Grateful-UnDead, you might want to check out Endless Forms Most Beautiful, a really good layperson’s book on developmental biology that shows how the genome steers the timing and chemistry of developmental events and gives some good examples of how small genetic mutations in key places can alter body plans, number of limbs, bone lengths, &c.
Particularly interesting to you should be the part about mutants and monsters–while I promise that magicking your morphic resonances won’t do any harm, there’s quite a nice gallery in the book that shows how tinkering with genes and chemistry can make fruit flies with feet instead of eyeballs and glow-in-the-dark spotted butterflies. Pretty cool stuff, and I encourage you to take a little break from Sheldrake and read about it.
The thing I object to most is patronizing ignorance.
You may note in the posts above, that I have made a point of the fact that I know little about Rupert Sheldrake, and even less of his theory. I ordered his book in order to read about it, and learn something of what he has to say. You may be well advised to do the same.
What he may, or may not have to say, has no bearing on the questions I asked.
Your patronizing response demonstrates that not only do you fail to understand the questions, but you also fail to appreciate the complexity of biochemical processes, both in isolation, and within living entities.
The questions I have asked are being asked by scientists all over the world, and the taxpayer pays millions of dollars a year in research grants in order to progress science towards answering those questions.
The fact that such research continues is a clear indication that the answers to the questions I have asked are not expected to be forthcoming in the foreseeable future, and your glib response is little more than a demonstration of arrogant ignorance.
(a-ha! you just hit the bit of developmental biology where I know anything worth a damn…)
Careful there. The example you picked is from C. elegans development, and though it’s a useful model system it’s quite unlike vertebrate development in many ways. In C. elegans, every cell type at every step in development is specifically defined, and cell lineages are invariant*. Cell fate decisions are made with each cell division, from the very beginning. Figure 1 from the page you cite describes the cell lineages for the first few divisions, and the entire lineage looks something like this.
In contrast, vertebrate development is a lot less rigid. You have populations of cells that can develop into all sorts of different tissues, depending on where they happen to be in the embryo and what developmental cues the receive from other tissues. So for example you can take a clump of cells from one part of the embryo and move them somewhere else, and in many cases they’ll develop into a structure appropriate for the new location.
So C. elegans embryo polarity is really determined by the first cell division, which (I believe) isn’t the case with vertebrate embryos. Early cell divisions in vertebrate embryos are completely undifferentiated until a certain point, though as you mention there are some early cues from the zygote that remain and eventually determine embryo polarity.
*at least as far as anyone knows. Some poor bastard named John Sulston spent years watching cells divide under a microscope, tracking each one through the entirety of development. Oh and he discovered apoptosis along the way and won a Nobel prize for it…
It is ad hoc and random and exquisitely baroque, because that’s how evolution produces new forms from existing ones. Every mutation that alters an existing structure or creates a new one does so in the context of all of the other developmental processes that are still going on. So if a segmented worm, for a hypothetical example, evolves into something with legs and a head, it’ll do so by building on the existing genetic logic that produces segments. There might be a new gene that specifies lateral outgrowth from certain parts of certain segments. It might be activated only in the absence of some developmental signal that’s present in the midline of the organism, and also in the absence of signals that mark the boundaries of each segment. When those conditions are met, this new gene then activates growth of proto-limbs by activating yet another developmental signal that promotes growth of skin and muscle. Presto, this segmented worm now has stubby little bumps on its side, and it’s on its way to continue evolving into something like a velvet worm.
And everything is still tightly controlled – only mutations that still result in a viable and successful organism can be passed on to the next generation. Evolving a new physical form is a bit like rebuilding a boat that’s floating far out at sea: you can only do so by preserving the structures that keep it afloat.
I do have to second the recommendation for “Endless Forms Most Beautiful” (d’oh… that one slipped my mind earlier).
As for Sheldrake’s “morphic resonance”, well… that idea is refuted by huge masses of evidence from over a hundred years of developmental biology. You’re right that there are lots of scientists that are currently performing experiments to learn more about development, but Sheldrake really isn’t one of them. His ideas are not backed by experimental data at all, particularly with regards to development, and are really just fanciful products of his imagination.
As a physicist, this was always one of the mysteries for me. How does left-right asymmetry emerge? For all practical purposes the laws of physics do not distinguish left from right, so how does the spherical embryo almost always decide correctly which side to put the spleen on? Of course, we have known since Pasteur that the molecules of life are handed (asymmetric with respect to right and left). Randomly, the most recent common ancestor of all life chose a specific handedness for amino acids, which all life forms have inherited. So the information about left-right asymmetry is in every cell, but it perplexed me what physical process takes this information and uses it to specify the left and right hand side of the embryo.
The recent discovery of the process involving cilia, that Smeghead described, explains it all. Cilia are helices. All helices are inherently handed, just like a screw - there are left handed helices and right handed helices. The molecular structure of a cilium is well understood. It is a complex, but regular collection of microtubules and other biomolecules. The microtubules are also helices, formed as polymers of protein subunits, each of which is handed because of the handedness of its amino acid constituents. Thus, it is clearly seen how the handedness of the amino acids, which was established by a molecular accident in our distant past, leads to handedness of microtubules, and thus the handed helical structure of cilia. As a small patch of cilia beat in the early embryo, it sets up a chemical gradient that establishes a center of asymmetry, leading to our bilaterally slightly asymmetrical bodies. “Endless forms most beautiful,” indeed!
The responses above address the issue of organism development in a macro sense; current theories of genetics provide a framework to explain why a mutation can cause a leg to grow out of a head, for example. In the context of this discussion, this is not an issue.
What I a still curious about are the issues of control, and the consequent consistency of product. So far we have discussed two factors of control: timing and concentration.
In order for any organism to develop, a number of events at the cellular level must occur in a precise sequence, and at a precise time in the overall time line of its development.
What is it that sets that clock, how are the timing signals transmitted, and how is the effect of that clock applied to all the processes on the time line? What happens if one particular process slips off the time line?
Secondly, it has been noted that concentration effects are critical. Different concentrations of components can result in different cellular outcomes. Since this is the case, how is concentration controlled; ie: without extremely precise concentration control, it should be impossible for any coherent organism to develop. So what is the controlling mechanism? I acknowledge the effects of sweeping celia, but this appears to a very limited mechanism considering the hundreds, if not thousands of reactions occurring at any given time.
These are not trivial questions. As anyone who has ever run a reaction in a test tube knows, timing and concentration are critical to the final product distribution.
In that biological processes occur in a “test tube” that normally would contain hundreds, if not thousands of reagents simultaneously, how is it that biological reactions so consistently produce the defined organism from that soup?
Obviously the cells communicate with each other using tiny, tiny PSI transceivers. The Architect Cells direct the Contractor Cells, which in turn direct the Sub-Contractor and Worker cells.
I would suggest that you are not entirely correct in this, in that you do not address the following issues:
a. Is the process of cell development a closed shop environment?
b. If not, how are demarcation disputes between unionized and non unionized workers resolved?
c. How are protection payments to the mob processed?
d. What mechanisms are in place in order to respond to “stop work” meetings and strikes?
e. In the case of a subcontractor dispute, what are the contingency plans in case of their withdrawing from the job?
f. How are occupational health and safety issues handled? Clearly, the environment contains a lot of “chemicals”, so the worker’s safety must be paramount.
g. When you refer to “cells” are you referring to worker’s democratic collective cells? Or running dog lackey cells?
Probably the simplest way to look at it is that developing embryos have cells which set up a chemical gradient to identify which end of the cell is going to turn into what. So one side of the cell will have a lot of chemical X whereas the opposite side will have very little. When they divide, naturally the first cell will have lots of the chemical and the other cell will have very little. These chemicals help tell the cell which genes get activated and which do not. Gradients can also exist across groups of cells. Also, sometimes the gradient exists not as a changing concentration along the length of the cell, but instead as differing amount of concentration in the various cell organelles.
These chemicals are called morphogens. Often they will be a protein which binds to the promoter, or part of a gene that controls it’s transcription. The initial gradient can be established by mRNA and helper proteins moving along microtubules, the internal support structure of the cell. Usually some sort of gradient is already present in the fertilized egg.
Your response encapsulates the state of scientific knowledge regarding biological processes: we have a lot of fragmentary descriptive knowledge of individual processes, but we have virtually no knowledge of the actual driving forces behind those processes.
In other words, we know a bit about the “what”, but very little about the “why” or the “how”.
Any human activity requires the input of managers; the greater the complexity of the activity, the more conspicuous management is required.
Even the most basic of cells is a hugely complex organization, involving a myriad of interrelated processes. All of these processes require very finely tuned and efficient organization and co-ordination, otherwise the cell dies.
The logistical and process complexities of the internal functions of any living cell exceed anything so far conceived, let alone executed, by humanity.
Yet, despite the application of the intelligence of thousands of scientists over a period of at least a hundred years, we have no coherent plausible explanation for its operations.
The usual glib explanation is that it is all driven by DNA; “DNA” is the answer to all questions.
However, DNA is little more than an agglomeration of inert atoms; it can be duplicated and replicated in a test tube from its base atoms, just like many other inert molecules. When observed in a test tube, it just sits there; just like any other dead thing.
There is no dispute that the function of DNA is to create proteins. In terms of process, there seems little dispute that DNA is a template for RNA, which in turn is a template for proteins. The resultant proteins function as either building blocks for tissues, or enzymes for chemical processes.
Beyond being a template for proteins, DNA is also attributed with breathtaking powers of design, organization, execution and control; these powers exceed anything humanity has ever been able to effect.
Yet, in that DNA is a template for proteins, no explanation is forthcoming as to how these proteins or enzymes can transmit all the powers attributed to DNA.
So how is it that an inert, dead molecule, displays more intellectual power than that of all of humanity combined?
Most scientists scoff and sneer at the very concept of “magic”; yet the powers they attribute to DNA are nothing short of magical.
Not really. All it encapsulates is my attempt to give a very simplified overview of the process. Developmental biology textbooks are quite thick. There’s plenty more detail out there for anyone who is curious for a more extensive understanding.
We know quite a bit. Most of our ignorance is in details.
Not really. A lot of human behavior is more or less self organizing. You need some sort of rule book or relaying of instructions (like DNA!) and some sort of signaling like announcements or clocks (chemical signals for the most part).
Which is why cellular clocks were evolved and refined very very early and have remained relatively unchanged since then, because they are so essential and unforgiving of error.
Cities are far more complicated.
Ha! Maybe you just don’t like the explanations? They are certainly there, at whatever level of detail you are willing to read.
No. Each part of the cell has an important function. DNA is the part with the instructions, so it tends to get special attention, but noone is saying it’s the only player.
There’s no such thing as an inert molecule. Even ignoring all of the various chemical reactions and inter molecular forces, at such a small scale and reasonably high temperature, all liquids are incredibly active, just from thermal motion. And things have extremely rapidly compared to our scale.
And while DNA does do a few things on it’s own owing to it’s structure and molecular attraction to itself, most of the interactive things it does, it does with the help of other chemicals.
Think of it this way - suppose you have a bunch of small sticks with rows of magnets on them, but the magnets aren’t all facing the same way, so you might have a stick with magnets lined up as NSSSNSNSSSSN. Now it might partially stick to other randomly arranged sticks, but it’s only going to stick really tight to a magnet with the exact opposite N-S arrangement. Now suppose you put a whole bunch of sticks with different arrangements in a tub of water and shake it or swirl it vigorously. Most of these “inert” sticks are going to pair up with their counterparts.
There is no dispute that the function of DNA is to create proteins. In terms of process, there seems little dispute that DNA is a template for RNA, which in turn is a template for proteins. The resultant proteins function as either building blocks for tissues, or enzymes for chemical processes.
I believe human DNA could fit on a single CD-ROM. It’s not actually that complicated.
The cool thing is that proteins translate really simple construction data into incredibly complex molecules. Pretty much all proteins are just strings. The complexity comes from the way they fold up.
You’ve gotten quite a few examples in this thread. Do you really want us to list every single gene in sequence followed by it’s purpose? I think you can extrapolate from the examples already given.
It’s not inert, and it doesn’t demonstrate any intellectual power at all. It’s just a list of instructions.
Is an airplane magical? It seems pretty neat, but it wasn’t invented wholesale. It gradually got to it’s current level of complexity after many many smal improvements over the years.
Humans are so complex because they have evolved for billions of years. The earliest life forms were single celled and had a much shorter and less complex DNA strand.
I think you are confusing “I haven’t bothered to read a book about it” with “nobody knows anything about it and it must be the work of fairies”.
No, you seem to have got my point, then missed it again.
I am not disputing the fact that we have a huge body of knowledge regarding individual functions of biological systems; consistent with this, I am well aware of the explanations that you and others have previously posted.
However, I am also well aware of the boundaries of our current knowledge regarding the functions of biological systems.
So, to reiterate my point: while we have a large body of fragmented knowledge of individual processes, we are lacking a coherent explanation that ties it all together.
In other words, as you yourself said above: “most of our ignorance is in the details”.
It is the details that I am interested in; and when delving into the details the most common and glib explanation is “DNA”.
Grateful Un-Dead: speaking as a PhD student in molecular biology, I can state that you’re severely overstating the level of our ignorance. Nobody believes that DNA has “magical” powers, and a massive amount of work is going on to understand exactly how these things that seem so magical to you work. Here’s the thing: a lot of this work has been and continues to be successful. We know much MUCH more about how the system works than we used to. We’re beginning to understand the importance of things like epigenetics, with codes of histone modifications beginning to be worked out, or chromatin structure, or the roles and prevalence of transcription factors.
Do we understand the whole system enough to be able to describe every last detail or model it in a computer? No, of course not. Science is quite happy to acknowledge what we don’t know - after all, that’s where our funding lies. No one’s going to pay for us to study something we already understand. But to make the leap from that to say that we’re just handwaving away complexity with mutters about “DNA” is just silly and wrong. It’s an absolutely fascinating area of research.
What does that even mean? Can you give an example of a ‘coherent explanation that ties it all together’ for any thing which you feel humans do understand well? What would that look like to you?
This sounds like the complete opposite of your statements “we are lacking a coherent explanation that ties it all together” and “Large body […] individual processes”.
If you are getting glib answers then you must be asking glib questions. I think you’ve gotten fairly reasonable answers to your specific questions. It sounds like want you really want a magic wand to take away your astonishment. But that’s not necessary. Something can be astonishing without one assuming it’s also miraculous.
It only seems amazing because it’s fairly complicated. And it’s only complicated because it’s been changing by small steps for a very long time, and because it involves feedback loops. Any system that changes over a very long time and has feedback loops will get more complicated.
Think of the complexity of our technology. Even if you sent a genius engineer back in time, he couldn’t replicate our technology, because in addition to the knowledge, you also need the infrastructure. Better tech allows for better infrastructure, which facilitates better tech, in a feedback loop. Similarly, if you just stuck the human genome in a bacteria cell, it wouldn’t function properly because it doesn’t have all the various bits of cellular infrastructure that have evolved in human cells over time.
“DNA” is ultimately the protagonist of this story. It’s both the plot and the main character. The basic raison d’être of all of life is to facilitate the replication of genes (see: Richard Dawkin’s The Selfish Gene"), except perhaps with humans who evolved another replicant, the meme. Cells and higher lifeforms pretty much boil down to being robots whose entire purpose is to create more copies of the genes they reside in.
DNA (or RNA in more primitive lifeforms) can’t act alone, and the other parts of the cell are also vital, but most important processes involve it in one way or another, mostly because it encodes the manufacture of proteins, which are incredibly simple to make but also incredible in the diversity of their final structures.
I really feel like people have done a fairly good job of answering your specific questions. You don’t seem to like the answers for some reason. You seem to simultaneously want an overall answer to everything and also more specific answers. I think you’ve gotten both. Scientists really do have a pretty good handle on how developmental biology works. I think if you read a book on it, you’d get a better sense of that. There’s plenty out there, from the simpler more conceptual text, to thick chock full of specific detail books. They explain in great detail the things that seem to be confounding you, like intra- and inter-cellular signaling, and biological clocks.
Before you get too bogged down with the ‘how’ and ‘why’ aspect of thing, consider modern organisms like they are wikipedia pages. You seem to be using a mistaken metaphor of 'there must be one author who thought out this really long article, but no one is smart enough to write such a long well thought out article!" whereas as the truth is, the article started out as a single simple sentence, and only came to become this long complicated intricate article after billions of tiny simple edits one at a time, over a long period of time.
There’s no ‘overall plan’. There’s many independent yet interdependent agents which have modified their relationship in increments. DNA is just the instruction book for how to put your IKEA furniture together. It has nothing to say about the purpose of your couch.
It should also be pointed out that cellular biology is often very sloppy and does not proceed in the most efficient and logical manner. You have genes that can only be expressed if micro interfering RNA from another gene blocks the activity of still other genes. If you were going to design a a biological system from scratch, I think you would opt for a much simpler approach to producing that particular protein. This tells you that a certain amount of random chance was probably involved in the evolution of this process. The fact that the procedure became reliable and reproducible over the millenia is simply a testament to its importance and not necessarily the wisdom of it’s design.
In light of the fact that we seem to have become somewhat bogged down here; and the fact that “jackdavinci” and others have made some comments that sent up some flares, I went down to the library this morning.
I ended up spending the whole day there, until the very cute librarian kicked me out and turned out the lights.
Boy is my face ever red!
Seems that in the years since I last cracked a bio text book, many of the issues that have been nagging at the back of my mind, have been addressed and moved along. There is a lot more clarity now, than there was then.
While there is still a gap in our knowledge, it is a lot smaller than it used to be. It also explains why there has been this conceptual gap between my questions and the responses given.
As result, my reading list has just become a couple of books longer, and Amazon is celebrating.
