Cells and life

[mellestad]

Pretty fascinating stuff.  The idea that the cells in critters (including us) function as autonomous entities that do not receive input from the brain is rather trippy.  It certainly makes you think about what it means to be alive when the bulk of our bodies run on their own, relying on the greater body only for energy.

The stuff about neurons is neat too, if he is right and an individual neuron cell is actually a complex mechanism that operates distinctively that means 'intelligence' is far more complex than we've thought previously.  Instead of 100 billion organic transistors in the brain we would have 100 billion individual processing units in the brain.

http://www.newscientist.com/article/mg20627571.100-the-secrets-of-intelligence-lie-within-a-single-cell.html?full=true

LATE at night on a sultry evening, I watch intently as the predator senses its prey, gathers itself, and strikes. It could be a polecat, or even a mantis - but in fact it's a microbe. The microscopic world of the single, living cell mirrors our own in so many ways: cells are essentially autonomous, sentient and ingenious. In the lives of single cells we can perceive the roots of our own intelligence.

Molecular biology and genetics have driven the biosciences, but have not given us the miraculous new insights we were led to expect. From professional biologists to schoolchildren, people are concentrating on the minutiae of what goes on in the deepest recesses of the cell. For me, however, this misses out on life in the round: it is only when we look at the living cell as a whole organism that wonderful realities emerge that will alter our perception not only of how single cells enact their intricate lives but what we humans truly are.

The problem is that whole-cell biology is not popular. Microscopy is hell-bent on increased resolution and ever higher magnification, as though we could learn more about animal behaviour by putting a bacon sandwich under lenses of increasing power. We know much about what goes on within parts of a cell, but so much less about how whole cells conduct their lives.

Currently, cell biology deals largely with the components within cells, and systems biology with how the components interact. There is nothing to counterbalance this reductionism with a focus on how whole cells behave. Molecular biology and genetics are the wrong sciences to tackle the task.

Let's take a look at some of the evidence for ingenuity and intelligence in cells that is missing from the curriculum. Take the red algae Rhodophyta, in which many species carry out remarkable repairs to damaged cells. Cut a filament of Antithamnion cells so the cell is cut across and the cytoplasm escapes into the surrounding aquatic medium. All that remains are two fragments of empty, disrupted cell wall lying adjacent to, but separate from, each other. Within 24 hours, however, the adjacent cells have made good the damage, the empty cell space has been restored to full activity, and the cell walls meticulously realigned and seamlessly repaired.

The only place where this can happen is in the lab. In nature, the broken ends of the severed cell would nearly always end up remote from each other, so selection in favour of an automatic repair mechanism through Darwinian evolution would be impossible. Yet something amazing is happening here: because the damage to the Antithamnion filament is unforeseeable, the organism faces a situation for which it has not been able to adapt, and is therefore unable to call upon inbuilt responses. It has to use some sort of problem-solving ingenuity instead.

We regard amoebas as simple and crude. Yet many types of amoeba construct glassy shells by picking up sand grains from the mud in which they live. The typical Difflugia shell, for example, is shaped like a vase, and has a remarkable symmetry.

Compare this with the better known behaviour of a caddis fly larva. This maggot hunts around the bottom of the pond for suitable scraps of detritus with which to construct a home. Waterlogged wood is cemented together with pondweed until the larva has formed a protective covering for its nakedness. You might think this comparable to the home built by the testate amoeba, yet the amoeba lacks the jaws, eyes, muscles, limbs, cement glands and brain the caddis fly larva relies on for its skills. We just don't know how this single-celled organism builds its shell, and molecular biology can never tell us why. While the home of the caddis fly larva is crude and roughly assembled, that of the testate amoeba is meticulously crafted - and it's all made by a single cell.

The products of the caddis fly larva and the amoeba, and the powers of red algae, are about more than ingenuity: they pose important questions about cell intelligence. After all, whole living cells are primarily autonomous, and carry out their daily tasks with little external mediation. They are not subservient nanobots, they create and regulate activity, respond to current conditions and, crucially, take decisions to deal with unforeseen difficulties.
Just how far this conceptual revolution about cells could take us becomes clearer with more complex animals, such as humans. Here, conventional wisdom is that everything is ultimately controlled by the brain. But cells in the liver, for example, reproduce at just the right rate to replace cells lost through attrition; follicular cells create new hair; bone marrow cells produce new circulating blood cells at a rate of millions per minute. And so on and on. In fact, around 90 per cent of this kind of cell activity is invisible to the brain, and the cells are indifferent to its actions. The brain is an irrelevance to most somatic cells.

So where does that leave the neuron, the most highly evolved cell we know? It ought to be in an interesting and privileged place. After all, neurons are so specialised that they have virtually abandoned division and reproduction. Yet we model this cell as little more than an organic transistor, an on/off switch. But if a red alga can "work out" how to solve problems, or an amoeba construct a stone home with all the "ingenuity" of a master builder, how can the human neuron be so lowly?

Unravelling brain structure and function has come to mean understanding the interrelationship between neurons, rather than understanding the neurons themselves. My hunch is that the brain's power will turn out to derive from data processing within the neuron rather than activity between neurons. And networks of neurons enhance the effect of those neurons "thinking" between themselves. I think the neuron's action potentials are rather like a language neurons use to transmit processed data from one to the next.

Back in 2004, we set out to record these potentials, from neurons cultured in the lab. They emit electrical signals of around 40 hertz, which sound like a buzzing, irritating noise played back as audio files. I used some specialist software to distinguish the signal within the noise - and to produce sound from within each peak that is closer to the frequency of a human voice and therefore more revealing to the ear.

Listening to the results reprocessed at around 300 Hz, the audio files have the hypnotic quality of sea birds calling. There is a sense that each spike is modulated subtly within itself, and it sounds as if there are discrete signals in which one neuron in some sense "addresses" another. Could we be eavesdropping on the language of the brain?

For me, the brain is not a supercomputer in which the neurons are transistors; rather it is as if each individual neuron is itself a computer, and the brain a vast community of microscopic computers. But even this model is probably too simplistic since the neuron processes data flexibly and on disparate levels, and is therefore far superior to any digital system. If I am right, the human brain may be a trillion times more capable than we imagine, and "artificial intelligence" a grandiose misnomer.

I think it is time to acknowledge fully that living cells make us what we are, and to abandon reductionist thinking in favour of the study of whole cells. Reductionism has us peering ever closer at the fibres in the paper of a musical score, and analysing the printer's ink. I want us to experience the symphony.

[AJ Dual]

I really want to hear that audio. Can't find any links... 

And OTOH, Jupiter and Earth's magnetosphere produce "dawn whistlers" which are sometimes evocative of bird or whalesong...  but are devoid of any higher purpose and meaning.

[mellestad]

I really want to hear that audio. Can't find any links... 

And OTOH, Jupiter and Earth's magnetosphere produce "dawn whistlers" which are sometimes evocative of bird or whalesong...  but are devoid of any higher purpose and meaning.

I agree, it would be an interesting thing to hear. 

This is exciting research in general though, not just relating to the brain.  Lots of research has been going into monitoring the activity of cells in the body for medical puroposes.  To me what is interesting is that this field has not been investigated very well until recently, and it makes me wonder why.  Maybe we didn't have the technical ability in the past?

The implications are huge though.  If we can figure out exactly how a particular type of cell behaves throughout the entire body we can have a leg up on creating treatments for when those processes break down.  I'm not a biologist but when I was in school they just sort of glossed over cells and explained their function as if they were single-purpose things that were 'sent' from here to there with a specific job.  Stuff like this is a big eye opener for me.  (My school had a poor science department though, so ymmv)

[roo_ster]

Let's take a look at some of the evidence for ingenuity and intelligence in cells that is missing from the curriculum. Take the red algae Rhodophyta, in which many species carry out remarkable repairs to damaged cells. Cut a filament of Antithamnion  cells so the cell is cut across and the cytoplasm escapes into the surrounding aquatic medium. All that remains are two fragments of empty, disrupted cell wall lying adjacent to, but separate from, each other. Within 24 hours, however, the adjacent cells have made good the damage, the empty cell space has been restored to full activity, and the cell walls meticulously realigned and seamlessly repaired.

The only place where this can happen is in the lab. In nature, the broken ends of the severed cell would nearly always end up remote from each other, so selection in favour of an automatic repair mechanism through Darwinian evolution would be impossible. Yet something amazing is happening here: because the damage to the Antithamnion  filament is unforeseeable, the organism faces a situation for which it has not been able to adapt, and is therefore unable to call upon inbuilt responses. It has to use some sort of problem-solving ingenuity instead.

This is fascinating on several levels.

First, I am ambivalent WRT Darwinian evolution, less so due to my religion and more so due to my physics/hard science training that emphasized empirical data...and Darwinian evolution relies more on shaky hypothesis, logic, and vigorous hand-waving for me to be comfortable with its conclusions.

The above is observed behavior of a cell.  I think declaring it "impossible" via Darwinian processes is a stretch, but it surely does not support the Darwinian conception.  Observed reality trumps the intellectual squid-ink that passes for Darwinian evolution.

Second, that is awfully complex behavior for a single-celled critter in an unlikely circumstance. 

For me, the brain is not a supercomputer in which the neurons are transistors; rather it is as if each individual neuron is itself a computer, and the brain a vast community of microscopic computers. But even this model is probably too simplistic since the neuron processes data flexibly and on disparate levels, and is therefore far superior to any digital system. If I am right, the human brain may be a trillion times more capable than we imagine, and "artificial intelligence" a grandiose misnomer.

IME, contemporary science has scratched the surface of the brain, understanding-wise.  That is one reason I consider psychology akin to astrology: both rely on a limited & faulty understanding of the subject matter and fill the voids with self-serving hokum.  Slather on a veneer of mystery (astrology) or scientific rigor (psychology) and call it good.

[mellestad]

This is fascinating on several levels.

First, I am ambivalent WRT Darwinian evolution, less so due to my religion and more so due to my physics/hard science training that emphasized empirical data...and Darwinian evolution relies more on shaky hypothesis, logic, and vigorous hand-waving for me to be comfortable with its conclusions.

The above is observed behavior of a cell.  I think declaring it "impossible" via Darwinian processes is a stretch, but it surely does not support the Darwinian conception.  Observed reality trumps the intellectual squid-ink that passes for Darwinian evolution.

Second, that is awfully complex behavior for a single-celled critter in an unlikely circumstance. 


IME, contemporary science has scratched the surface of the brain, understanding-wise.  That is one reason I consider psychology akin to astrology: both rely on a limited & faulty understanding of the subject matter and fill the voids with self-serving hokum.  Slather on a veneer of mystery (astrology) or scientific rigor (psychology) and call it good.

I don't know how you could get more empirical proof about Darwinian evolution jf, we've seen it happen, it has successfully born out predicted hypothesis and it successfully unifies the entire field of biology.

I’m a bit confused as to what more you could want?  The complexity of a single celled organism does not run counter to evolutionary biology in any way.

[Balog]

I don't know how you could get more empirical proof about Darwinian evolution jf, we've seen it happen, it has successfully born out predicted hypothesis and it successfully unifies the entire field of biology.

Umm, what? When have we observed one type of animal change into another? I'm going to need to see this reference.

[mellestad]

Umm, what? When have we observed one type of animal change into another? I'm going to need to see this reference.

http://lmgtfy.com/?q=speciation

 

[Balog]

Long on smart ass, short on facts. Yeah, sounds about right.

[mellestad]

Long on smart ass, short on facts. Yeah, sounds about right.

On the first page of that search there are over a dozen links to specific speciation events.  Some examples:

Very simple:  http://evolution.berkeley.edu/evosite/evo101/VSpeciation.shtml
In Depth: http://www.talkorigins.org/faqs/faq-speciation.html
A Video: http://www.youtube.com/watch?v=YCoEiLOV8jc
Broad with many sources: http://en.wikipedia.org/wiki/Speciation

I'm not sure what else you want, unless you want me to pull quotes and paste them, or write a summary of the peer reviewed papers in my own words. 

If you ask, I'll do either of those things, but it seems like a waste of time when Google makes it easy to do it yourself.

[AmbulanceDriver]

mellestad, I hate to point this out to you, but none of those links show evidence of Darwinian evolution via speciation.  At *best*, they show micro-evolution amongst a species, or perhaps differentiation.  I.E., one species of orchid developing into two different types of orchids, or fruit-flies, or house-flies.  While it's true that the new "species" cant' interbreed, which is one of the tests of speciation, the fact remains that they are at best showing micro-evolution. 

The argument remains that there exists no evidence of macro-evolution.  No skeletal remains of an intermediate species, at least none without some kind of controversy, have been found.  We don't see today any kind of intermediate species between, say, birds and reptiles, as has been posited by Darwinian evolution. 

[Balog]

What AD said.

I also not that most "advantages" are in fact severe detriments until fully developed. Flying being the biggest example.

[Regolith]

The argument remains that there exists no evidence of macro-evolution.  No skeletal remains of an intermediate species, at least none without some kind of controversy, have been found.  We don't see today any kind of intermediate species between, say, birds and reptiles, as has been posited by Darwinian evolution. 

http://en.wikipedia.org/wiki/Archaeopteryx

[AmbulanceDriver]

In line with the argument of cellular complexity, I'd like to present a molecular structure.

It's the F1/F0 ATPase.  A molecular generator, if you will, in the mitochondrial walls.  I don't remember the exact details, as it's been a few years since I took molecular/cellular biology.  But if I recall, there are three subsections to this molecular generator.

I'm gonna try to condense a week of classes/lectures into a single post, so bear with me if I gloss over a few of the finer details.  This molecular generator has 8 minor subunits, composing 2 major subunits, F0 and F1.  This molecular generator is what is responsible for the generation of ATP in the mitochondria, the "power plant" of the cell.  

The problem for evolution is that this generator ONLY is useful to aerobic organisms.  Anaerobic organisms, which according to evolutionary theory were the "basic building blocks" for evolutionary first life, can't use it.  There's no selective pressure for an anaerobic organism, in an anaerobic environment, to switch to an aerobic metabolism.  Furthermore, you can't have aerobic metabolism without this little generator.  In fact, EVERY aerobic metabolism mechanism has some variant of the F1/F0 ATPase.  

So you reach a quandary.  It's the classic "chicken and the egg" problem.  You can't have aerobic metabolism without the F1/F0 ATPase.  But you can't use the F1/F0 ATPase unless you have aerobic metabolism....

[mellestad]

There is no difference between microevolution and macroevolution, that is a false argument as evolution is evolution, there is no micro/macro.

Every species that produces offspring using DNA is a transitional form between its ancestor and its progeny.  The fact that we have as many transitional forms as we do is actually pretty amazing, since fossilization is not a common event.  http://en.wikipedia.org/wiki/List_of_transitional_fossils  (this includes examples of reptiles to birds)

The links I provided certainly do show examples of speciation.  For example, ring species.

Balog(or anyone):  You might benefit from this http://www.talkorigins.org/origins/faqs-qa.html since most of your questions/comments thus far are covered, often in great detail.  Your last post was covered under an idea called "irreducible complexity", which is the idea that certain traits could not have intermediate forms and functions and so could not evolve.  The popular exampels of the eye, wings, etc. all have rebuttals.  Reading that list might save some time so we don't have to go through them one at a time here.

[mellestad]

In line with the argument of cellular complexity, I'd like to present a molecular structure.

It's the F1/F0 ATPase.  A molecular generator, if you will, in the mitochondrial walls.  I don't remember the exact details, as it's been a few years since I took molecular/cellular biology.  But if I recall, there are three subsections to this molecular generator.

I'm gonna try to condense a week of classes/lectures into a single post, so bear with me if I gloss over a few of the finer details.  This molecular generator has 8 minor subunits, composing 2 major subunits, F0 and F1.  This molecular generator is what is responsible for the generation of ATP in the mitochondria, the "power plant" of the cell.  

The problem for evolution is that this generator ONLY is useful to aerobic organisms.  Anaerobic organisms, which according to evolutionary theory were the "basic building blocks" for evolutionary first life, can't use it.  There's no selective pressure for an anaerobic organism, in an anaerobic environment, to switch to an aerobic metabolism.  Furthermore, you can't have aerobic metabolism without this little generator.  In fact, EVERY aerobic metabolism mechanism has some variant of the F1/F0 ATPase.  

So you reach a quandary.  It's the classic "chicken and the egg" problem.  You can't have aerobic metabolism without the F1/F0 ATPase.  But you can't use the F1/F0 ATPase unless you have aerobic metabolism....

You can do this all day AD.  This is a Gaps argument, where you can bring up an unlimited line of examples about how modern evolution does not specifically explain some particular thing and say that because a particular thing is not (Edit: Yet) known, the theory must be false.  As in my last post where I mention irreducible complexity, this has been done most famously by Behe and and the flagellum in Darwin's Black Box.  Well now people have taken the time to create rebuttals for that argument.

Essentially, your argument isn't proof of anything, all you've done is created a potential line of study for an evolutionary biologist.  That is assuming the question has not already been answered, and I am not qualified to comment on that.

http://www.talkorigins.org/faqs/behe.html

[AJ Dual]

The problem for evolution is that this generator ONLY is useful to aerobic organisms.  Anaerobic organisms, which according to evolutionary theory were the "basic building blocks" for evolutionary first life, can't use it.  There's no selective pressure for an anaerobic organism, in an anaerobic environment, to switch to an aerobic metabolism.  Furthermore, you can't have aerobic metabolism without this little generator.  In fact, EVERY aerobic metabolism mechanism has some variant of the F1/F0 ATPase.  

So you reach a quandary.  It's the classic "chicken and the egg" problem.  You can't have aerobic metabolism without the F1/F0 ATPase.  But you can't use the F1/F0 ATPase unless you have aerobic metabolism....

Yes, but mitochondria have their own DNA in them, which suggest they may have at one point been independent organisms of their own, invaded other cells, and found a symbiotic relationship to the point that they're now just one of the many organelles. Such predation/parasitism/symbiosis may have gotten it's start at a boundary condition where anaerobic conditions gave way to aerobic ones.

Maybe right around the time the green photosynthetic single cell organisms killed off all the purple ones with waste 02.

[makattak]

You can do this all day AD.  This is a Gaps argument, where you can bring up an unlimited line of examples about how modern evolution does not specifically explain some particular thing and say that because a particular thing is not (Edit: Yet) known, the theory must be false.  As in my last post where I mention irreducible complexity, this has been done most famously by Behe and and the flagellum in Darwin's Black Box.  Well now people have taken the time to create rebuttals for that argument.

Essentially, your argument isn't proof of anything, all you've done is created a potential line of study for an evolutionary biologist.  That is assuming the question has not already been answered, and I am not qualified to comment on that.

http://www.talkorigins.org/faqs/behe.html

Hmm... sounds like you just have to take it on faith, then.

[mellestad]

What AD said.

I also not that most "advantages" are in fact severe detriments until fully developed. Flying being the biggest example.

How do you explain modern flightless birds then?  They don't seem inhibited.

[AmbulanceDriver]

mellestad, we're gonna have to agree to disagree on this one.  I really don't want to turn this thread into a Creation/Evolution hashfest, because neither one of us is gonna move the other's position.  And I really don't want to get this thread locked down.  

The OP has some very interesting connotations regardless of which side of the Evolution/Creation debate you fall on.  Which is where I *DO* agree with you.  We've hardly scratched the surface in understanding WHY the cell works as it does.  We've made a little more of a dent in the HOW, but there's still huge gaps in our knowledge.  

[mellestad]

Hmm... sounds like you just have to take it on faith, then.

No, Mak, it doesn't.  Please read some of the links to talk.origins.

@AD:  K.

[Balog]

Once again, what AD said. :D

[mellestad]

Once again, what AD said. :D

That's fine.  I would encourage you to do some reading on your own though, even if only through talk.origins.  Or sign up for a class at a local community college.

Heck, send me a PM and I'll mail you a book.

It just bugs me because evolution isn't a 'theory', it is a fact.  It is proven, it works, it explains and it unifies.  Evolution is to biology what plate tectonics is to geology and it drives me a little nuts to see people shrug it off like it is some random thing with no emperical backing, or because it doesn't match their intuition or their religion.

[AmbulanceDriver]

mellestad, I really don't wanna continue to argue this point with you, but I have to say one more thing here....  What you consider "fact", others DO consider theory, myself included.  And it isn't only due to religious belief (as was pointed out on talk.origins, there are evolutionist Christians) but because of definition.  Evolution is un-proveable, as is Creation.  We can't apply the scientific method to either belief and directly observe the results of it.  No human witnessed the birth of the universe.  You cannot call it a scientific fact when it is not, on the whole, proveable.  Much as Einstein's theory of General Relativity, it cannot be proven.  Does it attempt to answer some of the questions we have?  Absolutely.  Is it proven?  No.

[mellestad]

mellestad, I really don't wanna continue to argue this point with you, but I have to say one more thing here....  What you consider "fact", others DO consider theory, myself included.  And it isn't only due to religious belief (as was pointed out on talk.origins, there are evolutionist Christians) but because of definition.  Evolution is un-proveable, as is Creation.  We can't apply the scientific method to either belief and directly observe the results of it.  No human witnessed the birth of the universe.  You cannot call it a scientific fact when it is not, on the whole, proveable.  Much as Einstein's theory of General Relativity, it cannot be proven.  Does it attempt to answer some of the questions we have?  Absolutely.  Is it proven?  No.

I'm sorry AD, that simply is not true.  Evolution and creation are not the same, one is about cosmology and the other is about how species change and adapt over time due to pressure and genetic drift.  Evolution also isn't about the origins of life, that is abiogenesis.

We are not talking about something that cannot be seen or measured or rationally studied.  Evolution can be seen, it can be measured, it can be rationally studied, it makes predictions that are born out emperically.

What do you want?  Speciation?  We have that.  Beneficial changes?  We have that.  Transitional fossils?  We have those.  Controlled examples of artificial evolution?  We have those.  Being able to explain the origins of many species?  We can do that.  I honestly don't know what information you could want that isn't available.  You can just respond to my PM if you'd rather.

----

Also, the theory of (special) relativity certainly has been proven by real experiments.  It breaks down at a micro-level and then you get into quantum mechanics, but otherwise it tests out to be true.  Some of the real life experiments that have been done are totally trippy.  Like this one http://en.wikipedia.org/wiki/Hafele-Keating_experiment where they actually recorded time dialation!  This stuff blows my mind, but it is real and has been reproduced multiple times.  (Sumary:  Fly two atomic clocks around the world in opposite directions, then measure their times against a stationary atomic clock.  In all tests, the clocks show time shifts where stationary clocks do not.  Time isn't slowing down, but time is different because the travelling clocks have a seperate frame of reference.)  There are other examples, but most of them are beyond my physics level, so I'm not qualified to yack about them.  

Edit: More current examples exist, like http://einstein.stanford.edu/MISSION/mission1.html which confirmed other aspects of special relativity.

(If you really want in-depth: http://www.desy.de/user/projects/Physics/Relativity/SR/experiments.html)

[AmbulanceDriver]

On General Relativity and Special Relativity:  The caveat is that they are still theories because while *so far* every experiment on them has proven correct, not every experiment has been run on them.  The problem is, we don't know what we don't know about them yet.  They can't be called Laws, or proven facts, yet, because they haven't been tested to completion (the fact that we don't know all the questions yet just goes to show how much we don't know).  So far, every experiment proves out, but what happens if, "Whoops!  That wasn't supposed to happen!" happens?  Do we throw out the entire theory?  No, absolutely not.  But do we readjust the theory if the "whoops" is repeatable, independently verifiable, and ultimately measurable?  Absolutely!