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It's not a surprise that the number of genes does not determine complexity of an organism. The humble C. elegans (roundworm) has ~20000 genes, similar to human

by j7ake 8y ago

It's not a surprise that the number of genes does not determine complexity of an organism. The humble C. elegans (roundworm) has ~20000 genes, similar to humans. The complexity comes with the regulation of these genes, which are in the noncoding regions of DNA.

j16sdiz 8y ago
The question is: how organism evolve complexity if no new genes are added? You can regulate the genes to "disable" the complexity, but those genes need to be there in the first place....
- 0-_-0 8y ago
  Check out Saplosky's lectures on Youtube, he deals with this question. Particularly this one: https://www.youtube.com/watch?v=_dRXA1_e30o https://www.youtube.com/watch?v=_dRXA1_e30o
- j7ake 8y ago
  Proteomic diversity can be generated through alternative splicing of genes. Functional diversity of the same gene can be generated through context-specific regulator-to-promoter interactions.
trashtester 8y ago
True, and at least at two levels: 1) The amount of DNA does not determine the complexity of an organism. 2) Also, the number of protein-coding genes does not determine the complexity of an organism. You may have meant (2), and only (2). If so, this is clearly true, as much of the complexity comes from non-protein DNA. Still, (1) is also true, but one could argue, more due to random inefficiencies, or alternatively if you rank degree of complexity based only on phenotypes. My preferred definition of complexity, or rather of irreducible complexity, is to say that complexity is determined by the minimum number of bits of information that is needed to create an equivalent output. (where, naturally, the definition of equivalence needs to be supplied for a given domain) By this definition, DNA length (not number of genes) places an upper bound on complexity an organism can have.
- karmakaze 8y ago
  I was in part saying (2) with the main point being something else, that complexity of the rules i.e. amount of total/active DNA does not have to be the same as the complexity of what's produced. As an analogy, the literal rules of Go are simpler than any other game I know, the gameplay that results from those rules are the most complex. Another example might be rules for how to construct a deeply conneced NN can by very simple, once built and trained it can exhibit complex behaviour not seemingly bounded by the size of the rules of construction.
  - trashtester 8y ago
    Ok, interesting point. Ultimately, one could say that a fairly simple set of rules (the laws of physics), generate all complexity in the universe. To take the NN example: Clearly it applies to species, like humans, with a significant cultural and learning element to our being. Much of our complexity is learned socially or by interacting with our environment. In fact, this is done by training the NN in our brains. Edit: Note that our brains can store much more information than our DNA, making the upper bound on complexity for a human the sum of storage capacity in the DNA + the sum of storage capacity in the brain. But for species with little ability to learn, like jellyfish, wouldn't it be more appropriate to say that the "training of the NN" is analogous to evolution optimizing the DNA? That would mean that, for a given individual, their complexity is all included in their DNA at birth? In that case, one could argue that the length of the DNA string does create an upper bound on how much complexity it can contain. I suppose that is the case for the NN, too. The total number of bits in the weights of the network is an upper bound on the complexity a given, already trained, network can have. (Of course, the possible complexity of the network is way, way higher than that of the program that creates it.)
amacbride 8y ago
Exactly. Not too terribly long ago, estimates for the number of human genes ranged as high (or higher) than 100,000. Instead, we found significantly fewer genes, but with much more complicated regulatory networks and novel mechanisms (such as whole classes of regulatory RNAs.)

by j7ake 8y ago

j16sdiz 8y ago

The question is: how organism evolve complexity if no new genes are added? You can regulate the genes to "disable" the complexity, but those genes need to be there in the first place....

0-_-0 8y ago
Check out Saplosky's lectures on Youtube, he deals with this question. Particularly this one: https://www.youtube.com/watch?v=_dRXA1_e30o https://www.youtube.com/watch?v=_dRXA1_e30o
j7ake 8y ago
Proteomic diversity can be generated through alternative splicing of genes. Functional diversity of the same gene can be generated through context-specific regulator-to-promoter interactions.

trashtester 8y ago

True, and at least at two levels: 1) The amount of DNA does not determine the complexity of an organism. 2) Also, the number of protein-coding genes does not determine the complexity of an organism. You may have meant (2), and only (2). If so, this is clearly true, as much of the complexity comes from non-protein DNA. Still, (1) is also true, but one could argue, more due to random inefficiencies, or alternatively if you rank degree of complexity based only on phenotypes. My preferred definition of complexity, or rather of irreducible complexity, is to say that complexity is determined by the minimum number of bits of information that is needed to create an equivalent output. (where, naturally, the definition of equivalence needs to be supplied for a given domain) By this definition, DNA length (not number of genes) places an upper bound on complexity an organism can have.

karmakaze 8y ago
I was in part saying (2) with the main point being something else, that complexity of the rules i.e. amount of total/active DNA does not have to be the same as the complexity of what's produced. As an analogy, the literal rules of Go are simpler than any other game I know, the gameplay that results from those rules are the most complex. Another example might be rules for how to construct a deeply conneced NN can by very simple, once built and trained it can exhibit complex behaviour not seemingly bounded by the size of the rules of construction.
- trashtester 8y ago
  Ok, interesting point. Ultimately, one could say that a fairly simple set of rules (the laws of physics), generate all complexity in the universe. To take the NN example: Clearly it applies to species, like humans, with a significant cultural and learning element to our being. Much of our complexity is learned socially or by interacting with our environment. In fact, this is done by training the NN in our brains. Edit: Note that our brains can store much more information than our DNA, making the upper bound on complexity for a human the sum of storage capacity in the DNA + the sum of storage capacity in the brain. But for species with little ability to learn, like jellyfish, wouldn't it be more appropriate to say that the "training of the NN" is analogous to evolution optimizing the DNA? That would mean that, for a given individual, their complexity is all included in their DNA at birth? In that case, one could argue that the length of the DNA string does create an upper bound on how much complexity it can contain. I suppose that is the case for the NN, too. The total number of bits in the weights of the network is an upper bound on the complexity a given, already trained, network can have. (Of course, the possible complexity of the network is way, way higher than that of the program that creates it.)

amacbride 8y ago

Exactly. Not too terribly long ago, estimates for the number of human genes ranged as high (or higher) than 100,000. Instead, we found significantly fewer genes, but with much more complicated regulatory networks and novel mechanisms (such as whole classes of regulatory RNAs.)