DNA Encoding of Human Body Structures - A Question

[HAL]

First, I don't know what I'm talking about in this area, so that's why I'm asking for opinions on this. I know it isn't known yet but I'd appreciate your speculation.

I was thinking about human body parts, and the fact that they must somehow be encoded in the DNA. Somehow, the structure of things must be defined in the DNA. Take for example the bones of the ear. They are pretty exacting structures.

For example the Incus bone. It has a 3D shape and thus certain dimensions that can't vary too much. Do you think it's a code that starts/stops in the DNA? That somehow if the coding was known, it could be plugged into a computer interpreter and drawn on a computer screen? Or am I completely off-base here. Help me out with your opinions.


http://www.learnbones.com/middle-ear-bones-anatomy

[Tero]

No it does not work quite that way. There is interaction at all levels. Proteins formed by DNA inertact aftewards.
http://en.wikipedia.org/wiki/Developmental_biology

see also hox gene.

[Tero]

the fly embryo developing

[Tero]

I could not find a video for bone, but it is kind of late in the embryo development
http://www.ncbi.nlm.nih.gov/books/NBK10056/

[HAL]

No it does not work quite that way. There is interaction at all levels. Proteins formed by DNA inertact aftewards.

But what data set is controlling the formation? Where is the design for the bone located? Doesn't the design have to be encoded somewhere?

[wright]

Correct me if I'm wrong, but you're wondering about how body parts have their growth regulated to a given dimension, or range of size / volume? In other words, how a gene or series of genes lets an organism's body know when to stop?

An interesting question. Understand that this is coming from a curious layman with no formal background in biology.

Wikipedia had this about gene regulation networks, which govern when certain proteins are produced and when that production stops... http://en.wikipedia.org/wiki/Gene_regulatory_network

If I understand that entry, the regulation process depends not only on genetic information, but on feedback from an organism's environment.

Then there are morphogens, which act directly on cells to produce specialized tissues... http://en.wikipedia.org/wiki/Morphogen

Do you think it's a code that starts/stops in the DNA? That somehow if the coding was known, it could be plugged into a computer interpreter and drawn on a computer screen? Or am I completely off-base here. Help me out with your opinions.

That last would seem to be more of a programming question; a field I know even less about than biology / genetics.

[HAL]

Correct me if I'm wrong, but you're wondering about how body parts have their growth regulated to a given dimension, or range of size / volume? In other words, how a gene or series of genes lets an organism's body know when to stop?

Yes.

The coding is in the DNA, right? So doesn't the design of the bone have to reside there from the very beginning, even though it may have many steps involved. How else could the information for the bone formation be transmitted?

[Tero]

Watch he videos. The bone was not designed. DNA produced the growth and it follows in a certain order. But the interaction of the cells is not designed, it evolved. Each organism changed it a bit. So the mapping of DNA to structure is not there. DNA is not a blue print.



There is another video on the human heart. It makes two chambers, then three then four. I imagine each step is a bit of new DNA but it goes thru the discarded models to get to our heart.

[HAL]

Watch he videos. The bone was not designed.

Oh I don't mean I believed it was "designed". I mean there is a design that is carried forward though.

DNA produced the growth and it follows in a certain order.

That's what I'm asking about.

But the interaction of the cells is not designed, it evolved.

Yes I know this.

Each organism changed it a bit. So the mapping of DNA to structure is not there. DNA is not a blue print.

Start over - I'm not asking the question very well, I admit. How can the bone be formed without information? It can't - that's impossible. So, where does the information come from initially in the organism?

[Tero]

The instuctions are there but it all has to do with starting and stopping cell division. Nerves grow from the spine to the target organ.

[Tero]

The heart tissue has to divide just in this order to make 4 chambers.

[shnozzola]

Thanks for the videos, Tero.   Mouse eye gene inserted in a fruit fly makes a compound eye for a fruit fly -  Hey anti evolution folks - GET OVER HERE!!

[Tero]

We are getting into text book stuff here, so no free videos. The most studied embryo is the cchicken, the wing bud story:
http://www.nature.com/nrm/journal/v7/n1/box/nrm1830_BX1.html

If you cut tissue and paste it wrong, it will grow parts here and there in the wrong shape.

Beyond that you have to buy textbooks to get some more pictures.
http://onlinelibrary.wiley.com/doi/10.1002/cne.903020316/abstract

[HAL]

The instuctions are there but it all has to do with starting and stopping cell division. ...

Yes, of course, and thanks for the videos. But I'm asking a question at a way, way lower level. Basic instruction level. I know everything develops, and it's fascinating.

That's not what I'm asking, really. I'm asking where the code would be that gets the body to a heart or incus bone. It has to be there from the start. Has to be - right? So, in the DNA, isn't the code for a heart or specific bone there, in some basic primeval form? I don't know how else to ask the question.

[Tero]

No, there is no code for a bone. There is only code to divide the cells in a certain order. Then there is code inside each cell as to what type of cell it becomes. It turns off all the genes it longer needs as a skin cell, muscle cell or nerve cell. Some cells are in the area where they make bone, but bone is also cellular matter, it is not dead.

[Cyberia]

Think of DNA as a ".zip" file, that decodes to a BUNCH of smaller RNA ".rar" files, that decode to an astronomical amount of Protein ".exe" files.

It's the proteins that are functional, but they can do a HUGE range of functions, and in order to be able to simulate it ona  computer, you need to know EVERY POSSIBLE type of "function" that can be preformed, without exception, and we don't although it's theoretically possible.

This is the kind of mess you get after 4 billion years of evolution, NO designer would do this.

[Tero]

There's no more pictures, so read this
http://www.amazon.com/Developmental-Biology-Ninth/dp/0878933840/ref=sr_1_1?ie=UTF8&qid=1330999213&sr=8-1

or this:
http://www.amazon.com/Developmental-Biology-Short-Introduction-Introductions/dp/0199601194/ref=sr_1_2?ie=UTF8&qid=1330999213&sr=8-2

I only read the 7 dollar book.

Hal, no problem. I kept asking the same question. The answer is that the question is wrong! We can give you answers but not the ones you want.

[HAL]

No, there is no code for a bone. There is only code to divide the cells in a certain order. ...

Think of DNA as a ".zip" file, that decodes to a BUNCH of smaller RNA ".rar" files, that decode to an astronomical amount of Protein ".exe" files.

OK, got it. How would you describe the initial DNA code? Is it just an instruction set for when (or where) to divide cells?

[Tero]

DNA can only make proteins, via RNA. The interaction of all these is all the starts and stops and inactive parts. Naked DNA has start and stop codes. See genetic code in Wiki. So those are the proteins it can make but it does not make all of them.

[Cyberia]

OK, got it. How would you describe the initial DNA code? Is it just an instruction set for when (or where) to divide cells?

The proteins control cell multiplication/division/etc.  DNA is just a compressed container format for them.

[Tero]

Would this help, HAL?
http://ds9a.nl/amazing-dna/

he recommends Dawkins, but the only book with any DNA discussion is this
http://www.amazon.com/Greatest-Show-Earth-Evidence-Evolution/dp/B004AYCWY4/ref=sr_1_1?ie=UTF8&qid=1331000802&sr=8-1

[HAL]

Would this help, HAL?
http://ds9a.nl/amazing-dna/

LOL - it will - tomorrow morning. I've had a couple glasses of wine, so it's best read in the morning, but I will do it!

[Tero]

Many genes are the code for a specific protein. It makes enzyme such and such, in every cell. It is these proteins involved in the growing embryo that are hard to track down as a specific effect.

[Fiji]

In The Greatest Show On Earth, Dawkins draws the analogy that DNA is like the recipe for a cake rather than the blueprint for a building. In a finished cake, you can't possibly say which parts are the egg and which the butter.
I guess that theoretically it would be possible to write a program that reads DNA and produces the resulting phenotype. But it's going to be QUITE a program. And you'd need to add loads of rules about how this and that works in the real world. Rules that essentially are not in the DNA itself.
(and now, I've probably gone and made things less clear!)

[HAL]

In The Greatest Show On Earth, Dawkins draws the analogy that DNA is like the recipe for a cake rather than the blueprint for a building. In a finished cake, you can't possibly say which parts are the egg and which the butter.

Yes but, your missing one thing - the instructions for making the cake aren't in the cake. If you have the instructions to make the cake - you can reverse-engineer how it came to be a cake. For the cake example, the instructions are outside the cake, in a person's memory, or on a piece of paper.

In the body, we do have the initial instructions - the DNA. So I guess I still would say, however complex it would be, that a program should be able to read the DNA sequence and make a model of a human body on a computer. maybe not today but in the future.

[monkeymind]

In The Greatest Show On Earth, Dawkins draws the analogy that DNA is like the recipe for a cake rather than the blueprint for a building. In a finished cake, you can't possibly say which parts are the egg and which the butter.

Yes but, your missing one thing - the instructions for making the cake aren't in the cake. If you have the instructions to make the cake - you can reverse-engineer how it came to be a cake. For the cake example, the instructions are outside the cake, in a person's memory, or on a piece of paper.

In the body, we do have the initial instructions - the DNA. So I guess I still would say, however complex it would be, that a program should be able to read the DNA sequence and make a model of a human body on a computer. maybe not today but in the future.

Well, scientists are on their way to doing something similar to this already. Craig Venter Institute and Synthetic Genomics have reversed engineered a bacteria using a computer program and generated synthetic DNA. There was a press conference on TED, I believe.
http://www.jcvi.org/

Synthetic Genomics developed the first self replicating bacterial cell. It has been referred to as a “self replicating species whose parent was a computer.” Using four chemicals, they created a synthetic bacterial chromosome and inserted it into a bacteria, “booting it up."

They used yeast which assembled the gene sequences in steps. In order to make sure they were
looking at a synthetic chromosome without contamination (a molecule of organic bacteria that
was replicating) they inserted watermarks.

The watermarks consisted of a code within a code within a code which allowed them to use DNA
code and create groups of nucleotides corresponding to Greek characters. They then “wrote
in” the names of 46 authors and contributors, their website, and three quotations:

To live, to err, to fall, to triumph and to recreate life from
life.-James Joyce

To see things not as they are but as they might be. - From the book by
American Prometheus
(about Oppenheimer).

What I can not build I can not understand.- Richard Feynman

[Tero]

DNA is just code for proteins. How they interact with each other and DNA is called emergence. The interactions are so complex you wont be able to count and list them all. Proteins have a life of their own. There is in fact mote info than just in the DNA.

Hox genes are just the tip of the ice berg, but they are all building instructions: turn on eye or leg construction etc. But DNA does not control all directly. Proteins evolve...dna help needed.. to produce best organim.

[Tero]

One thing that is never clear to creationists is that all our ancestors were winners. All were functional, each tiny change in proteins was tested. So there is change in both DNA and proteins.

[inveni0]

Yes, it's coded into DNA.  But DNA isn't the end-all for structure.  Environment, diet, and other outside forces can change structure.

When I was growing up, I had twin neighbor friends.  Identical.  But not EXACTLY identical.  I could tell them apart because their moles were different.  Shouldn't the moles be hardcoded in the DNA?  No.  It's mutation that causes moles.  Just like mutation can cause bone malformation.

Can we use this code to grow bone?  Sure.  In fact, we've done this on the backs of mice to grow new ear tissue for humans.  It's the DNA in the cells that are transplanted that cause an ear to grow where it should not be growing.  That's why stem cells are so important.  They can become any kind of cell...meaning that they contain all of the code necessary to grow a human body.