[_ Old Earth _] No more universal common ancestor

[Vaccine]

"We have no evidence at all that the tree of life is a reality." Dr Eric Bapteste

"There is a longstanding and increasing realization among microbiologists that the mechanisms of gene spread among prokaryotes across evolutionary time are multiple and are different from those of eukaryotes. As a consequence, the gene histories for a large majority of their genes are discordant, which means that the traditional tree of life model is very much a problematic framework to study microbial evolution. Many of the primary tenets and major assumptions of this theoretical framework have been refuted or have undergone drastic modification since its first formulations in Darwin's notebooks. Yet today belief in a single universal tree of life remains largely unaffected, and the strong evidence-driven alternative is often still seen as competition rather than the successor. This persistence of the tree of life model could partly be explained by the fact that it is difficult to fully dislodge an old problematic model without replacing it with a better guiding metaphor. Our discussion above has proposed or implied several potential successors of the tree of life model"
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761302/

Proof, from a peer reviewed journal not some creationist site, that scientists clinging to universal common ancestry are a barrier to scientidic progress.
"But given what we now know about prokaryote genome evolution and the contribution of endosymbiosis to eukaryote evolution, it seems rather unlikely that biologists in 20 years will still be using the language of strictly bifurcating trees to describe the relatedness of prokaryotes, and to develop models of microbial evolution."
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761302/


"Having uprooted the tree of unicellular life biologists are now taking their axes to the remaining branches. Dr Bapteste said: 'If you don't have a tree of life what does it mean for evolutionary biology. At first it's very scary – but in the past couple of years people have begun to free their minds'."
Charles Darwin's tree of life is 'wrong and misleading', claim scientists - Telegraph

This will have a huge impact on origin of life experiments. They were working with just the simplest prokaryote genome now they have to account for the origin of eukaryotes.
"Networks" are going to replace the tree of life. What does that mean for common ancestry? It means hybrids, horizontal gene transfers, viral gene transfers, and endosymbiosis all which could common ancestry. It will be interesting to see where this goes but I think it will probably go something like this, an extremely unlikely event such as a pig and ape mated to produce a neanderthal. Of course, it was a male and all alone in the world so nothing happened. Although, whatever the problem for evolution, time is the cure. So the unlikely even happened again, pigs mated with apes, and now we have a male and female neanderthal. Of course, they were on opposite ends of the continent so nothing happ- just kidding, deep time trumps any issue for evolution. So we have figurative Adam and Eve, but is their common ancestry with pigs or apes? Or since humans share so much DNA with mice maybe the unlikely event was a mice with swine flu that mated with an ape to produce homosapiens. Would the common ancestry be with apes, pigs, or mice? Maybe our shared DNA with chimps is just convergent evolution.

 

[Barbarian]

"We have no evidence at all that the tree of life is a reality." Dr Eric Bapteste

"There is a longstanding and increasing realization among microbiologists that the mechanisms of gene spread among prokaryotes across evolutionary time are multiple and are different from those of eukaryotes. As a consequence, the gene histories for a large majority of their genes are discordant, which means that the traditional tree of life model is very much a problematic framework to study microbial evolution. Many of the primary tenets and major assumptions of this theoretical framework have been refuted or have undergone drastic modification since its first formulations in Darwin's notebooks. Yet today belief in a single universal tree of life remains largely unaffected, and the strong evidence-driven alternative is often still seen as competition rather than the successor. This persistence of the tree of life model could partly be explained by the fact that it is difficult to fully dislodge an old problematic model without replacing it with a better guiding metaphor. Our discussion above has proposed or implied several potential successors of the tree of life model"
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761302/

Proof, from a peer reviewed journal not some creationist site, that scientists clinging to universal common ancestry are a barrier to scientidic progress.
"But given what we now know about prokaryote genome evolution and the contribution of endosymbiosis to eukaryote evolution, it seems rather unlikely that biologists in 20 years will still be using the language of strictly bifurcating trees to describe the relatedness of prokaryotes, and to develop models of microbial evolution."
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761302/

Since the early 1900s, scientists have known that Darwin's tree of life is a less accurate metaphor than a bush. Which is what the above is talking about. However, Bapteste acknowledges common descent:

Gene similarity networks provide tools for understanding eukaryote origins and evolution.

2013: David Alvarez-Ponce; Eric Bapteste; Philippe Lopez; James O McInerney

Proceedings of the National Academy of Sciences of the United States of America 2013;110(17):E1594-603.

Abstract
The complexity and depth of the relationships between the three domains of life challenge the reliability of phylogenetic methods, encouraging the use of alternative analytical tools. We reconstructed a gene similarity network comprising the proteomes of 14 eukaryotes, 104 prokaryotes, 2,389 viruses and 1,044 plasmids. This network contains multiple signatures of the chimerical origin of Eukaryotes as a fusion of an archaebacterium and a eubacterium that could not have been observed using phylogenetic trees. A number of connected components (gene sets with stronger similarities than expected by chance) contain pairs of eukaryotic sequences exhibiting no direct detectable similarity. Instead, many eukaryotic sequences were indirectly connected through a "eukaryote-archaebacterium-eubacterium-eukaryote" similarity path. Furthermore, eukaryotic genes highly connected to prokaryotic genes from one domain tend not to be connected to genes from the other prokaryotic domain. Genes of archaebacterial and eubacterial ancestry tend to perform different functions and to act at different subcellular compartments, but in such an intertwined way that suggests an early rather than late integration of both gene repertoires. The archaebacterial repertoire has a similar size in all eukaryotic genomes whereas the number of eubacterium-derived genes is much more variable, suggesting a higher plasticity of this gene repertoire. Consequently, highly reduced eukaryotic genomes contain more genes of archaebacterial than eubacterial affinity. Connected components with prokaryotic and eukaryotic genes tend to include viral and plasmid genes, compatible with a role of gene mobility in the origin of Eukaryotes. Our analyses highlight the power of network approaches to study deep evolutionary events.

It's like your claim that Koonin rejected common descent, only to discover that Koonin considers the evidence for common descent to be "overwhelming." Likewise, I'm sure you're surprised to see that Bapteste has found compelling evidence for the common descent of eukaryotes.

The issue is something you rejected earlier, the fact of endosymbiosis. The salamanders, for example, our mitochondria, and plant chloroplasts. And the directly-observed evolution of this process in amoebae. You see, Darwin knew nothing of genes and DNA, but we have since learned that lateral gene transfer is common in prokaryotes, and does sometimes happen in eukaryotes. But as Koonin (to whom you attributed denial of common descent) observes, the evidence for common descent remains overwhelming.

"Having uprooted the tree of unicellular life biologists are now taking their axes to the remaining branches.

Surprise. It turns out you're chopping a dead bush. The "tree" hasn't been part of common descent for a long time.

This will have a huge impact on origin of life experiments. They were working with just the simplest prokaryote genome now they have to account for the origin of eukaryotes.

See above. The guy you're touting, has found evidence that shows the process. Ironic, um?

"Networks" are going to replace the tree of life. What does that mean for common ancestry? It means hybrids, horizontal gene transfers, viral gene transfers, and endosymbiosis all which could common ancestry.

It's not news. A long time ago, I showed a creationist here, the evidence for endosymbiosis. And now I've shown you a short time ago. As Koonin and Bapteste point out, it complicates the picture, but also gives us a clearer view of the way common descent works.

It will be interesting to see where this goes but I think it will probably go something like this, an extremely unlikely event such as a pig and ape mated to produce a neanderthal.

I've actually had some creationists demand that something like that was part of the theory. Amusing, um? Anyway, you're much more likely to score points by learning what evolutionary theory actually is, than by imagining what it must be, and attacking that.

Just saying...

 

[Barbarian]

".. it is no longer safe to assume that those (mitochondria and chloroplasts) were the only lateral gene transfers that occurred after the first eukaryotes arose. Only in later, multicellular eukaryotes do we know of definite restrictions on horizontal gene exchange, such as the advent of separated (and protected) germ cells...


If there had never been any lateral gene transfer, all these individual gene trees would have the same topology (the same branching order), and the ancestral genes at the root of each tree would have all been present in the last universal common ancestor, a single ancient cell. But extensive transfer means that neither is the case: gene trees will differ (although many will have regions of similar topology) and there would never have been a single cell that could be called the last universal common ancestor..."
W. Ford Doolittle
http://www.nature.com/scientificamerican/journal/v282/n2/pdf/scientificamerican0200-90.pdf

And even more enlightening...

Ge F, Wang L-S, Kim J (2005) The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. PLoS Biol 3(10): e316. doi:10.1371/journal.pbio.0030316
Abstract
With the availability of increasing amounts of genomic sequences, it is becoming clear that genomes experience horizontal transfer and incorporation of genetic information. However, to what extent such horizontal gene transfer (HGT) affects the core genealogical history of organisms remains controversial. Based on initial analyses of complete genomic sequences, HGT has been suggested to be so widespread that it might be the “essence of phylogeny” and might leave the treelike form of genealogy in doubt. On the other hand, possible biased estimation of HGT extent and the findings of coherent phylogenetic patterns indicate that phylogeny of life is well represented by tree graphs. Here, we reexamine this question by assessing the extent of HGT among core orthologous genes using a novel statistical method based on statistical comparisons of tree topology. We apply the method to 40 microbial genomes in the Clusters of Orthologous Groups database over a curated set of 297 orthologous gene clusters, and we detect significant HGT events in 33 out of 297 clusters over a wide range of functional categories. Estimates of positions of HGT events suggest a low mean genome-specific rate of HGT (2.0%) among the orthologous genes, which is in general agreement with other quantitative of HGT. We propose that HGT events, even when relatively common, still leave the treelike history of phylogenies intact, much like cobwebs hanging from tree branches.(My highlighting)

"Species are labeled with different colors based on their inferred HGT rates: red, >4%; yellow, 3%–4%; pink, 2%–3%; blue, 1%–2%; green, <1%. Taxonomy labels are (A) Euryarchaea, (B) Proteobacteria, (C) Chlamydiae, (D) Spirochaetes, (E) Thermotogae, (F) Aquificae, (G) Actinobacteria, (H) Deinococcus, (I) Cyanobacteria, (J) Firmicutes, and (K) Fungi."

 

[Milk-Drops]

Vaccine, if you had read the actual article, you would have noticed that most of what Bapteste was talking about was before the divergence of Fungus, plants, and animals from Bacteria and the expansion of eukaryote.

 

[Milk-Drops]

This will have a huge impact on origin of life experiments.

Not really, considering that this is relatively old news and doesn't change the concept of how life began.

They were working with just the simplest prokaryote genome now they have to account for the origin of eukaryotes.

Well, that is being studied.

"Networks" are going to replace the tree of life.

Only at the prokaryote level.

What does that mean for common ancestry?

Not much at all really. Considering that most models dealing with common ancestry deals with Eykaryotes.

It means hybrids, horizontal gene transfers, viral gene transfers, and endosymbiosis all which could common ancestry.

For Prokaryotes

It will be interesting to see where this goes but I think it will probably go something like this, an extremely unlikely event such as a pig and ape mated to produce a neanderthal.

No, because Humans, apes, and Pigs are all eukaryotes and nothing involving eykaryotes has changed.

Of course, it was a male and all alone in the world so nothing happened.

Where did this Ray comfort nonsense come from?

Although, whatever the problem for evolution, time is the cure. So the unlikely even happened again, pigs mated with apes, and now we have a male and female neanderthal. Of course, they were on opposite ends of the continent so nothing happ- just kidding, deep time trumps any issue for evolution. So we have figurative Adam and Eve, but is their common ancestry with pigs or apes? Or since humans share so much DNA with mice maybe the unlikely event was a mice with swine flu that mated with an ape to produce homosapiens. Would the common ancestry be with apes, pigs, or mice? Maybe our shared DNA with chimps is just convergent evolution.

What a bunch of nonsense. I wonder. Do you understand what a Prokaryotes and Eukaryotes are?

 

[Sparkey]

What a bunch of nonsense. I wonder. Do you understand what a Prokaryotes and Eukaryotes are?

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Definition of Derisive: expressing contempt or ridicule.

 

[Vaccine]

I was half-joking about the mice/pig/chimp thing. I say half because a pig-chimp hybrid theory for the origin of humans is a real thing:
http://phys.org/news/2013-07-chimp-pig-hybrid-humans.html
http://www.macroevolution.net/human-origins-2.html#.Un4AfuLflGk

Under that scenario, would the common ancestor be a chimp or pig?

Networks are going to replace a tree of life, it just might take 20 years. Not just for bacteria but multicellular life as well.

"But given what we now know about prokaryote genome evolution and the contribution of endosymbiosis to eukaryote evolution, it seems rather unlikely that biologists in 20 years will still be using the language of strictly bifurcating trees to describe the relatedness of prokaryotes, and to develop models of microbial evolution."
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761302/

"Having uprooted the tree of unicellular life biologists are now taking their axes to the remaining branches. Dr Bapteste said: 'If you don't have a tree of life what does it mean for evolutionary biology. At first it's very scary – but in the past couple of years people have begun to free their minds'."
Charles Darwin's tree of life is 'wrong and misleading', claim scientists - Telegraph

I'm not saying Dr Bapteste is a creationist, I think he's just being honest and objective about the evidence for Darwin's tree of life. Let them search all they want, but unless they offer something other than "suggestions" for the origin of life I remain skeptical. I quote them because it's like a stipulation in a court of law, it saves time when evolutionists like Koonin say:
"the idea of evolution being driven primarily by infinitesimal heritable changes in the Darwinian tradition has become untenable."
"The discovery of pervasive HGT and the overall dynamics of the genetic universe destroys not only the Tree of Life as we knew it but also another central tenet of the Modern Synthesis inherited from Darwin, gradualism."
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784144/pdf/nihms147680.pdf

Or when a secular geologist like Ager points out a major flaw in the pancake layer theory:
"Ager made it clear and repeated it in this and his second book followed up in 1990 to say he was no a young earth geologist or creationist and knew that what he was about to reveal would be used by creation scientists to damage the geology of Lyell."

As if using the truth is a bad thing. The truth is a spotted salamander uses photosynthesis within its cell and nobody knows how this happened. The INFERENCE is endosymbiosis, in other words evolution is used to prove evolution. Just another exercise in circular reasoning.

 

[Barbarian]

I was half-joking about the mice/pig/chimp thing. I say half because a pig-chimp hybrid theory for the origin of humans is a real thing:

So is the belief that there was a universal flood. The problem is, the same as the above. Lack of evidence.

Networks are going to replace a tree of life, it just might take 20 years. Not just for bacteria but multicellular life as well.

As you see, even Bapteste agrees that we have a common ancestor among eukaryotes, and even shows the evidence for this fact. So it doesn't seem very likely that common descent is in any trouble.

"But given what we now know about prokaryote genome evolution and the contribution of endosymbiosis to eukaryote evolution, it seems rather unlikely that biologists in 20 years will still be using the language of strictly bifurcating trees to describe the relatedness of prokaryotes, and to develop models of microbial evolution."

Pretty safe bet, since scientists were talking about this when I was an undergraduate,nearly 50 years ago. But as Bapteste said, the process is almost non-existent in eukaryotes, and the comprehensive study I showed you, shows that even in the prokaryotes, the amount of lateral gene transfer is perhaps 2 percent on average. Which means you can do a lot of mischief by cherry-picking data, but if you use whole genomes, the picture remains pretty clear.

I'm not saying Dr Bapteste is a creationist, I think he's just being honest and objective about the evidence for Darwin's tree of life.

As Gould wrote decades ago, the "tree" had long been abandoned. Common descent calls for a more bushlike metaphor, with a few "cobwebs" of lateral gene transfer and a number of endosymbiotic events.

Let them search all they want, but unless they offer something other than "suggestions" for the origin of life

This isn't about the origin of life.

I remain skeptical. I quote them because it's like a stipulation in a court of law, it saves time when evolutionists like Koonin say:
"the idea of evolution being driven primarily by infinitesimal heritable changes in the Darwinian tradition has become untenable."

He's about 30 years late. Punctuated equilibrium took that aside.

Or when a secular geologist like Ager points out a major flaw in the pancake layer theory:

It's not about geology, either. And Ager was no threat to modern geology which moved on past Lyell a long time ago.

As if using the truth is a bad thing. The truth is a spotted salamander uses photosynthesis within its cell and nobody knows how this happened.

We've directly observed the evolution of endosymbiosis. No magic. Would you like me to show you again?

The INFERENCE is endosymbiosis, in other words evolution is used to prove evolution.

It's like finding a tree burned and split after a thunderstorm, and inferring a lightning strike. We've observed that to happen, and since the evidence is consistent with observed reality, we don't imagine Thor hit the tree with his hammer.

Reality, again.

Just another exercise in circular reasoning.

You've been misled on that. We see endosymbiosis, and we have in the past directly observed the evolution of endosymbiosis, so we aren't puzzled as to how it happens.

 

[Sparkey]

I say half because a pig-chimp hybrid theory for the origin of humans is a real thing:

Regarding the "pig/chimp hybrid theory for the origin of humans," Barbarian goes way out into Left-Field and quips:

So is the belief that there was a universal flood. The problem is, the same as the above. Lack of evidence.

Huh? What was that? Now there is a relationship between what? The concept of humans evolving from pig-chimps is tied to the belief that what God said is true?

If you're saying that God created things in such a way that those who don't want to believe in Him don't have to? Okay. I can see that. But to say, "No Evidence(!)" while simultaneously dismissing all evidence or attempting to explain it away?

Add to that the compound error of using the left-field observation in such a strange manner? How exactly does the Flood relate to the topic of humans coming from pig-chimps? I'd like to hear this one. It's gonna be good, I can tell.

 

[Barbarian]

Barbarian observes:
So is the belief that there was a universal flood. The problem is, the same as the above. Lack of evidence.

Huh? What was that?

Another, rather odd dissent from the evidence.

Now there is a relationship between what?

Just pointing out that people will believe all sorts of things, once freed of the constraints of evidence.

If you're saying that God created things in such a way that those who don't want to believe in Him don't have to? Okay. I can see that. But to say, "No Evidence(!)" while simultaneously dismissing all evidence or attempting to explain it away?

I'm just pointing out that there isn't any evidence that shows a worldwide flood. There isn't any evidence that shows pigs and apes hybridized, either. In fact, we know that in mammals, different chromosome numbers is pretty much a wall against hybridization. And many times, different things are on different chromosomes. The issue would be easy enough to test. See if in-vitro fertilzation between ape and swine gametes would produce a viable embryo. I think I know why this guy has never done it.

 

[Vaccine]

Fossils of sea creatures found in mountains all over the world is evidence of a worldwide flood. But go ahead and reach into the bag of endless assumptions to bury this truth with.

Thanks for pointing out just how absurd a pig-ape hybrid is too. The reason I pointed that out in the first place was to show the extremes science has to go to cling to common ancestry. We're probably going to see all kinds experiments where animals are mixed in an effort to "prove" Darwin was right and the bible was wrong about the origin of man. All that just makes the idea of man being formed from the dust all the more palatable.

 

[Barbarian]

Fossils of sea creatures found in mountains all over the world is evidence of a worldwide flood.

Nope. Those mountains are made of the fossils of sea creatures. The Himalayas, for example, are made of the folded remains of shallow sea bottoms, thrown up as India moved into Asia. How do we know? It's still going on. GPS sensors attached to bedrock measure the northward motion; the mountains are still growing.

But go ahead and reach into the bag of endless assumptions to bury this truth with.

Your assumption was incorrect, as the evidence I showed you makes clear.

Thanks for pointing out just how absurd a pig-ape hybrid is too.

Of course. But as you see, the genetic data makes clear that a common ancestor for chimpanzees and humans is as certain as science can be.

The reason I pointed that out in the first place was to show the extremes science has to go to cling to common ancestry.

No. If that were true, evolutionary theory would be in serious trouble.

We're probably going to see all kinds experiments where animals are mixed in an effort to "prove" Darwin was right

As you know, Darwin never said anything remotely like that. Just another weird idea that creationists try to graft on to Darwin. It's very transparent, and really very futile.

and the bible was wrong about the origin of man.

Many creationists think so, when they see what Genesis actually says. But God should know; He created evolution, after all.

 

[Sparkey]

... and the bible was wrong about the origin of man.

Many creationists think so, when they see what Genesis actually says. But God should know; He created evolution, after all.

I have never found that statement in the Bible. Seems like you're reading something that isn't there. Yes, I've heard your version and interpretation. That's exactly why I say that it seems you're reading into things again. It's perfectly okay to try to figure out the unknown things for yourself but to turn from that pursuit and begin to teach others that God 'created' evolution is folly. Have you checked with Him on that one?

 

[Sparkey]

Barbarian observes:
I'm just pointing out that there isn't any evidence that shows a worldwide flood.

If you don't recognize it must follow that it didn't happen and evidence to support the fact doesn't exist.

Sparrowhawke observed that some say, "No Evidence(!)" while simultaneously dismissing all evidence and/or attempting to explain it (the literal mountains of evidence) away.

In the above response we see inadvertent confirmation(s) where yet another example of abject denial is given.

 

[Barbarian]

Barbarian observes:
Many creationists think so, when they see what Genesis actually says. But God should know; He created evolution, after all.

I have never found that statement in the Bible.

You won't find a statement asserting that He created protons, either. But He did.

Seems like you're reading something that isn't there.

Lots of things are true that aren't in Scripture.

Yes, I've heard your version and interpretation. That's exactly why I say that it seems you're reading into things again. It's perfectly okay to try to figure out the unknown things for yourself but to turn from that pursuit and begin to teach others that God 'created' evolution is folly.

Evolution is an observed fact of nature. God created nature. Seems obvious to me.

Have you checked with Him on that one?

Since He says He created all things, that would include evolution as well.

 

[Barbarian]

Barbarian observes:
I'm just pointing out that there isn't any evidence that shows a worldwide flood.

If you don't recognize it must follow that it didn't happen and evidence to support the fact doesn't exist.

I'm just pointing out the evidence. No sign of a worldwide flood, and since the Bible doesn't say there was a worldwide flood...

Sparrowhawke observed that some say, "No Evidence(!)" while simultaneously dismissing all evidence and/or attempting to explain it (the literal mountains of evidence) away.

Notice the mistaken assertion that mountains are covered with the shells of marine animals. Rather, they are made of the shells of marine animals. And we know why. The mountains were folded up by movement of the continents. And it's still going on, so we can observe it happening.

In the above response we see inadvertent confirmation(s) where yet another example of abject denial is given.

Reality has a lot of drawbacks, but it is true. GPS sensors make it clear the movement of India into Asia continues. No point in denying the fact. Do you have any evidence for a worldwide flood?

 

[Sparkey]

Do you have any evidence for a worldwide flood?

Are you asking for incontrovertible evidence that does not include the Word of God? Seems maybe you are.

I have it on good authority that, "those who hopefully wait for Me will never be put to shame." Is it too much of a stretch for me to think this "hopeful waiting" includes our discussion and the eventual end of it?

In the meantime, you are welcome to your opinion, for what it is worth, and I expect that you would say same to me.

 

[Sparkey]

To the subject I firmly believe that we (mankind) all have a "common ancestor". That's what Jesus believed and said too.

 

[Barbarian]

Are you asking for incontrovertible evidence that does not include the Word of God?

The word of God contains no evidence for a worldwide flood. And there is no evidence for it in nature. So...

I have it on good authority that, "those who hopefully wait for Me will never be put to shame." Is it too much of a stretch for me to think this "hopeful waiting" includes our discussion and the eventual end of it?

Hard to say. The race is not always to the swift, and this is a marathon, not a sprint.

In the meantime, you are welcome to your opinion, for what it is worth, and I expect that you would say same to me.

As always. It matters in science, but it's not a salvation issue at all. God really doesn't care whether you accept evolution or not.

 

[Sparkey]

I know that's the popular thing to say these days but seriously? I think He does care. We are to model ourselves after His Son who took his Father's words to heart. Show me the argument from the words recorded and spoken by Jesus, if you don't mind. For my part? We have too many to choose from, "Man lives not from bread alone but from every word the comes from the Mouth of God."

I would agree with your assessment regarding your teaching and the teaching of others on the subject in that I don't think that our ultimate salvation is predicated on it. But it's not okay to say, "God doesn't care..."

I have no clue where you got that idea, but it didn't come from the Bible.