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DNA question


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#1 Lode   Members   -  Reputation: 982

Posted 10 February 2013 - 06:30 AM

Hello,

 

I know this is quite off topic, but this is the most intelligent and interesting forum I know, so ...

 

I've been reading some things about DNA, but nothing seems to answer my questions:

 

-DNA has "instructions" to create enzymes. These enzymes are then catalyzers of processes in the cell. However, this would mean the order in which the DNA codes appear does not matter, since catalyzers would operate all at once, isn't it? But afaik the order of the codes in DNA should matter, otherwise it wouldn't contain a lot of information. What am I understanding wrongly here?

 

-Apart from the ability of copying itself (which is needed to copy cells of course), DNA/enzymes also have functions for modifying DNA, like splitting or adding bases. What is the point of those, shouldn't DNA mainly have instructions that determine the shape of the organism or cells rather than itself?

 

-DNA determines processes within a single cell. Every cell of the organism has the same DNA. However, it affects the shape of the complete organism, and in differnt locations in the organism are different types of cells. How can something that is the same in every cell and only affects processes in a single cell, determine the whole shape of a complete organism with billions of cells?

Thanks!



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#2 frob   Moderators   -  Reputation: 22184

Posted 10 February 2013 - 10:32 AM

First, I have no idea about those specific items. I don't think we have any gamedev members who are also PhD's in biochemistry or DNA.

DNA research is just a form of reverse engineering. We have a massive executable and are trying to decode it.

A huge amount of DNA is "noncoding DNA", aka "junk DNA", which scientists know is important but have no idea what it does or why it does it. For humans it is currently about half of our DNA.


So far all we've been able to identify with reverse engineering are a few individual bits:

These six bits have a correlation to eye color. Those seven bits have a correlation to height. These other thirty bits have a correlation to a specific genetic disorder.

It would be like studying the executable and save files from a massive game. There is a huge executable and a huge amount of data files that we have no clue what they do or why they do it. We have figured out some bits of the save files. We have even figured out a handful of small functions in the executable.

We can identify what a few bits do here and there, and some of the small programmatic instructions have been decoded, but we are a LONG way from actually understanding how it actually works.

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#3 SiCrane   Moderators   -  Reputation: 9624

Posted 10 February 2013 - 11:13 AM

DNA in the cell isn't just long strands of nucleic acids. DNA coils around proteins and those coils themselves form coils. These tightly wound coils aren't transcribed. Some proteins will come around and uncoil certain sections marked by certain DNA prefixes for transcription. At any given time only a small fraction of the chromosome is actually exposed for transcription, so not every enzyme is coded at the same time.

As for how the same code in each cell will generate a complex organism, consider looking at cellular automata. Most cellular automata we study have extremely simple rules that can generate complex patterns, like Conway's game of life. DNA is much, much more sophisticated that these simple rules.

#4 szecs   Members   -  Reputation: 2170

Posted 10 February 2013 - 11:43 AM

Enzimes are pretty big molecules, so the sequence of the DNA "codes" do make up specific enzimes. As far as I know, there are "end of molecule" instructions.

Maybe the sequence of these big "strings" doesn't matter, or maybe it only matters in the order of syntetisation, or the "availability" of more common molecules.

 

But I'm surprised that this isn't explained somewhere


Edited by szecs, 10 February 2013 - 11:43 AM.


#5 sunandshadow   Moderators   -  Reputation: 4978

Posted 10 February 2013 - 12:07 PM

The order does matter locally, though the different chromosomes are not in any kind of order relative to each other.  Here look at the picture:

GP.GeneticCode.GIF

This is showing that three bases, in order (this is called a codon) result in an amino acid.  If they were in a different order it would be a different amino acid, or none.  Then the amino acids are hooked together in order like beads on a string to make a protein.

 

Here's another picture, showing how the three letter codes correspond to many different amino acids; that's how dna stores lots of information.

dna.jpg


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#6 minibutmany   Members   -  Reputation: 1640

Posted 10 February 2013 - 02:03 PM

Am I correct that the DNA does not determine the shape of the organism, but DNA just codes for proteins, which determines certain traits? In many experiments scientists inject the DNA of the glowing jellyfish that makes them glow into another organism, they now make the protein that glows but they do not turn into jellyfish.


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#7 TheChubu   Crossbones+   -  Reputation: 4544

Posted 10 February 2013 - 02:34 PM

they now make the protein that glows but they do not turn into jellyfish.

Yep, many dreams were crushed that day.


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#8 SiCrane   Moderators   -  Reputation: 9624

Posted 10 February 2013 - 02:35 PM

DNA is used to create RNA. Most RNA is used to create proteins, but some RNA can do things on its own like ribozymes. As far as we know, DNA is the prime driver behind the processes of cell division, apoptosis and cell specialization, which together as a whole control the shape of an organism.

#9 Lode   Members   -  Reputation: 982

Posted 10 February 2013 - 02:49 PM

Am I correct that the DNA does not determine the shape of the organism, but DNA just codes for proteins, which determines certain traits? In many experiments scientists inject the DNA of the glowing jellyfish that makes them glow into another organism, they now make the protein that glows but they do not turn into jellyfish.

 

But what if they inject it in the very first cell after fertilization?!



#10 SiCrane   Moderators   -  Reputation: 9624

Posted 10 February 2013 - 04:18 PM

Usually the egg dies. Even for DNA from the same species.

#11 laztrezort   Members   -  Reputation: 968

Posted 10 February 2013 - 04:53 PM

DNA research is just a form of reverse engineering. We have a massive executable and are trying to decode it.

Massive, and horrendously obfuscated. If a programmer came up with designs akin to what evolution has produced, we wouldn't know whether to fear him for his genius or institutionalize him for his madness. In any case, he would likely get fired. smile.png

Edited by laztrezort, 10 February 2013 - 04:54 PM.


#12 sunandshadow   Moderators   -  Reputation: 4978

Posted 10 February 2013 - 04:54 PM

Am I correct that the DNA does not determine the shape of the organism, but DNA just codes for proteins, which determines certain traits? In many experiments scientists inject the DNA of the glowing jellyfish that makes them glow into another organism, they now make the protein that glows but they do not turn into jellyfish.

DNA determines everything (if you include mitochondrial DNA, which is separate from the chromosomes in the nucleus, and if you exclude bacteria which have RNA instead of DNA).  HOX genes are the ones that determine major body areas; some of them are similar in organisms as different as insects and humans.

buswold_john_1.jpg

An error in this kind of gene is how you get flies with legs where antennae should be, and that sort of thing.

 

In the jellyfish example they are not injecting ALL of the jellyfish's DNA, only the small strand that is related to the glowing.


Edited by sunandshadow, 10 February 2013 - 04:56 PM.

Phone game idea available free to someone who will develop it (Alphadoku game - the only existing phone game of this type is both for windows phone only and awful. PM for details.)


I want to help design a "sandpark" MMO. Optional interactive story with quests and deeply characterized NPCs, plus sandbox elements like player-craftable housing and lots of other crafting. If you are starting a design of this type, please PM me. I also love pet-breeding games.


#13 BCullis   Crossbones+   -  Reputation: 1813

Posted 10 February 2013 - 11:38 PM

As for the reason behind DNA order:

 

(I briefly considered the idea of being a geneticist when I first went to college)

 

Proteins behaviors and structures of multiple proteins (like hemoglobin, the protein complex responsible for transporting oxygen in your blood) are due to their 3d structure, which is created according to a folding pattern, and that folding pattern is due to the order in which the amino acids are attached to the protein's AA chain.  Hydrophyllic vs hydrophobic sections will cause certain 3d structures as the protein folds up.  This is why the order of DNA encoding is so important, because proteins do just about everything important in our cells.

 

This is also why prions are so freakin' scary: they misfold proteins.  No cell functions for you, thanks.


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#14 BLM768   Members   -  Reputation: 295

Posted 11 February 2013 - 03:07 AM

HOX genes are the ones that determine major body areas; some of them are similar in organisms as different as insects and humans.

 

Just thought I'd add onto this point a bit:

 

Since all cells in the body contain the same HOX genes, there must be some external factor influencing which cells express specific HOX genes. One factor that controls the expression of the HOX genes is the presence of certain chemicals; in the embryonic environment, there is typically a gradient of chemical concentrations that gives the embryo a general idea of which directions are "up", "forward", "right", and so on. Once the cells begin differentiating, they produce additional chemicals that further refine their specialization.






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