Self cloning "blue" crayfish?

[ScatMan]

Pretty much. Way to simplify it!

I don't deny the instability of DNA in species that reproduce via other methods. I question the possibility of occurrance in a species that is proven to only reproduce apomictically.

Edit: Perhaps I should amend my stance to state that they are 100% identical, with the possibility to go 99.9999999% identical if some environmental factor causes a change in the dna capable of being passed on to offspring?

another way to say it is: they are 99.99999% identical with an almost zero chance of being 100% identical, considering the improbability (virtual impossibility) of every single one of the billions of base pairs (t,c,g,a) replicating themselves perfectly.

 

[Dark Jester]

it's more than a possibility, it's almost a certainty that some of the billions of base pairs will be changed during the process of dna duplicating itself.

'Almost a certianty' (interesting wording) that something random will happen and be passed on to offspring. Even if 1, 10, or 100 base pairs might change, you then have to worry about whether that potential change can affect the organism in any significant way and also whether that change actually will be passed on to any offspring.

From http://www.talkorigins.org/faqs/mutations.html (linked from your berkely example)

"[4] The human genome has 3 billion base pairs. The average rate of point mutations is about 20-30 in a billion per individual. Almost all point mutations in multi-cellular organisms are strictly neutral. In human beings 90-97% of the DNA is "junk DNA" that does nothing (as best as can be determined.) One third of the changes to codons (sections of DNA that code for proteins) are silent; that is, the DNA changes, but the the amino acid coded for remains the same. Thus 93-98% of all point mutations in humans are strictly neutral."

Thus 93-98% of all point mutations in humans are strictly neutral. So, let's see, I'll go with the high average:

30/1,000,000,000 = 0.00000003 (.000003% chance a point mutation will occur in a base pair)

Potentially 7% of those point mutations are not neutral. 93-98% will have absolutely no effect at all, so I will discount them.

.00000003 / .07 = some infinately small percentage (4.285714285714286e-7)

Now maybe half of that miniscule percentage will be a harmful mutation, which very well might kill the specimen outright. Making sense?

For this next part we'll forget about the chances of whether a mutation is helpfull, neutral, or harmfull. We'll just go off of the .000003% chance a mutation might occur in a base pair.

Now an averave of 30 point mutations in 1 billion base pairs might present 'almost a certianty' to you. From the first paper I found on a crayfish genome, only 15,895 base pairs are present in Cherax Destructor. I can't imagine Marmokrebs' genome being all that dissimilar. 30 in 1 Billion is a .000003% chance of a base pair being subject to a point mutation. That is extremely low odds. When looking at billions of base pairs in a human, you likely will see it happen (though there is always the 'chance' that it won't). The 'average chance' would significantly drop in a species with only 15,895 base pairs. Overall there is a .047685% chance that ANY point mutation will develop at all in a crayfish. You have a much higher chance of absolutely no point mutations. This means that approximately 99.952315% of the time, marmokrebs will be 100% genetically identical.

So .047685% of individuals actually might develop one of these point mutations. Given the fact that only 7% of point mutations mentioned above are not neutral, and that half of those may outright kill the specimen, I think we can reasonably conclude that genetic variation within this species is extremely rare, borderline impossible.

The mutation then still needs the ability to be passed on to offspring too. Wow, that's a small number..

I feel fairly comfortable now stating that Marmokrebs are 100% Genetically Identical. Genetic diversity in this species may be possible, but it is an extremely remote chance.

look around man, i can't do all your homework. dna is not perfectly stable.

I do my own homework, thanks. Actually learned a bit about the human and crayfish genomes, and mutation effects on genetic diversity.

they're not my theories, they're scientific fact.

I like it when the facts come out.

another way to say it is: they are 99.99999% identical with an almost zero chance of being 100% identical, considering the improbability (virtual impossibility) of every single one of the billions of base pairs (t,c,g,a) replicating themselves perfectly.

No, with all of the above, I think I prefer my way of saying it.

 

[ScatMan]

'Almost a certianty' (interesting wording) that something random will happen and be passed on to offspring. Even if 1, 10, or 100 base pairs might change, you then have to worry about whether that potential change can affect the organism in any significant way and also whether that change actually will be passed on to any offspring.

why wouldn't it be passed on? is the mutation supposed to just change back to the way it was? why? how?

we don't have to worry about the mutation being expressed, unless you're only talking about visible difference between parent and offspring, which i'm not.

From http://www.talkorigins.org/faqs/mutations.html (linked from your berkely example)

"[4] The human genome has 3 billion base pairs. The average rate of point mutations is about 20-30 in a billion per individual. Almost all point mutations in multi-cellular organisms are strictly neutral. In human beings 90-97% of the DNA is "junk DNA" that does nothing (as best as can be determined.) One third of the changes to codons (sections of DNA that code for proteins) are silent; that is, the DNA changes, but the the amino acid coded for remains the same. Thus 93-98% of all point mutations in humans are strictly neutral."

Thus 93-98% of all point mutations in humans are strictly neutral. So, let's see, I'll go with the high average:

30/1,000,000,000 = 0.00000003 (.000003% chance a point mutation will occur in a base pair)

Potentially 7% of those point mutations are not neutral. 93-98% will have absolutely no effect at all, so I will discount them.

.00000003 / .07 = some infinately small percentage (4.285714285714286e-7)

Now maybe half of that miniscule percentage will be a harmful mutation, which very well might kill the specimen outright. Making sense?

For this next part we'll forget about the chances of whether a mutation is helpfull, neutral, or harmfull. We'll just go off of the .000003% chance a mutation might occur in a base pair.

it's irrelevant if the mutation is actually expressed or not. i think you might be arguing something different than me, so here's my point again:
they are not 100% genetically identical.

every organism has a different rate of error for copying base pairs and humans have a (relatively) very accurate system for reassembling their dna while other organisms don't (like a virus: 1 in 10,000)

20 - 30 (call it 25) in 1,000,000,000 = 1 in 40,000,000 lets remember this for later...

Now an averave of 30 point mutations in 1 billion base pairs might present 'almost a certianty' to you. From the first paper I found on a crayfish genome, only 15,895 base pairs are present in Cherax Destructor. I can't imagine Marmokrebs' genome being all that dissimilar.

ok, here's another mistake you've made: the 15,895 base pairs you're talking about are in the mitochondrial dna, a tiny tiny portion of dna in the cell wall, NOT i repeat NOT the whole genome(http://en.wikipedia.org/wiki/Mitochondrial_DNA). i'm shocked that you saw a number like 15,895 and didn't immediately think that something was wrong here!

now, i couldn't find how may base pairs are in a crayfish but a honey bee has 236,000,000 (http://en.wikipedia.org/wiki/Genome#Genomes_and_genetic_variation)

using a honey bee as a reasonable model:
236,000,000 / 40,000,000 = 5.9 or approximately 6 pairs per generation difference

assuming a 50-50 chance of there being NO (zero) change in 40,000,000 (this is a generous advantage to your argument because it is much more likely for there to be a change than no change); the likelihood of there being no difference is: 2 (50-50) to the power of 6 (236/40) = 64

a generous 1 in 64 chance of a honey bee being completely 100% genetically identical to it's parent.

now the rest of your argument makes no sense because your data was flawed.

30 in 1 Billion is a .000003% chance of a base pair being subject to a point mutation. That is extremely low odds. When looking at billions of base pairs in a human, you likely will see it happen (though there is always the 'chance' that it won't). The 'average chance' would significantly drop in a species with only 15,895 base pairs. Overall there is a .047685% chance that ANY point mutation will develop at all in a crayfish. You have a much higher chance of absolutely no point mutations. This means that approximately 99.952315% of the time, marmokrebs will be 100% genetically identical.

So .047685% of individuals actually might develop one of these point mutations. Given the fact that only 7% of point mutations mentioned above are not neutral, and that half of those may outright kill the specimen, I think we can reasonably conclude that genetic variation within this species is extremely rare, borderline impossible.

The mutation then still needs the ability to be passed on to offspring too. Wow, that's a small number..

I feel fairly comfortable now stating that Marmokrebs are 100% Genetically Identical. Genetic diversity in this species may be possible, but it is an extremely remote chance.

I do my own homework, thanks. Actually learned a bit about the human and crayfish genomes, and mutation effects on genetic diversity.

i'm glad you're learning but you still have more to learn.

I like it when the facts come out.

good, then you should like that. try having a little humility next time, it helps the with the sting that comes along with making mistakes.

No, with all of the above, I think I prefer my way of saying it.

still?

 

[Dark Jester]

i'm shocked that you saw a number like 15,895 and didn't immediately think that something was wrong here!

I'm still learning.

I guess we were both off the mark. You were comparing them to humans with billions of base pairs, I underestimated the count due to inexperience.

I think we can both agree that a crayfish is not nearly as complex as a human. Comparing to honeybees cannot be used as a basis either though, they're on a completely different branch of the tree.

I'll keep looking for a complete cray genome.

why wouldn't it be passed on? is the mutation supposed to just change back to the way it was? why? how?

I'm pretty sure I read it on that berkely site. Will try to find the link.

Ah, found it: http://evolution.berkeley.edu/evosite/evo101/IIIC1Mutations.shtml

"Not all mutations matter to evolution.
Since all cells in our body contain DNA, there are lots of places for mutations to occur; however, not all mutations matter for evolution. Somatic mutations occur in non-reproductive cells and won’t be passed onto offspring."

So, I guess we need to find out how many base pairs are in reproductive cells? If a mutation occurs in any other cell, it won't be passed on and the child will have the exact same genetic blueprint that the parent started with. Would that be accurate?

i'm glad you're learning but you still have more to learn.

At this point its starting to look like we both do. We keep finding flaws in each others' logic.

 

[ScatMan]

I'm still learning.

I guess we were both off the mark. You were comparing them to humans with billions of base pairs, I underestimated the count due to inexperience.

I think we can both agree that a crayfish is not nearly as complex as a human. Comparing to honeybees cannot be used as a basis either though, they're on a completely different branch of the tree.

I'll keep looking for a complete cray genome.

you wont find it because they haven't been sequenced yet, so i picked the honey bee as a stand in because they have a small genome.

true the crayfish genome is probably somewhere between a human and a bee.

so for the sake of the argument, i picked the honey bee because it has a very small genome and even with such a small genome, it still proves my point that (even under the best case scenario for you) it would be very rare to produce a 100% genetic clone.

I'm pretty sure I read it on that berkely site. Will try to find the link.

Ah, found it: http://evolution.berkeley.edu/evosite/evo101/IIIC1Mutations.shtml

"Not all mutations matter to evolution.
Since all cells in our body contain DNA, there are lots of places for mutations to occur; however, not all mutations matter for evolution. Somatic mutations occur in non-reproductive cells and won’t be passed onto offspring."

So, I guess we need to find out how many base pairs are in reproductive cells? If a mutation occurs in any other cell, it won't be passed on and the child will have the exact same genetic blueprint that the parent started with. Would that be accurate?

the numbers i gave would apply to every dividing cell in their body, not just 1. every time the dna replicates itself, it will have the same rate of error.

At this point its starting to look like we both do. We keep finding flaws in each others' logic.

i'll admit that i don't know everything, but even my flawed logic was considerably more accurate than what you were claiming.

conclusion: while my numbers aren't exact, they are still very conservative and easily demonstrate just how unlikely a 100% genetic clone would be. add in chemical and radiation factors of change and the odds are that much slimmer for a perfect clone.
so lets just to learning!

 

[Dark Jester]

Here's where I am now. Let me know if I'm on track.

So basically, outside of things like single celled bacteria and very simple multi-celled organisms (maybe nematodes are about as complex as it would get?), there really is no chance of a perfect clone.

Can we agree that they are genetic clones for all intents and purposes (just not 100%)? I think the 100% is where we have been differing. Considering that the children do inherit the exact DNA blueprint that the parent has, by any definition I can find, that is cloning. (AKA, Dolly the sheep, etc).

Any mutations that happen after that embryo starts developing will cause some genetic differences. At the point that the embryo is created, it would be a 100% genetic clone of it's parent though? That would be the best point for the potential of being 100% anyway.

Most mutations that do happen are neutral and have no effect on the creature at all. Most of the rest may not have any appreciable affect, very few may have a severe affect. Mutations will not be passed to any offspring unless the reproductive cells are directly affected.

so lets just to learning!

I can agree to that. Learned a lot about genetics this weekend.

 

[ScatMan]

Here's where I am now. Let me know if I'm on track.

So basically, outside of things like single celled bacteria and very simple multi-celled organisms (maybe nematodes are about as complex as it would get?), there really is no chance of a perfect clone.

even in the simplest organisms like a virus, there is an extremely low chance of there being a perfect 100% genetic clone. look at how variable hiv is. they're extremely tiny differences in the big picture but still significant.

Can we agree that they are genetic clones for all intents and purposes (just not 100%)? I think the 100% is where we have been differing. Considering that the children do inherit the exact DNA blueprint that the parent has, by any definition I can find, that is cloning. (AKA, Dolly the sheep, etc).

yes, the offspring get a "xerox" of their parents dna, and like a xerox copy, it's never exactly the same as the original but still the same for all intents and purposes.

Any mutations that happen after that embryo starts developing will cause some genetic differences. At the point that the embryo is created, it would be a 100% genetic clone of it's parent though? That would be the best point for the potential of being 100% anyway.

no, the blueprint that the offspring starts with is slightly different than the parents from the very beginning. the parent cell gives half of its dna strand to the new baby cell to construct a full copy from, and when the new cell, that is to become the baby, reconstructs the complete dna it will make some small errors.

Most mutations that do happen are neutral and have no effect on the creature at all. Most of the rest may not have any appreciable affect, very few may have a severe affect. Mutations will not be passed to any offspring unless the reproductive cells are directly affected.

mutations are any differences in the dna from parent to child, expressed or not. it might not effect the body of the new baby but the mutation is still there laying dormant in the dna.

I can agree to that. Learned a lot about genetics this weekend.

there's an almost endless supply of info on the subject of dna and i learn new crap every day about it. if you're interested, http://www.teach12.com/ttcx/coursedesclong2.aspx?cid=1533 will give you a really good grasp of almost everything dna. if the sticker price scares you as much as it scared me, you can get it somewhere else cheaper or even pirate it. i would check out their other lectures too, they are truly informative.

 

[Dark Jester]

there's an almost endless supply of info on the subject of dna and i learn new crap every day about it. if you're interested, http://www.teach12.com/ttcx/coursedesclong2.aspx?cid=1533 will give you a really good grasp of almost everything dna. if the sticker price scares you as much as it scared me, you can get it somewhere else cheaper or even pirate it. i would check out their other lectures too, they are truly informative.

Watching the videos now.. On lecture 5 toward the end, he talks about mutations being automatically repaired by some sort of active scanning system. If a T-A base pair is mutated to C-A, the system will autocorrect and replace the C with a T as it was originally. Not much more detail than that though (yet). I think mutations are covered more around lectures 12 or something, so it'll be a few hours before I get there. Hopefully it goes into some more detail.

Do you have any info on the rate at which those repairs take place? It would help explain why species seem to evolve extremely slowly given the rate at which mutations can happen.

I'd think at that rate, a snake could morph into a lizard over the course of a hundred generations, rather than thousands or millions of years. It would be extremely chaotic. An active DNA repair system running would prevent as many changes as possible, but some still can slip through. Maybe when both bases of the pair are mutated at the same time?

Still learning. Thanks for turning me on to this. Interesting stuff.