About Cells

Why do cells exist? Why are they ubiquitous in living organisms?

I am a serious plant scientist in search of a forum to discuss some non-standard ideas. I am new to the Wiki world and just trying to get an initial page set up to put some ideas out. I have done quite a lot of writing in other publication formats on this and related topics, but I want to see what kind of interaction I can get going.

Here are the first two questions:

Why are all living things composed of cells? Even viruses need cells to complete their life cycles! There is no theory that adequately explains this.
Why is there is no real functional theory of cells and cellularity? Even in courses on "Cell Biology" we deal mostly with the mechanics of what goes on inside cells and do not approach the basic question of why cells exist in the first place.

-- PhilLintilhac

You need to clarify what parts of existing theory are inadequate.

As you are well aware, cells are in one sense defined by their walls/membranes, which protect them from noxious chemicals and pathogens, provide mechanical protection to the interior, provide mechanical structuring, control intake of nutrients and expulsion of waste, control reception and emission of messenger molecules, etc.

In another sense, cells are the physical unit of viable reproduction, and enclose the various machinery necessary for ongoing metabolism and reproduction: groups of interdependent but genetically separate organelles (mitochondria, chloroplasts, plasmids, nuclear DNA and related machinery) need to be segregated from the environment, and transmitted as a group during cell division.

All of this is in some sense explains the necessity for cells, but obviously you're aware of all of that and are looking for something more - like what???

-- DougMerritt

Doug, you are correct that the common usage of the word cell in biology says something about what is contained in the cell. Another way to look at it is that the cell is like the "Quantum of Life", the smallest unit of living structure and function that can still be considered to be alive. However, in plants for instance, all the cells in the plant body are connected by very tiny cytoplasmic channels called plasmodesmata. This has led to the concept of the "Symplast" in plants. (The notion is not so well defined in animals, but there are other kinds of connections between cells there, junctions of various sorts.) So, the plant then becomes a giant cytoplasmic continuum, and cells cease to have meaning. And yet, it is clear, that in many cases differentiation of cells in plants goes on in a cell-by-cell manner. There is a logic of differentiation which is more clearly visible in plants than in animals, and that is what I am interested in.

There is really no existing theory of cells. The famous "Cell Theory" of Schleiden and Schwann, is actually just an aphorism which states that all cells come from pre-existing cells. If we go back to the 1830s we find that the concept of cellularity was actively debated. The great 19th century pathologist Rudolph Virchow said that "the organism is a state in which every cell is a citizen." Implying that individual cells have decision-making power and so-forth. On the other hand his contemporary Anton DeBary? said: No-no the developmental decisions are made at the organismal level and the cells just divide up the space for structural reasons - they have minimal significance in development.

But, in modern biological science, as taught to your sons and daughters in college, there is no such thing as cell theory. There is an enormous amount of detail available as to what is inside the cell and what it does, but no discussion of what a cell really is - no attempt to build some kind of a logic of cellularity that has predictive power or which can simplify understanding.

So, anyway, how do I create a wiki forum that is not off-topic? Should I create a dedicated wiki from scratch, or is there one out there with a reasonably close match that I can join?

[There are some wikis Google finds which at least have a page about what a cell is.]

Please forgive me for being presumptuous, but I must disagree with your statement: "So, the plant then becomes a giant cytoplasmic continuum, and cells cease to have meaning"

I note that surprising developments have occurred with animal cells, e.g. Scientific American Feb. 2006 "Intrigue at the Immune Synapse" - it turns out that somewhat parallel phenomenon occur in animal cells, not just plant cells.

In particular see the extraordinary photomicroscopic illustration on pg 55, showing the microtubule nanotube communication pathways formed between adjacent animal cells.

As I see it, the synthesis of the most cutting edge results across all Kingdoms shows that messenger molecules, and highly active metabolic machinery assisting in sending and receiving molecular messengers, is in fact a universal across Kingdoms.

In summer of 2005 or perhaps 2004, there was a very interesting conference in Italy regarding the ways in which colonies of bacteria act collectively as a parallel to neural networks; eukaryotes and prokaryotes alike, by exchanging messenger molecules - by diffusion, so far as has been proven, but speculatively, by pseudopod exchange, not too different than that of plasmid exchange across membranes.

To summarize, although there are far-ranging communicational networks between cells in all of the Kingdoms, and some are highly dependent upon metabolic/structural context, there appear to be broad principles that apply across all these mechanisms in all these Kingdoms.

I suspect that, at this point in history, there is enough evidence to show that DeBary? was simply wrong, overall. -- DougMerritt

Quite true, I don't agree with it either. On the other hand there is an alga, (Caulerpa, which is a pest in the Mediterranean and now in California) which can attain several meters in size, complete with leaf-like fronds, stem-like stipes, and root-like holdfasts, which is totally acellular! No cells at all. The point is that we need to be able to define a cell in a rigorous way, and build a logic of cellularity that has predictive power and meaning.

I am completely astonished, and will do some Google searching before saying more (if you have some educational URLs on the topic, please feel free to share). -- Doug

[Isn't Caulerpa one big cell?]

Yes - I think that is the most straightforward interpretation, but then how do you deal with the problem of individual cell specialization - Cellular differentiation - where you have a single cell surrounded by other identical cells which differentiates into an unique cell type. What are the signals that prompt differentiation? I'm not sure that it is really a problem. Obviously it isn't a problem for the organisms which do it routinely. The problem lies in the nomenclature we have developed which favors calling things cells.

See http://en.wikipedia.org/wiki/Morphogenesis for a very brief introduction to the mechanics of cellular differentiation.

Yes, the Wikipedia definition does a pretty good job of outlining the traditional view. An interesting aside that they do not mention relates to the origin of the word "Morphogenesis" which was actually coined by the German poet Johann Wolfgang von Goethe. He disdained to use the microscope but nevertheless contributed one of the most significant advances in our thinking. He studied plants, and was the first to really understand that you cannot simply view the plant as a static subject, but rather it is a concatenation of sequential forms one leading directly to the next. In plants, this is more apparent because of the modular construction of the plant body, internode - node - internode - node, with new form being continuously developed at the tip.

Wikipedia also falls for the usual oxymoron that development is controlled by the genome, which is often stated by saying that the genome is a blueprint for the mature organism, which is not true of course. There is nothing in the genome that remotely resembles a blueprint. They soften it a bit by saying that genelevel control is modified by the developmental environment. The reality is much more interesting than that, and in plants, where all the cells are trapped in rigid cellulose walls, firmly attached to each other, and are pressurized with up to 10 Bar (1.0MPa) of pressure (!) you have a perfect setup for a beautiful system of mechanical signals which can act to direct local cell behavior in a very precise way. Genetic switching mediates the process, but the source of the control signals is clearly non-genetic.

The genome makes for "Smart Cells" which then respond to their surroundings in various ways. For a cell embedded in other cells, that environment has evolved to provide certain signals at certain times; a form of organismal control, if you will. Not to deny the significance and power of the genome, which is fundamental of course! But, it does not do justice to the intricate, flexible, and varied levels of control that emerge at higher levels of organization and which are where the real action is.

In animals, these cell-by-cell control processes are not as readily apparent, because animal cells are free to move and can therefore place themselves in different eliciting environments, thereby triggering differentiation, but in plants the cells are permanently glued to their neighbors. There is no relative cell movement. None. So the significance of the logic underlying the differentiation of one cell from its genetically identical neighbor is thrown into relief.

I am tempted to think that cellularity IS a real and obligatory property of living organisms for reasons that go beyond just holding enzymes together in a bag. For reasons that extend beyond the contents of the cell, for instance. How to articulate those reasons? Phil L.

You might begin by telling us why you are tempted to think that.

"but the source of the control signals is clearly non-genetic" - this is true for all cells, not just plant cells. A big paradigm shift over the last 10-20 years has been seeing messenger molecules (including but not limited to traditional hormones) as central rather than secondary.

This is quite true in general, messenger molecules are key - but (although it is not my area of expertise) I think there are "reflexive" control signals that both originate in and act on the genome.

The breakthroughs in genomic analysis have shown that many messenger molecules have homologues in all species in all kingdoms/super-kingdoms, and therefore derive from shared ancestors that pre-date the split of cells into kingdoms, so this is truly basic stuff, applying equally to yeast and to humans (between which many homologues have been found).

Quite true!

The mechanical forces you mention (and just about everything else, too) trigger emission of messenger molecules, which may diffuse to neighboring cells or may diffuse toward receptors in organelles and/or the nucleus.

This can be true, but they can also act as direct signals acting on the cytoskeleton for instance (by some as yet unknown mechanism) to orient the plane of division, most likely without the intermediary of diffusible messsengers. This brings up an interesting question: How can a diffusible messenger specify a precise plane of division orientation (spindle orientation). I challenge you to come up with one! It may be possible but it is difficult.

Sounds like an excellent challenge - I sure don't have an answer off the top of my head! -- Doug
- See pattern development in early Drosophila embryos for lots of information on how this can be accomplished in a cellular organism. Maybe this is why cells are necessary - to allow precise molecular gradients to be set up?

When organelles/nuclei receive messenger molecules, it triggers enzymatic action via pre-existing enzymes, some of which are used for transcribing sections of the genome - so we have the interesting inversion that the action of the genome is in the middle of the sequence, rather than being the origin of the sequence, so in a sense, the genome is not fundamental; the nuclear machinery including transcriptase is perhaps even more fundamental.

The genome is just a memory store; the vastly complex nuclear (or organelle) enzymatic machinery is the actual workhorse that gets things done (including by reading the genome and e.g. sending mRNA to ribosomes, etc).

Yes, as Paul Green used to like to say "The genome just make for smart cells".

That underlies almost all processes, ranging from juvenile growth to apoptosis (which is primary in forming e.g. feathers, and correct me if I'm wrong, also in seasonal deciduous leaf loss). Also of course, the water conducting vessels in all living plants are dead - Interesting aside: the water in the transpiration stream can be under high negative pressure of as much as neg 15 Bar adjacent to living cells with Pos 10 Bar or more! How 'bout that? Cell differentiation is triggered by gradients of messenger molecules (zillions of them, and thus zillion-dimensional), in all multi-cellular organisms, across kingdoms, as with the famously correct guess as to the origin of the leopard's spots.

Those pressure differences are baffling to me; that's one for Ripley's Believe it or Not. :-) -- Doug

I have some quibbles with how we use the word **Differentiation**. Is spore differentiation in Bacteria equivalent to multicellular differentiation? I think not. Spore differentiation proceeds autonomously, under the correct environmental conditions, whereas multicellular differentiation is a contract between two entities, cells perhaps, where one says: OK, Ill do the cooking if you clean up afterwards - A division of labor. Very different methinks!

Ah, but they are in fact the same! I alluded to this earlier, but more specifically, searching on "bacterial neural networks" finds e.g. this meeting report in Nature:
- http://www.nature.com/cgi-taf/DynaPage.taf?file=/embor/journal/v4/n1/full/embor702.html
- The recent EURESCO Conference on Bacterial Neural Networks heralded broadly the inescapable truth that bacteria cooperate in both uniform and mixed societies, sabotage the relatively mammoth creatures that they colonize, modify their own living spaces, and anticipate predictable changes in their surroundings. They achieve these feats with a clear sense of time and place, both within and outside their small but well-organized bodies, and send and receive messages across comparatively vast space.
- Major themes of the meeting were the interconnected phenomena of signalling, behaviour and development, with just enough emphasis on technological advancements to presage how much more bacterial complexity is yet to be discovered as the tools improve.
In all cases, there's a fundamental similarity: exchange of messenger molecules between cells; issues of "contracts" are somewhat metaphorical, but in any case apply just as well to the bacteria colony differentiation (and aptopsis of bacteria lining the colony to provide a barrier, which turns out to be a major issue with e.g. arterial infections!) and to slime mold sessile to motile to sessile macro-body formation and sporing, as to traditional multicelluar organisms. It's a unification of what was once disparate. -- Doug

"that go beyond just holding enzymes together in a bag" - Given the above, this is not a "just", it may in fact be the whole point. If we transplant the DNA from a monkey into the nucleus of an echinoderm, the result will be non-functional; the nuclear machinery is incompatible. It's important to transmit the functioning enzymatic machinery of nuclei and organelles during cell division, not just the genome itself.

It is also important to provide the correct epigenetic enviroment, so that the properly equipped cells make the correct decisions at critical moments.

Holding all of the critical stuff together in a bag may, therefore, indeed be exactly the point.

To speculate, it's even possible that some nuclear enzymes are not transcribed from the genome; it is theoretically possible for them to independently reproduce via some kind of reverse-transcriptase targeted purely at that one process, in which case the nuclear machinery would be self-perpetuating, but still utterly essential.

The point of that speculation is that it would reflect on the definition of "species"; it would show quite clearly that compatibility of the classic genome is insufficient, one would have to consider the compatibility of the nuclear machinery, as well - which I believe is in fact already the case, but that would underscore it.

P.S. I keep mentioning organelles - Lynn Margulis' radical hypothesis that they originated as utterly independent cellular species is, these days, regarded as orthodox. I have been implicitly taking that for granted, as well as what that implies for e.g. mitochondria - machinery parallel to that of the nucleus (albeit simpler) is at work, whether well-studied or not.

P.P.S. I created a home page for you here, populated with a small amount of information I found via Google; I hope I was not too presumptuous in doing so. Click on PhilLintilhac to see my attempt.

-- DougMerritt

I appreciate your help and your interest Doug. It looks good. Actually I have started a wiki at Peanut Butter Wiki. It was easier than I thought. I have put it out to faculty in my department for beta-testing, and will circulate it if it looks interesting. You need a password which is **phyton** The whole thing is quite cool I must say!

http://plantdevelopmentwiki.pbwiki.com/

But I don't have any discussion going there yet!

-- PhilLintilhac

FebruaryZeroSix

I'm not even convinced this is OffTopic. Could the evolutionary success of cellular structure be nature's way of telling us that modularity and encapsulation are fundamental virtues for organizing complex interacting subsystems to form even more successful larger systems? -- IanOsgood

Thanks Ian, -- More later! PL

Phil said:

Doug, here is a link to a 1999 paper on Cell theory. http://www.uvm.edu/~plantbio/faculty/lintilhac.cellularity.pdf

As I look back on it now, I find it a bit pretentious and of too broad a scope. It should really have been two papers. The part that relates to developmental logic is really the second half of the paper. You can see how much of what we have discussed comes from that same thinking. The underlying questions are just as valid now as they were then however.

...and despite Phil's self-critique, and despite the difficulties in attacking the subject he is addressing, I find it a very interesting paper.. -- Doug

AlanKay's original vision of ObjectOrientedProgramming was strongly influenced by biology (and some other things, such as the early ArpaNet?). It was focussed on encapsulation and MessagePassing; each object is a cell, the whole system is a biological organism. He hoped that OO systems could have the fault-tolerance and plasticity of plants and animals: "you never have to take a baby down for maintenance". He talks a lot about the analogy in his OOPSLA '97 TheComputerRevolutionHasntHappenedYet video - see http://video.google.co.uk/videoplay?docid=-2950949730059754521 and also AlanKayOnMessaging, and look at EarlyHistoryOfSmalltalk too.

While SmalltalkLanguage's message-passing model was inspired by biology, CarlHewitt was influenced by physics in his ActorsModel work. (Also, Hewitt's PlannerLanguage? influenced Kay's SmalltalkLangue? which influenced the ActorsModel.)

ErlangLanguage programming has a LetItCrash idiom which exploits Erlang's highly-concurrent, shared-nothing message-passing model to attain high robustness in the (arguably) biological manner foreseen by Kay; see JoeArmstrong's PhD thesis. (LetItCrash is DontCatchExceptions's bigger brother.)

SteveBurbeck also has some ideas about applying the biological analogy to computing: see http://evolutionofcomputing.org/.

CategoryBiology CategoryOffTopic OffTopicIsOkay