Junk DNA, High R, Pinnipeds, and the Multiverse

[Giltil (Gilbert Thill)]

@Rumraket

@Giltil

First, it comes from the observation that there is no example of an organism with complex ontogeny having a low ratio of non protein coding to protein coding DNA (let’s call R this ratio), whereas there are many examples of organisms with simpler ontogeny having a low R.

This pufferfish with it’s 400 Mbp genome laughs at that statement:

Given that the fraction of non protein coding DNA in pufferfish is probably around 85%, I don’t think this example falsify the hypothesis that complex ontogeny requires high R.

[Giltil (Gilbert Thill)]

@John_Harshman

That’s because you naturally consider your species to be the pinnacle of evolution. Since fugu are not human, they must therefore be less complex

I consider humans to be the pinnacle of creation, but not necessarily in the biological sense. By this, I mean that if it could be demonstrated that some other species was biologically more complex than humans, I would still place humans at the top of creation.

@John_Harshman

So you have just admitted that at least 80% of the human genome is junk

Ok, I think I see why you are saying this. It is probably true that if fugu was biologically as complex as humans, then, given my hypothesis, one may infer that about 80% of the human genome is junk. But I don’t think it is at all irreasonable to hypothesize that human are biologically more complex than fugu.

[Rumraket (Mikkel R.)]

@Giltil

Given that the fraction of non protein coding DNA in pufferfish is probably around 85%, I don’t think this example falsify the hypothesis that complex ontogeny requires high R

1. “Probably”?
2. Who knows what you consider “high R”?
3. Or what you consider “complex ontogeny”?
4. Why can it make do with so much less than some species that have between ten times, and in some cases over a hundred times more non-coding DNA, yet don’t appear to have more complex ontogeny?

[John_Harshman]

@Giltil

Given that the fraction of non protein coding DNA in pufferfish is probably around 85%, I don’t think this example falsify the hypothesis that complex ontogeny requires high R.

However, it does suggest that most of the human genome is junk. Remember that current estimates are that about 10% of the human genome is functional, while only 2% is protein-coding. That means that about 80% of functional DNA is non-coding. Fugu just happen to have very little junk. The supposed correlation between non-coding DNA and complexity just doesn’t exist.

@Giltil

By this, I mean that if it could be demonstrated that some other species was biologically more complex than humans, I would still place humans at the top of creation.

Naked speciesism.

@Giltil

But I don’t think it is at all irreasonable to hypothesize that human are biologically more complex than fugu.

If it’s reasonable, you should probably be able to provide a reason. But you’re still clinging to this spurious relationship? If so, you must allow that salamanders and lungfish are by far the most complex vertebrates, since they have by far the largest genomes.

[Giltil (Gilbert Thill)]

@Rumraket

@Giltil

Given that the fraction of non protein coding DNA in pufferfish is probably around 85%, I don’t think this example falsify the hypothesis that complex ontogeny requires high R

1. “Probably”?

This value of 85% is obtained by assuming that humans and pufferfish have about the same number of protein coding genes.

@Rumraket

Who knows what you consider “high R”?

Let’s say above 80%

@Rumraket

Why can it make do with so much less than some species that have between ten times, and in some cases over a hundred times more non-coding DNA, yet don’t appear to have more complex ontogeny?

My claim is that complex ontogeny requires high R, not that high R necessarily indicates complex ontogeny.
Don’t forget that
If « A then B » is true, it doesn’t follow that if « B then A » is true.

[John_Harshman]

@Giltil

Let’s say above 80%

That means that any organism with more than 300MB of DNA has “high R”, which includes almost every eukaryote. Congratulations: you have hit upon a meaningless standard.

@Giltil

My claim is that complex ontogeny requires high R, not that high R necessarily indicates complex ontogeny.

So you finally agree that within eukaryotes there is no correlation between complexity and R, and that there is no reason not to believe that 90% of the human genome is junk.

[Rumraket (Mikkel R.)]

@Giltil

My claim is that complex ontogeny requires high R, not that high R necessarily indicates complex ontogeny.
Don’t forget that
If « A then B » is true, it doesn’t follow that if « B then A » is true.

But that’s exactly the problem. Since the pufferfish appears able to make do with so little non-coding DNA compared to many other species that have way more genome but aren’t more complex, it would then follow that most species have way more DNA than is strictly required to specify their physiology. So the pufferfish would be closer to the amount of genome that is required.

Again, the question isn’t whether there is some direct prortionality between the complexity of an organism and the amount of genetic material that is required to specify it. But the part that is required can easily be a fraction of the actual measured genome size, even for the pufferfish.
The question is if the range of observed genome sizes is at all an indication of this requirement, or is better explained as being mostly the product of chance events.

Given how much genome size can vary even between species that appear almost identical (and a lot of other types of data), the evidence is actually more consistent with variations in genome size being mostly the product of the more or less random actions of selfish genetic elements such as transposons, whole genome duplications, and stuff like that.

[MrAnderson (Mathew)]

@Giltil

@Rumraket

Who knows what you consider “high R”?

Let’s say above 80%

It sounds like you have a theory, and you are here to expose it to criticism. That’s good!

In order to do this fairly, I think you have to give a bit more of a robust definition of what you mean by “high R” than just picking a number. We need to know what is “high R” what is “medium R” what is “low R”, and we need to be given reasons for why the categories are being set where you are setting them. Right now, it just looks like you picked 80% because it is less than the 85% that you have calculated for the pufferfish that you want to reject as a counter-example.

Edit:

@John_Harshman

@Giltil

Let’s say above 80%

That means that any organism with more than 300MB of DNA has “high R”, which includes almost every eukaryote. Congratulations: you have hit upon a meaningless standard.

This post was made after I had already submitted and I want to go on the record as saying “CALLED IT”
End of Edit

The reason they want to pin you down here is that right now your hypothesis isn’t really worth anything because it can’t be used to do anything. If we are trying to see whether your theory can sort A’s from B’s, and all we know is that not all A’s are B’s, but all B’s are A’s, then the theory is worse than wrong. It’s not even wrong. It’s just a thing that you say.

Edit: Called it again! I’m on fire today!

@Rumraket

But that’s exactly the problem.

@Rumraket

Again, the question isn’t whether there is some direct prortionality between the complexity of an organism and the amount of genetic material that is required to specify it. But the part that is required can easily be a fraction of the actual measured genome size, even for the pufferfish.
The question is if the range of observed genome sizes is at all an indication of this requirement, or is better explained as being mostly the product of chance events

Remember that we are talking to scientists right now. They want to “science” the things you say, which means you have to back everything up with reasons, data, examples, that sort of thing.

You also need to be very clear and precise in your language with them. So if we are going to use words like “complex ontogeny” as part of our theory, then we need to know what that means in scientific (and that probably means measurable and quantifiable) terms. Also, just like the last time, the next thing they are going to ask you for again is a reason why you have defined the term that way, and there needs to be a rationale to back that up.

I imagine these guys are probably going to insist on that stuff before they give you any more counterexamples. I would. Otherwise, it just becomes a game of “nope, that doesn’t count either” which really isn’t that fun to play.

[Giltil (Gilbert Thill)]

@John_Harshman

So you finally agree that within eukaryotes there is no correlation between complexity and R

Yes, mostly. I say mostly because there may be a trend.

@John_Harshman

and that there is no reason not to believe that 90% of the human genome is junk.

Under the design perspective, there is obviously a good reason not to believe the junk paradigm. Another reason is to realize that the junk paradigm is dangerous for science because it discourages exploration of the so called genomic dark matter.

[colewd (Bill Cole)]

@Rumraket

Again, the question isn’t whether there is some direct prortionality between the complexity of an organism and the amount of genetic material that is required to specify it. But the part that is required can easily be a fraction of the actual measured genome size, even for the pufferfish.
The question is if the range of observed genome sizes is at all an indication of this requirement, or is better explained as being mostly the product of chance events.

Hi Rum
If it were chance events wouldn’t you expect genome size variation in specific animal populations?

[Dan_Eastwood]

@Giltil

Another reason is to realize that the junk paradigm is dangerous for science because it discourages exploration of the so called genomic dark matter.

I’m pretty sure that’s not a thing. Junk DNA was first proposed about 1970, and by the early '80’s it was already known that not all of it was really “junk”. I don’t think researchers ever stopped looking for more function, but they may have lowered their expectations.

[AnEvolvedPrimate]

@Giltil

Under the design perspective, there is obviously a good reason not to believe the junk paradigm.

What reason is that?

Another reason is to realize that the junk paradigm is dangerous for science because it discourages exploration of the so called genomic dark matter.

How does it discourage this? I’ve seen this claim a lot, but I’ve never seen any examples of where this has been demonstrated to be the case.

[John_Harshman]

@colewd

If it were chance events wouldn’t you expect genome size variation in specific animal populations?

There’s plenty of genome size variation within species. Science wins again!

[MrAnderson (Mathew)]

Speaking only for myself, I would expect size variations between individuals, and if I understand things correctly, we do see size variations between individuals.

This is not surprising as insertions and deletions are pretty common types of mutations. Heck, even the cells in a person could vary to some degree in length (just not by very much. Big changes take a longer time to add up).

[CrisprCAS9]

@colewd

If it were chance events wouldn’t you expect genome size variation in specific animal populations?

There is genome size variation in animal populations.

[John_Harshman]

@Giltil

Yes, mostly. I say mostly because there may be a trend.

So you say yes but no? You’re not making a lot of sense here.

@Giltil

Under the design perspective, there is obviously a good reason not to believe the junk paradigm.

Is there? What is that reason? And since the evidence shows that there is plenty of junk in most eukaryote genomes, how is the design perspective looking now?

@Giltil

Another reason is to realize that the junk paradigm is dangerous for science because it discourages exploration of the so called genomic dark matter.

Nonsense. That’s just creationist propaganda, and you can’t support it with anything real.

[Giltil (Gilbert Thill)]

@MrAnderson

Remember that we are talking to scientists right now. They want to “science” the things you say, which means you have to back everything up with reasons, data, examples, that sort of thing

Do you think that these « science guys » always back up their claims with « that sort of thing »? For example when they posit a multiverse, or a naturalistic, unpurposeful origin of life, ATP synthase etc… . It seems to me there is a double standard here.

[Rumraket (Mikkel R.)]

@colewd

If it were chance events wouldn’t you expect genome size variation in specific animal populations?

Sure, and there is.

[Dan_Eastwood]

@Giltil

@MrAnderson

Remember that we are talking to scientists right now. They want to “science” the things you say, which means you have to back everything up with reasons, data, examples, that sort of thing

Do you think that these « science guys » always back up their claims with « that sort of thing »? For example when they posit a multiverse, or a naturalistic, unpurposeful origin of life, ATP synthase etc… . It seems to me there is a double standard here.

You might be off-topic. With respect to genetics and how much DNA in a genome is functional, we have data to test various hypotheses. In this situation we should expect “reasons, data, examples, that sort of thing.”

MODERATION NOTE: Expect a topic split for discussion of multiverses, etc…

[MrAnderson (Mathew)]

@Giltil

Do you think that these « science guys » always back up their claims with « that sort of thing »? For example when they posit a multiverse, or a naturalistic, unpurposeful origin of life, ATP synthase etc… . It seems to me there is a double standard here

Do they always back up their claims with evidence and rationales? Definitely not. But do they always expect each other to back up their claims with evidence and rationales?

YOU BETCHA.

This is the standard that scientists hold each other to, and if we expect to swim in their waters, it is the standard that we have to realize they are going to hold us to as well. I’ll give you a good example of where a scientist tried to make some claims and a whole bunch of other scientists freaked out at him for providing insufficient evidence and rationales, even though they thought his underlying find was really cool, and even though they didn’t necessarily disagree with his conclusions: Lee Berger and the Homo Naledi papers. Dr. Berger has this really cool site with these crazy fossils that may have something significant to say about human evolution. If we get in to the details this will definitely get punted to a side discussion, but the point is that he tried to publish in a journal that was experimenting with a “peer review - light” model. A whole bunch of people freaked out. @GutsickGibbon did a good video about it.

Peer review can be vicious my friend. Scientists, can you back me up on this?