Rapid Emergence

[Resha Caner]

The recognition in the late 1970s that Hbt. halobium (now renamed Hbt. salinarum) is a member of the Archaea was based on 16S rRNA oligonucleotide cataloguing, at the time the only method to obtain sequence information on rRNAs ( Magrum et al., 1978 ). Complete 16S rRNA gene sequences of Hfx. volcanii and Hbt. cutirubrum ( salinarum) became available in 1983 and 1985, respectively ( Gupta et al., 1983 ; Hui & Dennis, 1985 ).

This makes it unlikely that it will be found that this is a totally independent for of life.

I hope you didn't spend too much time digging that up for several reasons: 1) I don't need a list of challenges to the idea. I'm aware of what they are and I'm sure plenty of people are willing to line up and offer criticisms. 2) I was just spitballing. I'm not fixated on Archaea. 3) The example may have misled you a bit.

So, let me address these:
1) I'd be more interested in hearing examples of what you think could possibly work. Not why you think it won't work. So, let me ask a few questions.

2) All my example was trying to illustrate is that I'm not looking to propose something earth-shattering. I'd be happy if biology accepted a small change. At this point I can't imagine an experiment that would establish separate biogenesis events for existing life - even given the things you suggested. I only mentioned it to try to provide a framework into which the experiments I can imagine would fit.

However, let me ask you this: What do think would be the most plausible were a hypothesis presented for separate biogenesis events? For example, is someone suggested to me that wolves and the Alaskan Malamute came from 2 separate biogenesis events I wouldn't believe it. If however, someone suggested that Eukaryotes, Bacteria, and Archaea came from separate biogenesis events, I would accept that as a plausible idea. So, in your case, if you could imagine an experiment for separate biogenesis events, what 2 specimens would you select as the most plausible for that experiment?

3) Maybe someone else can devise that biogenesis thought experiment, but I haven't so far. So it may have misled you when I commented on a separate biogenesis event for Archaea. Therefore, let's back up and discuss an experiment I can imagine. Give me an example of the simplest nested hierarchy you know of. It would also need to be one where we have 2 living examples - one with the full hierarchy and one with only parts of the hierarchy.

 

[Loudmouth]

However, let me ask you this: What do think would be the most plausible were a hypothesis presented for separate biogenesis events?

The most plausible hypothesis is the one that has already been tested to death.

If there were different biogenesis events, then we would expect to see different codons, different amino acids, different tRNA, and perhaps even different genetic molecules. This hypothesis is tested by comparing the sequence of tRNA's across the major domains of life.

If that hypothesis fails, as it has, then it is going to be tough sledding. The first thing you need to do is show why you can have different biogenesis events and still have shared tRNAs et alia.

For example, is someone suggested to me that wolves and the Alaskan Malamute came from 2 separate biogenesis events I wouldn't believe it. If however, someone suggested that Eukaryotes, Bacteria, and Archaea came from separate biogenesis events, I would accept that as a plausible idea. So, in your case, if you could imagine an experiment for separate biogenesis events, what 2 specimens would you select as the most plausible for that experiment?

What you will accept as a plausible idea is not what a hypothesis is. What you will accept as plausible absent any evidence is really a measure of your own biases and not a measure of anything in reality. Please don't take this as an insult at all. This bias is something that scientists struggle with all of the time. Constructing good hypotheses is not easy to do.

 

[Resha Caner]

The most plausible hypothesis is the one that has already been tested to death.

That's not what I was asking, but that's OK. You don't have to make a suggestion.

What you will accept as a plausible idea is not what a hypothesis is.

OK. I was asking for what you think would be most plausible within the given framework. "Most plausible" might mean less chance than Donald Trump being President, but I'm OK with that. It's just a mental exercise, but again, you don't have to suggest anything.

 

[Loudmouth]

OK. I was asking for what you think would be most plausible within the given framework.

The most plausible idea is that all life shares a common ancestor because of the overwhelming genetic evidence.

 

[Resha Caner]

The most plausible idea is that all life shares a common ancestor because of the overwhelming genetic evidence.

I heard you the first time. You don't want to speculate on the first question (edit: separate biogenesis events). You seem to think the second question (edit: nested hierarchies) also deals with UCA, but it doesn't, so I'm not sure where you're at on that one, but I'll just assume you don't want to speculate on that either.

I realized I should have been more explicit, so I added edits to repeat the 2 areas I asked questions about.

 

[OliviaMay]

I hope you didn't spend too much time digging that up for several reasons: 1) I don't need a list of challenges to the idea. I'm aware of what they are and I'm sure plenty of people are willing to line up and offer criticisms. 2) I was just spitballing. I'm not fixated on Archaea. 3) The example may have misled you a bit.

So, let me address these:
1) I'd be more interested in hearing examples of what you think could possibly work. Not why you think it won't work. So, let me ask a few questions.

2) All my example was trying to illustrate is that I'm not looking to propose something earth-shattering. I'd be happy if biology accepted a small change. At this point I can't imagine an experiment that would establish separate biogenesis events for existing life - even given the things you suggested. I only mentioned it to try to provide a framework into which the experiments I can imagine would fit.

However, let me ask you this: What do think would be the most plausible were a hypothesis presented for separate biogenesis events? For example, is someone suggested to me that wolves and the Alaskan Malamute came from 2 separate biogenesis events I wouldn't believe it. If however, someone suggested that Eukaryotes, Bacteria, and Archaea came from separate biogenesis events, I would accept that as a plausible idea. So, in your case, if you could imagine an experiment for separate biogenesis events, what 2 specimens would you select as the most plausible for that experiment?

3) Maybe someone else can devise that biogenesis thought experiment, but I haven't so far. So it may have misled you when I commented on a separate biogenesis event for Archaea. Therefore, let's back up and discuss an experiment I can imagine. Give me an example of the simplest nested hierarchy you know of. It would also need to be one where we have 2 living examples - one with the full hierarchy and one with only parts of the hierarchy.

First your going about this the wrong way. You want consensus to change not because it is necessarily because it is incorrect, but it seems just because. You don't necessarily believe there was more event and have no evidence of multiple events. I just don't get the goal.

IMHO if you want to demonstrate a separate event you do it with life that is radically different from all other life. The leading contender for a seperate event of genesis currently are the creatures living with totally different energy sources not related to the sun. Those very strange things near geothermal vents.

To determine if they are indeed not related to other live the best way is to look at the DNA or if they even have DNA.

 

[Loudmouth]

I heard you the first time. You don't want to speculate on the first question (edit: separate biogenesis events).

I have speculated. I even came up with things that should be seen if there were separate biogenesis events.

You seem to think the second question (edit: nested hierarchies) also deals with UCA, but it doesn't, so I'm not sure where you're at on that one, but I'll just assume you don't want to speculate on that either.

I realized I should have been more explicit, so I added edits to repeat the 2 areas I asked questions about.

The speculations have already been done. The hypotheses have already been tested. If you are going to move forward, then you are first going to have to demonstrate why all of these previous hypotheses were wrong.

 

[Resha Caner]

First your going about this the wrong way. You want consensus to change not because it is necessarily because it is incorrect, but it seems just because.

I'm not asking for consensus. I'm asking if you want to participate in a thought experiment. If I've not given you enough to pique your curiosity, that's fine. I don't need to know the reason why you choose not to participate.

I have speculated. I even came up with things that should be seen if there were separate biogenesis events.

If you insist. But what about my nested hierarchy question? I'll repeat it: Give me an example of the simplest nested hierarchy you know of. It would also need to be one where we have 2 living examples - one with the full hierarchy and one with only parts of the hierarchy.

 

[OliviaMay]

I'm not asking for consensus. I'm asking if you want to participate in a thought experiment. If I've not given you enough to pique your curiosity, that's fine. I don't need to know the reason why you choose not to participate.

.

I gave you a clear way to show separate genesis. Why is that not an option?

 

[Resha Caner]

I gave you a clear way to show separate genesis. Why is that not an option?

First, because I'm more interested in the nest hierarchy question that has nothing to do with biogenesis.

Second, because your speculation is about life not yet found. I asked you for an example from known life. You did mention thermal vents, but I got the impression you didn't think such life had been analyzed and as such had the potential to be different. However, it has been analyzed: http://www.mbari.org/news/homepage/2013/vent-fossils/vent-fossils.html

If I misunderstood you, and you think animals near thermal vents are the ones most likely to have come from a separate event ... why do you think that?

 

[OliviaMay]

First, because I'm more interested in the nest hierarchy question that has nothing to do with biogenesis.

Second, because your speculation is about life not yet found. I asked you for an example from known life. You did mention thermal vents, but I got the impression you didn't think such life had been analyzed and as such had the potential to be different. However, it has been analyzed: http://www.mbari.org/news/homepage/2013/vent-fossils/vent-fossils.html

If I misunderstood you, and you think animals near thermal vents are the ones most likely to have come from a separate event ... why do you think that?

I think animals near thermal vents present the best chance of fining a separate genesis because their environment is so different and separate and extreme.

I thought the goal was to show a separate genesis?

 

[Resha Caner]

I think animals near thermal vents present the best chance of fining a separate genesis because their environment is so different and separate and extreme.

Then I misunderstood. My apologies, and thank you for the example.

I thought the goal was to show a separate genesis?

Well, we must crawl before we can walk ... and run ... and build spacehips to land people on Mars. Have I not been clear I'd rather focus on the first baby step than the end goal? That I've already chosen the first baby step? That to begin a thought experiment for that baby step I would like someone to suggest a simple nested hierarchy?

 

[Loudmouth]

If you insist. But what about my nested hierarchy question? I'll repeat it: Give me an example of the simplest nested hierarchy you know of. It would also need to be one where we have 2 living examples - one with the full hierarchy and one with only parts of the hierarchy.

What do you mean by simplest? A hierarchy with humans, chimps, and bonobos would be pretty simple. Is that what you are talking about?

Added in edit, in case you missed it. The nested hierarchy below has the human, chimp, bonobo triad on the right side.

 

[Loudmouth]

Well, we must crawl before we can walk ... and run ... and build spacehips to land people on Mars. Have I not been clear I'd rather focus on the first baby step than the end goal?

The first baby steps in this sort of endeavor is to review the research that has already been done.

 

[Resha Caner]

What do you mean by simplest? A hierarchy with humans, chimps, and bonobos would be pretty simple. Is that what you are talking about?

Added in edit, in case you missed it. The nested hierarchy below has the human, chimp, bonobo triad on the right side.

OK, I'll try to define it further. Your example might work, but I'm not familiar enough with the differences between those species to know for sure. So, I'll use a different example to explain.

And please bear with me. I'm not claiming I have all the relationships correct. I'm just trying to draw an illustration. So, all bats are mammals, all mammals are vertebrates, etc. I believe it has been proposed that one of the ancestors of the bat was some wingless shrew-like creature. So, again, I'm not saying biology claims shrews and bats had this kind of common ancestor, but let's suppose for the sake of argument they did and that the DNA of the bat has diverged farther from that ancestor than the DNA of the shrew. So, for this hierarchy we have a very close living relative of the predecessor (the shrew) and a living relative that has diverged significantly (the bat has wings). Now we need to go back one more step to, say, the split between marsupial and placental mammals and again find a living example that is close to the predecessor that existed before that split.

So, would that be true of the tree you show? That for humans, chimps, and bonobos one is distinctively closer to the common ancestor than the other two? And for those remaining two, one is distinctively closer to their common ancestor than the other?

If so, I was also asking for those distinctive differences to be as simple as possible. By that I mean the differences required in DNA to manifest those distinctions is as small as possible.

 

[OliviaMay]

This should help find what you are looking for.

http://tolweb.org/Life_on_Earth/1

 

[Resha Caner]

I'm concerned my example wasn't clear enough. So let me use an absurdly simple example to illustrate what I'm after.

Let's use the nested hierarchy that all convex polygons are made of straight lines and all lines are made of points. Let's suppose that existing today we have 2 "point" creatures. The DNA of P1 = PQRS and the DNA of P2 = PQPRPSPQRPQSPRS. P1 has the simpler DNA so we will chose P1 for the thought experiment.

From there the tree branches into straight and curved lines. We are only interested in straight lines, and existing today we have 2 "line" creatures. The DNA of L1 = PQRSRQP, and the DNA of L2 = PQPRRQQPSRQP. L1 has the smallest deviation from P1, so we choose L1 for the thought experiment.

Again the tree branches into convex and concave polygons. We are only interested in convex polygons, and exisitng today we have 2 "polygon" creatures. The DNA of polygon G1 has the smallest deviation from L1, so we choose it for the thought experiment.

 

[Resha Caner]

This should help find what you are looking for.

http://tolweb.org/Life_on_Earth/1

OK.

 

[Loudmouth]

And please bear with me. I'm not claiming I have all the relationships correct. I'm just trying to draw an illustration. So, all bats are mammals, all mammals are vertebrates, etc. I believe it has been proposed that one of the ancestors of the bat was some wingless shrew-like creature. So, again, I'm not saying biology claims shrews and bats had this kind of common ancestor, but let's suppose for the sake of argument they did and that the DNA of the bat has diverged farther from that ancestor than the DNA of the shrew.

If evolution were true, then they should have diverged equally from that common ancestor. If we were to use sloths as the group to compare to, since sloths diverged from that lineage before shrews and bats diverged, then I would expect shrews and bats to be equidistant from the sloth at the DNA level.

If we were to use humans and the other apes as our example, since we have a nice cladogram above this post, the traditional position is that chimps are more ape like. However, when we look at the DNA we see that chimps are closer to humans than they are to gorillas and orangutans. This is because we diverged equally from our shared ancestor, and that ancestor we share with chimps is more recent than the ancestor chimps share with gorillas and orangutans.

This isn't too surprising given the fact that the vast majority of the genome is not under selective pressure, and of the DNA that is under selective pressure only a fraction of that is directly tied to morphological features.

So, for this hierarchy we have a very close living relative of the predecessor (the shrew) and a living relative that has diverged significantly (the bat has wings). Now we need to go back one more step to, say, the split between marsupial and placental mammals and again find a living example that is close to the predecessor that existed before that split.

That would require us to go back in time. Genomes don't stop evolving after two species split. While morphological features may experience stasis, the genome does not. It ticks away at a much steadier pace. Shrews are just as distant from that common ancestor as bats are.

So, would that be true of the tree you show? That for humans, chimps, and bonobos one is distinctively closer to the common ancestor than the other two? And for those remaining two, one is distinctively closer to their common ancestor than the other?

Since you seem to have a more ladder-like view of evolution, it might be more useful to go back one step to the triad of chimps, gorillas, and humans. The common ancestor between chimps and gorillas was 7 or 8 million years ago. The common ancestor of chimps and humans was 5 million years ago. The DNA comparison follows the time line, with chimps sharing more DNA with humans than they do with gorillas even though laypeople tend to lump chimps and gorillas together as apes and have humans separate.

If so, I was also asking for those distinctive differences to be as simple as possible. By that I mean the differences required in DNA to manifest those distinctions is as small as possible.

There are going to be synonymous mutations which are changes DNA that don't even manifest as differences in protein sequence. Evolution doesn't really care how simple things are at the DNA level.

 

[Resha Caner]

... it might be more useful to go back one step to the triad of chimps, gorillas, and humans. The common ancestor between chimps and gorillas was 7 or 8 million years ago. The common ancestor of chimps and humans was 5 million years ago. The DNA comparison follows the time line, with chimps sharing more DNA with humans than they do with gorillas ...

OK, that's fine. We can try using those 3.

So, there is some DNA that all 3 share, yes? Let's call that strand A. Then there is DNA that chimps and humans share, but is excluded from gorillas, yes? Let's call that strand B. Finally, the gorilla, chimp, and human have additional DNA that is unique to that species, yes? Let's call those strands G, C, and H (for gorilla, chimp, and human respectively).

So, could we describe our 3 sample species as:
gorilla = AG
chimp = ABC
human = ABH
Does that work?