Scientific Evidence for Universal Common Descent

Subduction Zone · Aug 19, 2019

YoursTrue said:
I was asking you what you say the last problem is, not Szostak. Since you say abiogenesis is the last problem, again -- what do you mean that it's the "last problem"? Perhaps you think evolution can start all over again? Did Miller's experiment go along any further to make life?

Now you are playing silly games.

Jim · Aug 19, 2019

Does anyone have any comments on these two articles?

Jim said:
Ancient horizontal gene transfer and the last common ancestors | BMC Evolutionary Biology | Full Text

“Therefore, one cannot assume that the last common ancestors of each gene were all present in the same cell representing the cellular ancestor of all extant life.”

Jim said:
Perspectives on the Phylogenetic Tree | Boundless Biology

“The hypothesis is that eukaryotes evolved not from a single prokaryotic ancestor, but from a pool of many species that were sharing genes by HGT mechanisms. Some individual prokaryotes were responsible for transferring the bacteria that caused mitochondrial development in the new eukaryotes, whereas other species transferred the bacteria that gave rise to chloroplasts.”

Jim · Aug 19, 2019

Is there anything in any similarities between species that could not possibly be explained by horizontal gene transfer?

ImmortalFlame · Aug 19, 2019

Jim said:
Is there anything in any similarities between species that could not possibly be explained by horizontal gene transfer?

Yes, since liberal estimates of the amount of genes in bacterial DNA that have been transferred is only between just 5% and 6%.
SOURCES:
https://www.sciencedirect.com/topics/neuroscience/horizontal-gene-transfer
https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/bacterial-genome

For horizontal gene transference to account for the appearance of common ancestry, therefore, what we should expect to find are bacteria that have around 94-95% completely unique DNA - with the difference accounted for by horizontal gene transference. Not only do we not find this, but it also makes no sense, since a population with DNA that has an entirely unique genetic code is extremely unlikely to be able to transfer genes horizontally with a population of organisms that is entirely distinct from it. This indicates that all life shares common ancestry at the bacterial level.

Unless you want to claim that somehow there was a 95-96% DNA transference between separately arising organic life forms with entirely different DNA makeup, the idea that horizontal gene transference can explain this similarity is contrary to reality.

Jim · Aug 19, 2019

Now I see how evolution research without a premise of common ancestry could be happening already.

Jim · Aug 19, 2019

ImmortalFlame said:
Yes, since liberal estimates of the amount of genes in bacterial DNA that have been transferred is only between just 5% and 6%.
SOURCES:
https://www.sciencedirect.com/topics/neuroscience/horizontal-gene-transfer
https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/bacterial-genome

For horizontal gene transference to account for the appearance of common ancestry, therefore, what we should expect to find are bacteria that have around 94-95% completely unique DNA - with the difference accounted for by horizontal gene transference. Not only do we not find this, but it also makes no sense, since a population with DNA that has an entirely unique genetic code is extremely unlikely to be able to transfer genes horizontally with a population of organisms that is entirely distinct from it. This indicates that all life shares common ancestry at the bacterial level.

Unless you want to claim that somehow there was a 95-96% DNA transference between separately arising organic life forms with entirely different DNA makeup, the idea that horizontal gene transference can explain this similarity is contrary to reality.

Thank you.

Subduction Zone · Aug 19, 2019

Jim said:
Thank you.

Do you understand how DNA alone is evidence of common ancestry?

Polymath257 · Aug 19, 2019

YoursTrue said:
Because when I'm not conscious, I don't know if I'm alive. That's one thing. When I am in a deep sleep, I don't know I'm in a deep sleep. My next question is, do bacterium know if they are alive? Granted consciousness and life are two different things, but then, as I think about it, they are somewhat related. Of course, as I said, no one to my knowledge has spoken to a bacteria, although it may develop. Now you got me wondering about bacterium. What keeps them alive, even if they don't think (i.e., have consciousness). But then who knows? Maybe they do have consciousness. So they're alive, but not knowing they are alive. Do they sleep? I mean, that is the first organism scientists conjecture that have life, isn't that right?

A bacterium will respond to a chemical gradient by moving towards it (if it is a chemical needed for its life) or away (otherwise). I'm not sure I would classify that as consciousness, though. There isn't even a 'thought process' involved: the chemical makes the flaggelum turn so the backterium moves.

From what I can see, life and consciousness are *very* different things. For example, I would not classify many insects as conscious: they are 'too programmed' (although some others may be). I am pretty sure that sponges, for example, are not conscious, nor are fungi. But all of these are definitely alive.

As for 'knowing to be alive', I am guessing that happens only in much more complicated animals. For example, I'm not convinced an earthworm 'knows' itself to be alive. And if an earthworm doens't, then a bacterium definitely doesn't.

In any case, we have good definitions for 'life' and that is the topic here. I'm not even sure we have a good definition of 'conscious': how do we tell if something is conscious or not?

Polymath257 · Aug 19, 2019

YoursTrue said:
Oh, no, now I have to learn about prokaryotes? Oh, dear. And eukaryotes. Oh, it's involved with a hypothesis. Here's my question, based on what I'm learning and seeing here. Do these things (whatever you want to call them) sleep?

What do you mean by the term 'sleep'? Many living things have a daily cycle of activity with higher activity at some times and lower at other times during the day.

But, for example, I'm not convinced a sponge is ever 'awake', let alone that it sleeps.

And yes, if you want to discuss life intelligently, then you have to know some of the wide range of variants it can exhibit. Bacteria are 'simple' celled living things. Eucaryotes are those living things with 'complex' cells: the cells have internal organelles. Often those organelles have their own, independent DNA.

Polymath257 · Aug 19, 2019

YoursTrue said:
OK, looking at more definitions -- "The first living things on Earth, single-celled micro-organisms or microbes lacking a cell nucleus or cell membrane known as prokaryotes, seem to have first appeared on Earth almost four billion years ago, just a few hundred million years after the formation of the Earth itself." (From
The Beginnings of Life - The Physics of the Universe
The Beginnings of Life - The Physics of the Universe

My question -- how do they figure that they seem to have first appeared on earth about four billion years ago? Perhaps the hypothesis from outer space would seem relevant here, especially since it doesn't say a singular prokaryote appears to have appeared, but it uses the plural. And now my next question: how long might these prokaryotes have stayed alive, individually, that is? Because it seems the definition is, as I say, about more than one prokaryote.

Of course there was more than one individual!

The term 'seems' applies to the term 'first': it is possible that the fossils we have could have had precursors. We know life existed on Earth 3.8 billion years ago.

I'm not sure what you are asking about 'how these stay alive'. At least part of the question involves answering what it means to be alive: having a metabolism, the possibility of reproduction, etc. Well, all of those are aspects of the chemical reactions that happen inside of the cell membrane. So as long as nutrients are available and the cell membrane stays intact, they will stay alive.

Polymath257 · Aug 19, 2019

YoursTrue said:
I was asking you what you say the last problem is, not Szostak. Since you say abiogenesis is the last problem, again -- what do you mean that it's the "last problem"? Perhaps you think evolution can start all over again? Did Miller's experiment go along any further to make life?

Miller's experiment was an early one. It only produced amino acids (which was surprising at the time). But much more has been done, including experiment where such amino acids spontaneously form cell-like structures that can catalyze some basic reactions for life. These cell-like structures will bud off and 'reproduce', but the chemicals inside gradually become depleted over generations. So they don't quite qualify as life.

I really hope you didn't think that Miller's experiment was the last word on this topic.

tas8831 · Aug 19, 2019

YoursTrue said:
So - to the people that hate evolution because of their fragile faith - Why do you try to conflate abiogenesis with evolution?

Click to expand...

I don't. But I also see that you can't say what is the first "living matter."

Q:Why do you try to conflate abiogenesis with evolution?
A: I don't. (and then goes on to do so)

I guess no scientist really knows. But I was curious and so I asked here of those who believe in evolution. It actually has nothing to do with abiogenesis, but you made it so.

Right.... Because "fist living matter" and "abiogenesis" are totally different issues....

tas8831 · Aug 19, 2019

Jim said:
I noticed that too, in my Web searches on this topic.

I noticed in your reply to Dan that you totally ignored his question regarding your accusations of fraud against the authors of a paper that you had only seen the abstract of.

I guess if I had made such a dishonest fool of myself I would try to avoid bringing it back up, too.

TagliatelliMonster · Aug 19, 2019

Jim said:
All this time, I’ve been asking the wrong questions. What I want to see is not the reasons for believing in common ancestry. What I want to see is arguments against the idea of many lines of ancestry going back to the beginning of life. Some or all of the arguments might be the same, so I’ll repost the kinds of arguments that I’ve seen for believing in common ancestry, but considering them now as arguments against multiple lines of ancestry going all the way back to the beginning of life:
- Fossils.
- Similarities.
- How well it works not to think that way,

Can anyone think of any arguments against multiple lines of ancestry, apart from those three kinds of arguments?

A phylogenetic tree of all life. That is to say, of all the fully sequenced genomes so far, represented on a single tree of life.

It doesn't have 27 distinct roots. No data shows multiple distinct roots.
The data shows a single tree with a common root.

tas8831 · Aug 19, 2019

YoursTrue said:
So - to the people that hate evolution because of their fragile faith - Why do you try to conflate abiogenesis with evolution?

Click to expand...

You know what's interesting in relation to your question?

That you won't answer it?

It's that when scientists taught recapitulation regarding human growth in the womb, it was taught as truth, and to deny it would undoubtedly cause a little rumble in a school. But then later it was taught that it just isn't so -- that a fetus does not go through every stage of evolution in the womb until it, of course, evolves supposedly into a human being and, not a fish let's say at a certain point in the womb.

Ancillary question -

So - to the people that hate evolution because of their fragile faith - Why do you keep pretending that Haeckel's theory of recapitulation was taught as truth?

But it takes two cells to tango causing a baby to be develop in the woman. That, of course, of the male, and female. It's amazing, is it not? (I think so...) Irreducibly two cells to make a baby.

Wow, so amazing.... This happens in trees and worms, too. Great story, bro.

tas8831 · Aug 19, 2019

YoursTrue said:
Additionally, except, of course, in reportedly three cases (and I say reportedly since it is written, there were no human eyewitnesses to Adam's creation, but I believe it as written), Adam--no meeting of sperm and egg needed--and Eve (similarly with her) and Jesus Christ, since his birth as well as the other two, were made-designed-created by God the Almighty, who can do such wondrous things.
Notice:
Romans 5:12 - "Therefore, just as through one man sin entered the world, and death through sin, and thus death spread to all men, because all sinned"
Death spread through the sin of Adam.
"Let us make man in our image." Almighty God does not die. The Almighty is sinless. His son in heaven was sinless. Adam was sinless until he sinned. Same with Eve. Jesus was without sin, he died because he was killed. He was killed because of the sins of those around him, not because he sinned. He was blameless.

Cool.

Say, if I quote the Bhagavad Gita, will you totally accept my arguments as true?

Jim · Aug 19, 2019

YoursTrue said:
I don't. But I also see that you can't say what is the first "living matter." I guess no scientist really knows. But I was curious and so I asked here of those who believe in evolution. It actually has nothing to do with abiogenesis, but you made it so.

I believe in evolution in a way. It looks to me like evolution theory is very useful and widely used in some sciences, with beneficial results. Different researchers might draw the line between living and not living in different places, but there is matter that all of them call “living.” Does that have some relevance for you in what’s been discussed in this thread?

Jim · Aug 19, 2019

TagliatelliMonster said:
A phylogenetic tree of all life. That is to say, of all the fully sequenced genomes so far, represented on a single tree of life.

It doesn't have 27 distinct roots. No data shows multiple distinct roots.
The data shows a single tree with a common root.

Did you read these two articles?

Jim said:
Ancient horizontal gene transfer and the last common ancestors | BMC Evolutionary Biology | Full Text

“Therefore, one cannot assume that the last common ancestors of each gene were all present in the same cell representing the cellular ancestor of all extant life.”

Jim said:
Perspectives on the Phylogenetic Tree | Boundless Biology

“The hypothesis is that eukaryotes evolved not from a single prokaryotic ancestor, but from a pool of many species that were sharing genes by HGT mechanisms. Some individual prokaryotes were responsible for transferring the bacteria that caused mitochondrial development in the new eukaryotes, whereas other species transferred the bacteria that gave rise to chloroplasts.”

TagliatelliMonster · Aug 19, 2019

Jim said:
Did you read these two articles?

No, I did not read those articles and yes, I am aware of the mechanisms of HGT (and its limitations...)

Do you think anything in these articles poses a problem for the point I made? If yes, what is it?

I don't see how HGT somehow poses a problem.
High level phylogenetic trees still show that all life is interwoven with common roots.
We're not seeing various sets of "independent lines" of genetics, for example.

ImmortalFlame · Aug 19, 2019

Jim said:
Did you read these two articles?

I'm very curious. What is it that you think these two articles are saying with regards to common ancestry?

Scientific Evidence for Universal Common Descent

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