Pharyngula

Tuesday, August 16, 2005

Generating right-left asymmetries

We're only sorta bilaterally symmetric: superficially, our left and right halves are very similar, but dig down a little deeper, and all kinds of interesting differences appear. Our hearts are larger on the left than the right, our appendix is on the right side, even our brains have significant differences, with the speech centers typically on the left side. That there is asymmetry isn't entirely surprising—if you've got this long coil of guts with a little appendix near one end, it's got to flop to one side or the other—but what has puzzled scientists for a long time is how things so consistently flop over in the same direction in individual after individual. There has to be some deep-seated mechanism that biases developmental events to favor one direction over the other. We know many of the genes involved in asymmetry, but what is the first step that skews development to make consistent asymmetrical choices?

In mammals, we're getting close to the answer. And it looks to be beautifully elegant—it's a simple trick to convert an anterior-posterior difference into a left-right one.

Nonaka et al. have examined the node of the mouse embryo. At the time of gastrulation, the mouse embryo (and the human embryo as well) is essentially a flat, two-layered sheet, with a groove in the middle called the primitive streak, and a dimple at the anterior end called Henson's node. Looking down on the sheet of cells, we'd see something like this:

node

This particular diagram is a little cluttered because it's got all those curved arrows all over it; they're there because what's going on at this stage of development is a great deal of cell movement. Cells are moving on the surface layers towards the primitive streak (thick solid lines) and then diving down at the streak into the deeper layers, and migrating from there to various deep places in the embryo (thick dashed lines). This is what gastrulation is about, tucking cells from the surface into a middle layer, creating a three-layered embryo.

This is a cross section through the embryo above, clarifying what's going on. The blue cells are the superficial epiblast (roughly, the ectoderm), yellow is the hypoblast (endoderm), and the cells that have migrated through the streak are colored red, and are going to form mesoderm.

node

There's more than just simple movement going on, of course. The cells are also interacting with their neighbors and sending chemical signals back and forth; these inductive signals instruct cells in what tissues they should differentiate into. The node is a particularly important place for these signals, and cells going through there will become axial mesoderm—central structures like the notochord that will define the midline, and also will specify the formation of essential tissues like the nervous system.

node

So the node is important as a critical structure for setting up axial structures. It's also important for generating early asymmetries.

To the right is a scanning EM of a mouse node. Don't get too confused; the figure labeled B rotated so left is on top and bottom on the right, but the area we care about has an arrow pointing to it. Zooming in on that area of the node in C, you can see the tops of the epithelial cells looking vaguely like cobblestones, with white strings scattered around. These are ciliated cells, and the strings the whip-like cilia that would be swinging around in a clockwise rotation if the cells were alive. You can watch a QuickTime movie of node cilia to see it in action.

When you watch those cilia spin around, here's the subtle but important thing to look for: their paths don't form perfect circles, which would indicate that they are pointing straight up at you, but are instead deformed to varying degrees, showing that they are tilted at an angle…and they are all tilted in the same direction, towards the posterior end of the embryo.

node
Trajectory of Node Cilia Movement (A) Trace of node cilia in enhanced DIC images after background subtraction. Positions of root are indicated in black, and tip in blue, green, and orange. Most cilia have a pattern consistent with the projection of a tilted cone (blue and green, see text) whereas some cilia move in a D-shape (orange). A, P, L, and R refer to anterior, posterior, left, and right sides of the node, respectively. The direction of cilia rotation was clockwise (arrows). (B) Relationship between essentially rotatory movement of cilia and their projected images at various tilt angles.

That tilt is what generates the left-right asymmetry. The tilt isn't asymmetric—all of the cilia are aimed just a little bit posteriorly, rather than straight up—but because the cilia are also rotating in a clockwise direction, it generates unequal lateral forces.

node
Flow Generation Mechanism. Circular clockwise motion of a cilium can generate directional leftward flow if its axis is not perpendicular to the cell surface but tilted posteriorly. Due to distance from the cell surface, a cilium in the leftward phase (red arrow) drags surrounding water more efficiently than the rightward phase (blue arrow), resulting in leftward force in total (purple arrow).

Because of that tilt, the left-to-right stroke drags along the surface of the cell, and is less efficient at generating fluid flow. The right-to-left stroke, on the other hand, swings up and away from the cell and into the medium, and effectively pushes fluid to the left. It's a very elegant way to create handedness using an existing anterior-posterior axis to amplify the chirality of the rotating cilia into a directional shift.

The authors cleverly made a mechanical model of cilia with rotating wires in a viscous silicone medium (another QuickTime movie here), with glitter used as a marker that could be seen streaming specifically to one side. That's how this would work in a real animal: start with a symmetrical embryo which is secreting diffusible molecules from a central point like the node, and then the rotation of the cilia sends the bulk of those molecules streaming to just the left side. Those molecules then induce biases in the pattern of differentiation of one side over the other, leading to all our familiar internal asymmetries.

It should also be obvious why a rare genetic disease, Primary Ciliary Diskinesia, which causes defects in ciliary motors that prevent them from rotating, is also associated with a condition called situs inversus (not all cases of situs inversus are caused by PCD, however), in which humans have their internal asymmetries reversed—heart larger on the right, appendix on the left, etc. If the rotors aren't spinning properly, they don't generate the sideways force, so the molecules are randomly spread to both sides…and in those cases it's just luck which determines which way the asymmetries will form.


Nonaka S, Yoshiba S, Watanabe D, Ikeuchi S, Goto T, et al. (2005) De novo formation of left–right asymmetry by posterior tilt of nodal cilia. PLoS Biol 3(8): e268.


Trackback url: http://pharyngula.org/index/trackback/2747/BSVUeeML/

Comments:
#36012: — 08/16  at  02:49 PM
Lately it seems hearts really are larger on the Left.



#36013: — 08/16  at  02:51 PM
Oh boy...... this is going to send Charlie Wagner into conniptions. You heard it here first.



#36018: notheory — 08/16  at  03:41 PM
::laughs::

When i first saw this title, i thought it was regarding political differences.

This is cool even if it didn't connect with my original expectation ;)

In conclusion, David Horowitz is an intellectual pygmy.



#36023: — 08/16  at  04:12 PM
Very cool!!! I curious, though... does having a consistent left-right asymmetry confer a survival advantage, or is it just an evolutionary side effect? Or is it the developmental remains of a now-defunct adaptation, like a cat's broken sugar receptor? How far down the tree do you have to go to find the first consistent asymmetries?



#36025: Jeremy Henty — 08/16  at  04:27 PM
OK, so why do the cilia always rotate clockwise? Is it down to the chirality of proteins? And why do organisms develop a consistent chirality even when the cilia don't rotate? Surely if the cells are just wandering around any old how you'd get situs ambiguous rather than situs inversus?



#36028: — 08/16  at  04:38 PM
A note on all that cellular migration:

[Amoeboid properties of cells during early morphogenesis and the
nature of a possible protozoan ancestor of Metazoa]

[Article in Russian]

Seravin LN, Gudkov AV. 2005. Zh Obshch Biol. 2005 May-Jun;66(3):212-23.

Data analysis reveals that cells of most of the metazoans (especially
from the phyla Spongia, Placozoa and Cnidaria) at the early stages of
morphogenesis demonstrateas amoeboid properties i.e. ability to form
pseudopodia, to move by means of pseudopodia and to phagocyte. In
different degress these properties could be found at the late stages
of embryogenesis and even in adult organisms. Moreover, during
gastrulation and blastulation blastomeres is able to form flagellas
and than loose them and return to amoeboid activity. These and other
facts indicate that both amoeboid and flagellate types of cellular
organization are programmed in the genome of metazoan cells, as well
as their ability for mutual transformation. It leads to suggestion
that ancestors of Metazoa were amoeboflagellates. Anarchic cleavage
observed in some invertebrates evidences that separated blastomeres is
able to aggregate into the unite embryo due to cytotaxis. Aggregation
of artificially separated cells of sponges, trichoplax and cnidaria
results in complete recovery of the organism by cytotaxis. Thus, there
are reasons to suppose that ability of cell aggregation was inherited
by the Metazoan genome from the amoeboflagellate ancestors. Thus
amoeboflagellates may be considered as forerunners of Metazoa, i.e.
Prometazoa.

Publication Types:

* Review
* Review, Tutorial

PMID: 15977428
<url href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15977428&query_hl=4">Pubmed</url>



#36030: — 08/16  at  05:01 PM
I think I've mentioned this here before, but I once got to take a tour of a medical school's morgue and saw a lot of cool specimens, including the torso of a guy whose internal organs were a mirror image of what's common. They discovered the anomoly when he went in for gall bladder surgery and the surgeon couldn't find the gall bladder. It turned out to be on the opposite side.

It was pretty cool, which is why I talk about it a lot. That and the two-headed baby. (Well, fetus -- it was miscarried.)



#36033: Keith Sader — 08/16  at  05:14 PM
That is one of the coolest things I've read in quite some time. Thanks PZ!



#36034: ekzept — 08/16  at  05:26 PM
so, PZ, have the fields of "diffusible molecules from a central point like the node" been mapped? i'm not aware of practice in zoology and barely in plant work. but it seemed that the chemical fields governing taxis in plant has been mapped, last time i checked. that could be simply because they stay put.



#36061: rob loftis — 08/16  at  08:19 PM
Cool. I second Jeremy Henty's question, and want to see Mnemosyne's two headed baby.



#36063: Burt Humburg — 08/16  at  08:20 PM
It's worth mentioning that at least some of the asymmetries noted in Dr. Myers' essay are due to environment more than genetics. For example, it is thought that the heart's disproportionately large left side is due less to genes for "Big left heart" than it is due to the fact that the left side of the heart has a much bigger job to do. (The right side simply has to pump to the lungs and back. The left side has to pump to the whole body.)

An analogy would be primary pulmonary hypertension, where the circulatory system of the lungs requires a higher blood pressure to get the blood through. The heart responds by increasing the size (and thus the strength) of the right side of the heart.

This is not to detract from PZ's article. In fact, it's downright nitpicky in comparison. My only point, which I'm sure Dr. Myers knows only too well from his job, is that it's oftentimes hard to tell the difference between nature and nurture when looking at a single, simple phenotype.

Great essay, Dr. Myers!

BCH



#36074: coturnix — 08/16  at  09:56 PM
Great! When I saw this on PLoS I just had a feeling PZ would cover it here. Thank you.



#36075: — 08/16  at  10:17 PM
You're missing the forest for the trees, Burt. Yes, the right side of the heart is smaller because it only pumps to the lungs. But *why* does that side always pump only to the lungs, and the left side always to the rest of the body? That's just how it's 'wired' into the circulatory system; there's no reason why that shouldn't be flipped, and the pulmonary arteries & veins attached to the left side. Or rather, there is, way back when the heart was developing in the embryo ...



Trackback: It's just a jump to the left Tracked on: PhaWRONGula (72.9.234.70) at 2005 08 17 08:17:02
At your time of gastrulation, Feeling flattish, so to speak, You've a groovy indentation: Dare I say, "your primitive streak"? And a...



#36138: saurabh — 08/17  at  11:19 AM
Mnemosyne - musta been here. I remember that, as well as mention of the fact that identical twins are sometimes right/left mirrors.



#36143: charlie wagner — 08/17  at  11:25 AM
Andy Groves wrote:

" Oh boy...... this is going to send Charlie Wagner into conniptions. You heard it here first."

Not so.

A "conniption" is a "fit of violent emotion, such as anger or panic." An event like that would most likely kill me, so I avoid it at all costs. wink

Good hard science, however, still gives me a rush and this is no exception. Unfortunately, there's damn little of it in the so-called "debate" that rages on. From now on, I prefer to stick strictly to science and leave ideology to those with more energy.
Speaking of "you heard it here first", more than 10 years ago I wrote that what you refer to as evolution is the unfolding of a program that was already present at the time that life first arrived here on earth. Scientists are now using the term "evo-devo" to demonstrate the importance of studying the molecular and genetic signals that control developmental processes and are linking that to evolutionary processes. The parallel between developmental programs and evolutionary programs is becoming clearer.
It is time for science to attempt to regain its credibility by abandoning the ridiculous neo-darwinian paradigm and embracing the new "evo-devo" weltanschauung.
This is not a concession to creationists as much as it is an affirmation of the scientific method.



#36151: — 08/17  at  12:13 PM
Tell us more about the program that was present at the beginning, Charlie. Where did the program reside?



#36160: Kagehi — 08/17  at  01:13 PM
The only problem with your assertion being Charlie, that we know the program itself has changed over time and grown more complex. The more we come to understand the language, the less 'room' there ends up being for some sort of, "from the dawn of time", code. More so, since that would imply a total lack of one thing that is observed, multiple species. How after all can the program, unless it was thousands of times more complex (and therefor took up more code than found in any single cell organism) determine that there needs to be trees, but also squirrels. And that is the key problem. The most primitive single cell organisms have just enough code to define themselves, not everyone else that could have derived from them. So either every species in existance has 'lost' code over time, which completely contradicts the evidence, or the code has been growing over time, which 'is' supported by the evidence.

As for science throwing out the darwin paradigm, and embracing something else, it already has, which is what people like you and the nuts that support ID in general, don't get. The problem here is that evo-devo no more supports your version of facts than darwin did, so asking scientists to abandon something they don't use, to accept something they do, but which **still** contradicts your belief in some master program won't get you anything but laughed at.

Any priest or shaman must be presumed guilty until proved innocent - Robert A. Heinlein



#36178: charlie wagner — 08/17  at  02:46 PM
Andy Groves wrote:

" Tell us more about the program that was present at the beginning, Charlie. Where did the program reside?"

We don't even understand the molecular and genetic signals that drive the developmental programs and we've been looking at them for a very long time.
The neo-darwinian paradigm almost completely discounted developmental importance in understanding evolution. No one has ever looked for these programs, so none have been found. We're only just now beginning to look at epigenetic factors in development. Once we sort out the molecular and genetic aspects of developmental programs, we might begin to get some hint about evolutionary programs.
The important thing is that for science to move foward, neo-darwinism and the modern synthesis must be abandoned. While mutations, selection, drift, gene duplication are real phenomena, their role in evolution has been minimal and trivial.



#36181: charlie wagner — 08/17  at  02:53 PM
Kagehi wrote:

"The most primitive single cell organisms have just enough code to define themselves, not everyone else that could have derived from them."

Simply not true.

http://tinyurl.com/abvuo



#36187: — 08/17  at  03:42 PM
That's an interesting table that you link to Charlie.

Umm, Kagehi didn't say "single cell organisms have enough code.." Kagehi said "The most primiative single cell organisms..."

Whether this claim is true or not depends on the definition of primitive. I think that there is room to argue that some of those single cell organisms are not primative as such, at least in comparison to other single cell organisms. Or do you, Charlie, working on the assumption that all single celled organisms are primative?

A minor quibble perhaps.



#36190: Kagehi — 08/17  at  04:20 PM
Umm. Charlie, in case you haven't noticed a 'gene' is a 'series of base pairs'. You know, kind of like this sentence is a series of letters. With only 5,386 base pairs in 10 genes, there is hardly much 'information' in them. A rats gene for insulin contains 119 pairs by itself. http://t1dbase.org/bcgb/cgi-bin/gene_more.cgi?bc_ann_id=159 That is 518 119 instructions on how to 'produce' just one chemical. A program to print "Hello world" to a computer screen in DOS, using assembly took the equivalent of 30 instructions, but that *doesn't* include the int 21h code that performs a dozen other things at the same time (lets assume that is another 100, to be charitable). If you wrote one that does what the insulin gene does, which isn't to simply move the data, but take other chemicals and 'build' the result, you would easilly reach of exceed the 518 genes in rat insulin and still have something that **only** produced the words "Hello world". And coincidentally, 5,386 based pairs divides 'almost' perfectly by 10, that leaves maybe 206 base pairs for your 'master program', and that is only *if* you first assume that all 'genes' are exactly 518 base pairs in length.

But that hardly matters. We know that unused code for other things that species don't use is sometimes left over. Usually it ends up with a enough changes to take on a completely different function than before. But there simply isn't enough of it, or any single part of it that is so similar to what is in all other species, to be a master program. It does code for things all of them share in common, and rarely in 100% identical ways, but there is no evidence for it dictating that A will become B in X generations. There simply isn't any room for such code in the genomes.

Your chart only says that when species develop special features, like poisons to fend off other animals, the number of genes needed to make it work 'increases'. For your assumption to be correct. E. Coli would have to consist almost 'entirely' of your imaginary master code.

Any priest or shaman must be presumed guilty until proved innocent - Robert A. Heinlein



#36193: Kagehi — 08/17  at  04:36 PM
Here is an even better one:

http://www.biologie.uni-hamburg.de/b-online/e35/35c.htm

*two* genes, with around 2,500 base pairs.

Or even viriods, that rely on the host to replicate (they lack the 'copy' code needed to replicate themselves) and have only 240-400 necleotides (another word for base pairs). Hmm. Kind of hard to find a magic super program in that. lol

Any priest or shaman must be presumed guilty until proved innocent - Robert A. Heinlein



#36208: ekzept — 08/17  at  05:57 PM
so, charlie wagner when you write:
The important thing is that for science to move fo[r]ward, neo-darwinism and the modern synthesis must be abandoned. While mutations, selection, drift, gene duplication are real phenomena, their role in evolution has been minimal and trivial.
what do you mean? sorry if this physics-trained computer scientist is being dense. are you arguing for a teleological mechanism of some kind in the biological background, at least one that "seeks complexity" or something? if so, hasn't that been argued before?

or do you mean something else, something simpler?



#36209: ekzept — 08/17  at  06:01 PM
The most primitive single cell organisms have just enough code to define themselves, not everyone else that could have derived from them.
Simply not true.
well, isn't there a semantic dispute here about what "code" means? after all, as important and useful as a signature genetic information in DNA or RNA is, it's not much good without machinery to read it out, or with some kind of plasm about it to protect and manage replication. and any mechanism where non-adjacent codons cooperate to produce proteins suggests there's coding in the geometrical and mechanics of strand arrangements as well as in the existence of sequences of base pairs.



#36324: — 08/18  at  04:09 PM
Charlie - your answer was part no-answer-at-all, and part nonsense ("mutations, selection, drift, gene duplication are real phenomena, their role in evolution has been minimal and trivial."). Rather than going through it, let me rephrase the question.

Do you think your primordial ur-program was coded in genetic materal? If not, where was it coded.



#36364: charlie wagner — 08/18  at  07:44 PM
Andy Groves wrote:

"Do you think your primordial ur-program was coded in genetic materal? If not, where was it coded."

This is a most interesting question. Of course, I don't know the answer, but I'm not above speculation.

I believe that this program resides in the epigenome, which controls the differential expression of genes in specific cells, influencing the programming of gene expression profiles. Little is known about the non-covalent module of the genome, the chromatin and its associated chromatin modifying and remodeling activities although our understanding is rapidly increasing.
Acetylation, phosphorylation and methylation seem to be important players. They alter the structure of the chromatin and determine the state of activity of the genes by regulating the access of the transcription machinery to transcriptional regulatory regions.
Removing methyl groups has been shown to both activate and deactivate genes, but the deactivation aspect has been underappreciated. For example, it is well known that the genetic information in humans is present for hirsutism, but our lack of body hair is the result of the deactivation of existing genomic sequences.
Evolution and development are two sides of the same coin and epigenetics, which are inheritable modifications to chromosomes and genes other than changes in the DNA sequence itself, may be the key to understanding both.



#36379: Kagehi — 08/18  at  09:59 PM
While its not well known, this is nonsense. There is still **more** of that epigenome in animals that have evolved significantly, than in ones that have not and somehow I suspect that the data in the E. Coli for that is **still** far smaller that needed to contain your master code. Once again, for such a things to exist, it must be basically the same for all species. The real irony here is that from what I have seen, the unknown code you are talking about is even *more* different between species than the genetic code is, which would seem to completely contradict the idea that it contains such a predetermined path for everything to follow. Not to mention the other fly in the ointment, which is your admittance that it changes, due to the same mutations as regular genes do. I.e., it is just a susceptable to radiation, copying errors and other problems as the rest of the genes in an animal. Such a program would have to be a) fixed, b) contain, in some fashion, code for 'all' species, or at least how to make them, and c) completely immune to changes that would effect its proper operation. And you flat out admit 'we' can change it in a way that causes it to 'not' work as intended.

Try again.

Any priest or shaman must be presumed guilty until proved innocent - Robert A. Heinlein



#36421: charlie wagner — 08/19  at  09:27 AM
Kagehi wrote:

" While its not well known, this is nonsense."

Your statements seem to fall into two general catagories:

1. unsupported assertions and
2. so what?

For example, you state:

"There is still **more** of that epigenome in animals that have evolved significantly, than in ones that have not and somehow I suspect that the data in the E. Coli for that is **still** far smaller that needed to contain your master code."

This covers both catagories. You offer nothing more than "I suspect" as evidence. In addition, we know that lateral transfer of genetic information occurs all the time. It doesn't have to be the genome of one organism. Maybe there is a pool of genetic information that exists across multiple forms and is drawn upon by evolutionary algorithms. Sort of like a chinese menu: "one from column A, 2 from column B"

You write:
"for such a things to exist, it must be basically the same for all species."

Why so? What justifies this intrepid claim?

You write:

"from what I have seen, the unknown code you are talking about is even *more* different between species than the genetic code is, which would seem to completely contradict the idea that it contains such a predetermined path for everything to follow."

If the code is "unknown", then how do you know that there are more differences between species than in the genome itself? Again, you offer nothing more substantial than "seem to completely contradict".

You write:

"which is your admittance that it changes, due to the same mutations as regular genes do. I.e., it is just a susceptable to radiation, copying errors and other problems as the rest of the genes in an animal."

The fact that accidental errors can occur is not evidence that directed processes are not at work. The genome has a quite elegant mechanism in place for correcting the majority of these errors, so clearly they are undesirable and not beneficial.

You wrote:

"Such a program would have to be a) fixed, b) contain, in some fashion, code for 'all' species, or at least how to make them, and c) completely immune to changes that would effect its proper operation. And you flat out admit 'we' can change it in a way that causes it to 'not' work as intended."

It can be fixed by the DNA repair apparatus and most errors are.
Insofar as "code for 'all' species" is concerned, the cell and it's genetic apparatus is nothing less than a universal automaton. The protein synthetic apparatus alone can both replicate itself and also, given the correct information, construct any other biochemical machine, no matter how complex, as long as its functional units are proteins. Because of the almost unlimited number of ways in which proteins can be assembled and organized, this gives the cell almost unlimited potential. And the potential for assembly, organization and regulation lies in the epigenome.



#36504: Kagehi — 08/19  at  05:32 PM
"It can be fixed by the DNA repair apparatus and most errors are.
Insofar as "code for 'all' species" is concerned, the cell and it's genetic apparatus is nothing less than a universal automaton. The protein synthetic apparatus alone can both replicate itself and also, given the correct information, construct any other biochemical machine, no matter how complex, as long as its functional units are proteins. Because of the almost unlimited number of ways in which proteins can be assembled and organized, this gives the cell almost unlimited potential. And the potential for assembly, organization and regulation lies in the epigenome."

And all of this would make sense for 'any' system, not just one following some bizarre master code. And some of your statements are entirely contradictory. How for example can a program function properly if if depends on the interaction of two seperate species and say someone dynomites the valley in between them, cutting them off from each other. Or for that matter, landslide or other events that happen all the time naturally? For such a code to exist implies an active role in making sure nothing screws it up, by seperating critical species, which makes no sense. Why if some being can make 100% sure that species A and species B will 'always' be near each other, so that the needed cross-connections will happen, would it even need a program that would work that way in the first place. As for how much I do or don't know about epigenes, I never the less do know that they tend to make up maybe, at most, half the material in a species' chromosomes. This means you have a program that is still too small in something like E. Coli to do jack.

And your wrong, if there was an almost unlimited way proteins can be assembled, we wouldn't see such a large similarity between species. Chemically some proteins are more stable than others, this is a basic fact. Which means, in general, like everything else with genetics, only those that are 'stable enough' will be used, same reason why we even have proteins in the first place, instead of a miriad of both 'less' and 'more' stable chemicals instead. I might not be an expert, but even I know this. Your simply trying to argue from even greater ignorance that something should be possible, simply because you don't have a clue why its impossible.

Any priest or shaman must be presumed guilty until proved innocent - Robert A. Heinlein



#36513: ekzept — 08/19  at  06:16 PM
Insofar as "code for 'all' species" is concerned, the cell and it's genetic apparatus is nothing less than a universal automaton. The protein synthetic apparatus alone can both replicate itself and also, given the correct information, construct any other biochemical machine, no matter how complex, as long as its functional units are proteins.
umm, use of the term "automaton" triggered my interest. granting for the moment that the apparatus is equivalent to a universal automaton, which it may or may not be, that universality confers much less than it might first seem. for instance, synthesis of something might take longer than the time to next cell division.

but, besides that, i think it's pretty clear the protein synthesis mechanism in the cell for any particular species has severe limitations, and i'm almost tempted to add "thankfully".

so, i wonder, at what point and on what timescale does this hypothetical epigenetic information operate? does it operate at each moment during the life of a cell? does it operate just during cell replication? and what does the individual cell get out of having it?



#36515: charlie wagner — 08/19  at  06:48 PM
Ekzept wrote:

"so, i wonder, at what point and on what timescale does this hypothetical epigenetic information operate? does it operate at each moment during the life of a cell? does it operate just during cell replication? and what does the individual cell get out of having it?"

Good question.

Look at a human body. Although each cell has the exact same genetic information as every other cell, different cells are doing different things in different locations and at different times. So control of these "programs" involves delicate timing, in which genes are turned on and off at different places and at different times to generate the development and homeostasis of the organism. Some genes are used early in development and are never again used at all. Others activate or deactivate and different points in the life of an organism.
Transferring this thinking to an evolutionary perspective, it seems logical that the same kind of "timing" must occur in the emergence of new structures, processes and adaptations. I suspect that the majority of these programs have already run their course, that most, if not all of the major structures and processes have emerged and that evolution as we know it, is basically over.



#36519: ekzept — 08/19  at  07:02 PM
Good question....Transferring this thinking to an evolutionary perspective, it seems logical that the same kind of "timing" must occur in the emergence of new structures, processes and adaptations. I suspect that the majority of these programs have already run their course, that most, if not all of the major structures and processes have emerged and that evolution as we know it, is basically over.
whether the question was good or not, i wasn't seeking generalities. what i meant was, what selective advantage does the epigenetic information confer on the cell that bears or activates it? i don't necessarily mean a competitive advantage. i mean an advantage to outweigh the energy costs of copying and activating the epigenetic information.

even if this epigenetic stuff's copying costs are negligibly small, swept along with copying the remainder of the genome, at some point, if it is relevant, that epigenetic stuff has to be activated and do something. at that point it does cost energy. if the cell does not gain from its operation, that energy is withdrawn from other activities which are essential for survival. so, i ask again, what's the win for the cell?



#36520: charlie wagner — 08/19  at  07:15 PM
Ekzept wrote:

"what i meant was, what selective advantage does the epigenetic information confer on the cell that bears or activates it? i don't necessarily mean a competitive advantage. i mean an advantage to outweigh the energy costs of copying and activating the epigenetic information."

I simply don't think about this in terms of "selective advantage" or "energy costs". Those are neo-darwinian relics that I have long ago purged from my thinking.

You wrote:

"if the cell does not gain from its operation, that energy is withdrawn from other activities which are essential for survival. so, i ask again, what's the win for the cell?"

The win for the cell is that there's an almost unlimited amount of energy available to it, so who cares if some is wasted? If there was a limited supply of energy and machines had to compete for it, that might be an issue. But there is not and they do not, thanks to photosynthesis and chemosynthesis.



#36521: — 08/19  at  07:29 PM
Those are neo-darwinian relics that I have long ago purged from my thinking.
Yet you kept the bathwater ...



#36526: ekzept — 08/19  at  08:17 PM
I simply don't think about this in terms of "selective advantage" or "energy costs". Those are neo-darwinian relics that I have long ago purged from my thinking.
well, the model proposed invoked the concept of an automaton. i'm entertaining it as a serious hypothesis. as such, it needs to explain how a signal from a possible, remote future gets from there to the individual cell which acts upon the proposed epigenetic information in order to "induce it" to do so. the induction is, of course, statistical. that is, by implementing the hypothetical epigenetic program, the population of cells is drawing down on its energy resources and, so, is made more susceptible to challenges from competition and the environment. all i'm observing is that there are penalties for carrying out the postulated epigenetic program. what counteracts those penalties? in other words, what's the mechanism for carrying that information to the automaton?

consider a simpler case: why do trees on steep hillsides grow antiparallel to the gravity gradient and not perpendicular to the hillside?



#36530: ekzept — 08/19  at  08:19 PM
i should add that whatever your hypothesis is, if it cannot answer these questions which "neo-darwinian relics" can, it is already inferior by any scientific standard.



#36586: charlie wagner — 08/20  at  08:52 AM
Ekzept wrote:
"consider a simpler case: why do trees on steep hillsides grow antiparallel to the gravity gradient and not perpendicular to the hillside?"

Well, we know that this reponse is to gravity, but we have not yet answered the questions about how the stimulus is perceived and how it is transmitted.

You wrote:

"it needs to explain how a signal from a possible, remote future gets from there to the individual cell which acts upon the proposed epigenetic information in order to "induce it" to do so."

Probably the same way that signals get to the zygote and cause it to differentiate into the various structures, processes and systems of the developing organism.

You wrote:

"the population of cells is drawing down on its energy resources and, so, is made more susceptible to challenges from competition and the environment."

There is no support for this conclusion. The amount of energy used is of no consequence in an environment of unlimited energy resources. There is no "need", there is no "competition" and there is no "advantage". These are human qualities and to ascribe them to cells is anthropomorphic.

As I said before, we are barely beginning to understand the molecular and genetic signals that drive development. We are a long way off from understanding how they drive evolution. But I suspect that once we understand the former, we will be further along to understanding the latter.



#36591: ekzept — 08/20  at  09:50 AM
Well, we know that this reponse is to gravity, but we have not yet answered the questions about how the stimulus is perceived and how it is transmitted.
what absolute rubbish! gravitropism and its mechanism is standard curriculum in junior high school biology. if a growing tree tip tilts away from axis antiparallel to gravity the local concentration of the plant hormone auxin is increased on the side farthest away from vertical and its concentration decreased on the side nearest vertical. it's akin to oil in the bottom of a skillet. when the skillet is tilted, the oil runs to one side. for plant stems, auxin encourages cell growth. thus, the side away from the veritical experiences a flourish of cell growth, whereas the rate of growth on the opposite site is diminished. so, as the tree tip grows, it straightens. this is quantitative enough that it can be expressed as a differential equation.

of course without knowing this, charlie wagner had zero hope of explaining anything else. facts are, a mechanism for transmitting information of what is the local perpendicular to the surface is more complicated than a mechanism which relies upon an ever-present local signal like gravity. for the tip of a tree to "know" what is the local perpendicular, that information would need to be conveyed from the contact of the tree with the surface, near the roots, through the tree to the tips, using some signalling system. that's elaborate, complicated, and, so, undesirable.

it's hard to imagine taking anything you write seriously if the most basic biological knowledge is missing. the hypotheses posed are trying to explain a make-believe world.
Probably the same way that signals get to the zygote and cause it to differentiate into the various structures, processes and systems of the developing organism.
that's hand-waving, and useless as science. need to make a specific, verifiable prediction don't ya know. the power of natural selection is that it does provide a direct signal and mechanism locally available to each and every cell of each and every organism. it does not require any roundabout hand-waving. in cases where individual cells initiate processes harmful to themselves, like the apoptosis needed for differentiation during development of macroorganisms, the chemical signals of the cell's surround are choreographed to arrange the result. but apoptosis also serves a survival purpose, which the article cited describes, e.g., in the case of viral infection. in fact, if there are any global signals of the kind you're speaking of, the signaling pathways which initiate apoptosis are probably them.
There is no support for this conclusion. The amount of energy used is of no consequence in an environment of unlimited energy resources.
oh, i imagine physical laws don't apply to biological organisms. they imbibe energy for free from the environment. guess those mitochondria are really quite superfluous. eating is optional. get a clue.

biological cells need nutrients in order to produce energy, even if they are part of a macroorganism. again, without understanding the basics of biology or in this case biophysics, the hypotheses are constructed for a make-believe world.



#36606: charlie wagner — 08/20  at  11:38 AM
Ekzept wrote:

"what absolute rubbish! gravitropism and its mechanism is standard curriculum in junior high school biology. "

First of all, I would not rely on Wikipedia for my information.
While the statolith theory is one possible explanation, it is not a proven mechanism. The statolith theory claims that sedimentable amyloplasts in central cap cells (the statoliths) become aligned as a result of constant gravitational acceleration. This alignment then generates the production of auxins, which then dictate the direction of root growth.
As you probably know from your courses in physiology, most such chemical reactions in living organisms are carried out rather slowly, with a significant time lag, one of the reasons why there are enzymes to speed the reactions up.
In order for this mechanism to be useful in plants, these changes must occur very rapidly in reponse to changes in gravity. Roots will adjust at least 5 degrees towards the natural downward alignment within minutes, with a threshhold value for the gravity change that is dauntingly small.
Despite research that has strengthened the statolith theory, we have not yet answered the questions how the stimulus is perceived and how it is transmitted. And we have not explained the causal chain in multicellular roots where stimulus perception and gravitropic reaction take place. In short, a "black box" exists between stimulus perception and reaction and this "black box" can be assembled from any number of different system components.
Certainly, some kind of signaling system is necessary, perhaps one in which the sedimented amyloplasts and their cellular environment act as a signal transformer but the nature of this signalling system is as of now, unknown.

You wrote:

"in cases where individual cells initiate processes harmful to themselves, like the apoptosis needed for differentiation during development of macroorganisms, the chemical signals of the cell's surround are choreographed to arrange the result."

Choreographed by whom?
Arranged by whom? or what?



#36610: ekzept — 08/20  at  12:09 PM
While the statolith theory is one possible explanation, it is not a proven mechanism. The statolith theory claims that sedimentable amyloplasts in central cap cells (the statoliths) become aligned as a result of constant gravitational acceleration.
please cite one or more technical papers in refereed scientific journals disputing the statolith theory.
Choreographed by whom? Arranged by whom? or what?
i used the qualitative term "choreographed" to refer to, e.g., immune system mechanisms for initiating apoptosis. chemical signaling between cells or even between invading pathogens and immune systems are all about exchanges of markers and triggers that cause one or the other to do something. for pathogens, these are among their most important defenses, notably for viruses.



#36611: ekzept — 08/20  at  12:25 PM
regarding:

While the statolith theory is one possible explanation, it is not a proven mechanism. The statolith theory claims that sedimentable amyloplasts in central cap cells (the statoliths) become aligned as a result of constant gravitational acceleration.

and my request:

please cite one or more technical papers in refereed scientific journals disputing the statolith theory.

this is no longer necessary (see http://spacebio.net/modules/pb_resource/gravshortscript.doc). statoliths have nothing to do with auxins. they are the older theory which the Cholodny-Went hypothesis (see, e.g., http://tinyurl.com/d9tup) supplanted.

stop wasting my and everybody's time. i now choose to ignore you.



#36613: charlie wagner — 08/20  at  12:49 PM
Ekzept wrote:

"stop wasting my and everybody's time. i now choose to ignore you."

Thank you for taking the time to respond to my comments.

Just as the soft rains fill the streams,
pour into the rivers and join together in the oceans,
so may the power of every moment of your goodness
flow forth to awaken and heal all beings,
Those here now, those gone before, those yet to come.

By the power of every moment of your goodness
May your heart's wishes be soon fulfilled
as completely shining as the bright full moon,
as magically as by a wish-fulfilling gem.

By the power of every moment of your goodness
May all dangers be averted and all disease be gone.
May no obstacle come across your way.
May you enjoy fulfillment and long life.

For all in whose heart dwells respect,
who follow the wisdom and compassion, of the Way,
May your life prosper in the four blessings
of old age, beauty, happiness and strength.



#36639: Kagehi — 08/20  at  05:20 PM
Did I just imagine it, or has Charles just tried to imply the long debunked 'free energy' concept and some form of perpetual motion system to explain why his system can both function based on physical laws that demand that the majority of energy produced by 'all' known processes is lost, but it doesn't effect his imaginary system?

Any priest or shaman must be presumed guilty until proved innocent - Robert A. Heinlein



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