CharlieM has this strange habit of linking some obscure article with a number of quotes about how wonderful and complex living systems are, then back it up with some bits of vague and arbitrary declarations like the need for "incredible" organization.


Hmm, I see.

I wonder what properties this notion possesses over and above 'credible organisation'. I think it's quite safe to just remove the unnecessary adjective.

Organisation in nature is a product of conflicting forces, not an orchestrated intentional event.

Snow drifts are 'organised' by the wind, by the aerodynamic qualities of the various geometric shapes on the ground, and gravity. They come out fairly highly organised, and are quite repeatable given very similar circumstances. Something can be 'incredible' in the sense of looking at the final product, but perfectly mundane when looking at how it arrived at that level of organisation.
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Re: Molecular movement in living matter

#95  Postby Rumraket » May 16, 2012 6:32 pm

CharlieM wrote:
Rumraket wrote:CharlieM has this strange habit of linking some obscure article with a number of quotes about how wonderful and complex living systems are, then back it up with some bits of vague and arbitrary declarations like the need for "incredible" organization.

He seems to think this constitutes evidence for something, like his planning for perfection and love thingie or whatever it was. Somehow he just has this deep aversion to randomness. It just can't be probabilistic, it has to be planned. But as I've said before, the thing itself cannot be evidence of it having a planned/"primed" origin.


I have nothing against randomness, its a fact of life. What I am against is an unjustified assumption of randomness due to a prior belief in how things are supposed to operate. To give an example, here is quote from the book, Life Itself: Exploring the Realm of the Living Cell by Boyce Rensberger in 1998:

Whatever the source of the signal, its effect is to work within the nucleus, seeking out the regulatory portions of DNA
that govern the specific gene it "wants" to activate. The signal proteins must find and bind to the regulatory segments to cause a given gene's message to be "expressed" or, depending on the signal, to prevent expression. The sequence of DNA bases that constitute a gene's "on" switch is positioned next to the "go" signal at the beginning of the genetic sentence. Also taking part in the process are other regulatory sequences that are often situated some distance away from the gene. At one time it was assumed that the signal proteins wandered aimlessly within the nucleus until they chanced to bump into their target sequence. Now it is clear that they don't. They grab onto a DNA strand and "walk" along it, "looking" for the sequence - yet another example of the role of autonomous motion in life. Even though the molecule may have to walk a long way to find its gene (many miles in the living-room cell nucleus), the process is roughly 100 million times more efficient than simply bouncing around inside the nucleus.


Why did they automatically assume that the regulatory proteins just bounced around aimlessly? They could have said that they didn't yet know how these regulators found their target but they didn't; they assumed a blind unguided process at work. Their beliefs were found to be unjustified in light of the facts.

If we are not in possession of all the facts would it not be better to say that a certain process might turn out to be the result of random processes but on the other hand it might not.

What possible difference does it make? All the article says is that it was "thought". It's not like this thought hindered the discovery of the actual mechanism anyway.
Towards equilibrum-diffusion and brownian motion is the basic behavior of matter in liquids, this knowledge doesn't come with a dogmatic insistence that exceptions don't exist. And with regards to this specific example, there's still a possibility that the regulatory protein randomly drifts around in the nucleus until it hits DNA and then attaches and starts the "walk", instead of just drifting around until it happens to be lucky enough to hit the specific target sequence.
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Re: Molecular movement in living matter

#96  Postby CharlieM » May 16, 2012 10:02 pm

Spearthrower wrote:
Organisation in nature is a product of conflicting forces, not an orchestrated intentional event.


The organization is not so much the product of conflicting forces. It is more accurate to say that conflicting forces are used in the organization.

From [url]http://www.meduniwien.ac.at/homepage/news-and-topstories/en/?tx_ttnews[tt_news]=2270&cHash=2d042440f3[/url] MedUni Vienna: Key gene function against cell death discovered
The human body maintains a stable equilibrium between cell death and the breakdown of tissue and the regeneration of tissue from stem cells. Stem cells have the potential to develop into other types of cells such as skin, muscle or nerve cells and are therefore crucial for the rebuilding of tissue. A human stomach cells, for example, lives only two days. Skin cells live for up to four weeks. A lung cell dies after around 80 days and a red blood cell dies after around 120 days.

The two proteins TSC (tuberin) and PRAS40 are crucial for this development, deciding whether the stem cell develops correctly or undergoes apoptosis, a form of programmed cell death. They act, as it were, as ‘gatekeepers’.


The question is, what is doing the organizing? The researchers imply, in this case, that it is the human body. This is rather vague which isn't very surprising as it is something that's very hard to pin down. It is certainly not the genome that's doing the organizing. The genome of itself can do nothing and also the same genome sits in the stomach cells and in the skin cells.

Spearthrower wrote:
Snow drifts are 'organised' by the wind, by the aerodynamic qualities of the various geometric shapes on the ground, and gravity. They come out fairly highly organised, and are quite repeatable given very similar circumstances. Something can be 'incredible' in the sense of looking at the final product, but perfectly mundane when looking at how it arrived at that level of organisation.



You are comparing snow drifts with this!

[youtube]http://www.youtube.com/watch?v=yKW4F0Nu-UY[/youtube]
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Re: Molecular movement in living matter

#97  Postby Rumraket » May 17, 2012 5:53 am

CharlieM wrote:
Spearthrower wrote:
Organisation in nature is a product of conflicting forces, not an orchestrated intentional event.


The organization is not so much the product of conflicting forces. It is more accurate to say that conflicting forces are used in the organization.

From [url]http://www.meduniwien.ac.at/homepage/news-and-topstories/en/?tx_ttnews[tt_news]=2270&cHash=2d042440f3[/url] MedUni Vienna: Key gene function against cell death discovered
The human body maintains a stable equilibrium between cell death and the breakdown of tissue and the regeneration of tissue from stem cells. Stem cells have the potential to develop into other types of cells such as skin, muscle or nerve cells and are therefore crucial for the rebuilding of tissue. A human stomach cells, for example, lives only two days. Skin cells live for up to four weeks. A lung cell dies after around 80 days and a red blood cell dies after around 120 days.

The two proteins TSC (tuberin) and PRAS40 are crucial for this development, deciding whether the stem cell develops correctly or undergoes apoptosis, a form of programmed cell death. They act, as it were, as ‘gatekeepers’.


The question is, what is doing the organizing? The researchers imply, in this case, that it is the human body. This is rather vague which isn't very surprising as it is something that's very hard to pin down. It is certainly not the genome that's doing the organizing. The genome of itself can do nothing and also the same genome sits in the stomach cells and in the skin cells.

Of course it's the genome, or more correctly, it's the interaction of the genome with the environment of the cell. I've already given you an example of a regulatory mechanism. The stomach cells have a different environment than the skin cells. It's the interactions of the regulatory mechanism with their requisite cell environments that "produce" said organization.

CharlieM wrote:
Spearthrower wrote:
Snow drifts are 'organised' by the wind, by the aerodynamic qualities of the various geometric shapes on the ground, and gravity. They come out fairly highly organised, and are quite repeatable given very similar circumstances. Something can be 'incredible' in the sense of looking at the final product, but perfectly mundane when looking at how it arrived at that level of organisation.

You are comparing snow drifts with this!

Yes and it's essentially the same. Given the right conditions, however fucking many of them it takes and however specifically arranged they are, the unguided forces of nature can give rise to that. The thing itself isn't evidence that it was the product of a plan.
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Re: Molecular movement in living matter

#98  Postby DavidMcC » May 17, 2012 1:12 pm

CharlieM wrote:It is certainly not the genome that's doing the organizing. The genome of itself can do nothing and also the same genome sits in the stomach cells and in the skin cells.

Of course the genome does things. The different cellular environments (including the cell membrane) of different cell types produces different gene expression, apart from those genes that are essential to the functioning of the cell itself. In multicellular species, chromosomes have been selected for because they can and do turn most of theose genes that are not essential for a living cell permanently off in any one cell type. Organismal death would be rapid if this failed completely. Thus, the same genome can reliably do different things in different cell types.
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Re: Molecular movement in living matter

#99  Postby DavidMcC » May 17, 2012 2:36 pm

CharlieM, the "Inner Life of a Cell" video, whilst fascinating, is misleading in a particular way - almost the only the molecules that are shown are those for which the right domain happens to find the right domain in some other molecule for the given process to proceed. This gives the misleading impression of some kind of top-down co-ordination of molecular movement, which does not exist in reality. This may make the video appealing to "intelligent evolutionists", but it does not make it scientifically accurate. Remember the video on apoptosis some months ago? That was made along the same lines, but with the significant difference that it showed ALL the molecules, not just selected ones.
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Re: Molecular movement in living matter

#100  Postby Spearthrower » May 18, 2012 1:53 pm

CharlieM wrote:
Spearthrower wrote:
Organisation in nature is a product of conflicting forces, not an orchestrated intentional event.


The organization is not so much the product of conflicting forces. It is more accurate to say that conflicting forces are used in the organization.


No, you've added a teleology there that's not evident or supported.


CharlieM wrote:The question is, what is doing the organizing? The researchers imply, in this case, that it is the human body. This is rather vague which isn't very surprising as it is something that's very hard to pin down. It is certainly not the genome that's doing the organizing. The genome of itself can do nothing and also the same genome sits in the stomach cells and in the skin cells.


Not the human body, but the chemical environment within the human body, in an isolated package - the cell.


CharlieM wrote:
Spearthrower wrote:
Snow drifts are 'organised' by the wind, by the aerodynamic qualities of the various geometric shapes on the ground, and gravity. They come out fairly highly organised, and are quite repeatable given very similar circumstances. Something can be 'incredible' in the sense of looking at the final product, but perfectly mundane when looking at how it arrived at that level of organisation.



You are comparing snow drifts with this!

[youtube]http://www.youtube.com/watch?v=yKW4F0Nu-UY[/youtube]


Yes, that's precisely what I am comparing it to. Just think - what are the chances that all of those billions of flakes of snow, being blown about in the wind, will settle in such an ordered shape? Moreover, new drifts will form with the same contours in the same places again and again.

Obviously the 2 scenarios use completely different mechanisms, but the organisation element is functionally analogous. The result is not the consequence of intent, but of physical forces and constraints - in evolutionary terms, there's a mechanism you know as natural selection that provides the analogous walls, lean-to's, and eddies in the snowdrift scenario.

Also obviously, the entire point of living organisms is the hereditary retention of beneficial changes to the organisation process itself. In fact, snow flake settling is far harder to predict - it's far more chaotic, as it doesn't have a process that stabilises it over generations.
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