The Mystery of Evolution: 8. Common Descent-The Tree of Life or a Bush? An Orchard?

Special Update!!!

It turns out that professor Larry Moran of the University of Toronto agrees with Craig Venter. Thanks to Allan Miller, I discovered a blog on a similar theme at sandawalk link here 

This is what professor Moran says about the video (his video is 42 min long):

” Everything that Ventor says is correct. He didn’t need to quibble about the universality of the genetic code but it’s true that there are variants.”

“I’m pretty sure that Dawkins doesn’t agree (in reference to video) with those who question whether there’s a tree of life. One of the most profound implications of the net of life is that it’s consistent with several independent origins of life that preceded the rise of a modern genetic code and contributed to existing species. In other words, there may not be a single LUCA (Last Universal Common Ancestor). Dawkins does not like that. It’s not what he says on the lecture circuit.” (my emphasis)


There is probably no one in the world of biology today as respected as Craig Venter.

Why?

Well, his achievements are indeed great including being involved with sequencing the human genome and assembled the first team to transfect a cell with a synthetic chromosome, which some even went as far as calling the creation of artificial life…

Now apparently, he is involved in the anti-aging research…no surprise here…he is 70 and would like reach immortality like the jellyfish…Who can blame him…He is an atheist…

However, his also known for what some would call radical statements such as denying the common descent which is the very foundation of evolutionary theory…

“Common descent describes how, in evolutionary biology, a group of organisms share a most recent common ancestor. Common ancestry between organisms of different species apparently arises during speciation, in which new species are established from a single ancestral population. Organisms which share a more recent common ancestor are apparently closely related.” –Wiki

The apparent common descent of all organisms on earth doesn’t agree with Craig Venter’s research…

Here is what he says on the theme:

While some may object that this is an old and recycled subject, I would argue that to claim that, one would have to present the evidence that Venter’s claims have been refuted since…

I have noticed that the tree of life is being used on many threads, including miraculous insertions of genes into the tree of life that many, like Venter  and others had already buried… 

However, in view of my recent OPs The Mystery of Evolution # 6 especially, it doesn’t look like the issue of common ancestry has been resolved at all…The genes are still not accounted for and the proposed mechanism for the endosymbiosis seems sketchy… if not miraculous…

If anything, the supposed common ancestry got more complicated on the much deeper and deeper level in the history of life and no wonder that Venter claims that:

Venter: “…I’m not so sanguine as some of my colleagues here,” he said, “that there’s only one life form on this planet. We have a lot of different types of metabolism, different organisms. I wouldn’t call you [Venter said, turning to physicist Paul Davies, on his right] the same life form as the one we have that lives in pH 12 base, that would dissolve your skin if we dropped you in it.”

What does he mean by this? Is there more then one form life on earth?

Davies “Well, I’ve got the same genetic code, “We’ll have a common ancestor.”

Venter: “You don’t have the same genetic code,” replied Venter. “In fact, the Mycoplasmas [a group of bacteria Venter and his team have used to engineer synthetic chromosomes] use a different genetic code that would not work in your cells. So there are a lot of variations on the theme…”

Davies: “But you’re not saying it [i.e., Mycoplasma] belongs to a different tree of life from me, are you?”

Venter: There Isn’t a Tree of Life

“The tree of life is an artifact of some early scientific studies that aren’t really holding up…So there is not a tree of life.”

What Venter was talking about” is as good, if not better today, and it will look even better in the not that distant future…I can assure you of that… 🙂

More on the theme:

Uprooting the Tree of Life

“The tree of life is being politely buried..”- Evolution: Charles Darwin was wrong about the tree of life

 

Is the Bush of Life the answer? Venter says “…there may be a bush of life…”

Image result for sandwalk tree of life

Or is there a forest or orchard of life with many independent roots?

Has the base of the bush or orchard of life been a single root?

75 thoughts on “The Mystery of Evolution: 8. Common Descent-The Tree of Life or a Bush? An Orchard?

  1. Allan Miller:
    Venter wrong. Simple.

    Well…I assume you have your own research to prove Venter wrong…

    Let’s see…

    You wouldn’t be saying “Venter is wrong” without any bases just because you don’t like what he is saying, would you? On the other hand… 😉

  2. J-Mac,

    You’re right, I wouldn’t be saying he’s wrong without any basis, but essentially you are just trolling. You haven’t grasped a single word of anything else anyone has said to you, so why should anyone bother now?

    It’s just Kurland all over again. You don’t understand the argument yourself, can’t articulate why you think Venter is right, but since it’s Dawkins on the other side, todays’s pet evolutionist is … ta-dah! … Craig Venter. So, shove it. I will content myself with pointing and laughing.

  3. Allan Miller:
    J-Mac,

    You’re right, I wouldn’t be saying he’s wrong without any basis, but essentially you are just trolling. You haven’t grasped a single word of anything else anyone has said to you, so why should anyone bother now?

    It’s just Kurland all over again. You don’t understand the argument yourself, can’t articulate why you think Venter is right, but since it’s Dawkins on the other side, todays’s pet evolutionist is … ta-dah! … Craig Venter. So, shove it. I will content myself with pointing and laughing.

    So…where is it? Vent it out!!! I’m going golfing…bye..;-)

  4. This J-mac guy is my new favorite creationist.

    Keep going J-mac, by Christmas you’re sure to have made the whole rotten edifice come crashing down. This is where it all began, the collapse of Darwinism. And you’ll be the guy who did it.

  5. Allan Miller:
    J-Mac,

    So you’ve got to number 8; we haven’t seen anything new yet.

    Oh I dunno. I though #7 where J-Mac asked for ways to falsify evolution, was given a dozen or so ways, then flat out lied and said no one provided a method was kinda interesting.

  6. So J-mac in the previous thread thinks there’s no way to falsify evolution, but in this thread he thinks Craig Venter’s research has falsified it.

  7. Adapa: Oh I dunno.I though #7 where J-Mac asked for ways to falsify evolution, was given a dozen or so ways, then flat out lied and said no one provided a method was kinda interesting.

    Kinda like Behe on the witness stand at Dover, testifying that there was no evidence that the immune system had evolved. Then complaining that the 3-foot high stack of such evidence, papers and textbooks, were too heavy for his lap. And THEN testifying that all this evidence failed to address his claim that there was no such evidence.

    I’d say this is evidence that Morton’s Demon has infinite patience and never misses an opportunity.

  8. Rumraket:
    So J-mac in the previous thread thinks there’s no way to falsify evolution, but in this thread he thinks Craig Venter’s research has falsified it.

    Creationists aren’t the sharpest knives in the drawer.

  9. This was discussed at Sandwalk back in February 2013. 4 comments in, a chap called Allan Miller (he’s very good, isn’t he?) echoes my own opinions on the matter. Prof. Moran tried to slap me (I mean him!) down a bit, but gave no reason why one should suppose that LUCA was not a single cell.

    Miller says:

    I don’t read Dawkins as being overly concerned about the structure of the tree as opposed to its rooting. Does a bush/net mean more than one LUCA? The differences between codes are vastly over-hyped (eg EN&V, which links to the whole video, tries to lecture Dawkins that there are !!!17!!! variant codes). But any two codes differ by two or three bases [meant codons!] at most – it is only by comparing all codes that one can determine that in all 9 (out of 64) codons vary. Which is still sod all, really.

    If there are separate origins, we might also wonder how the base pairs were arrived at – convergent evolution? There are theoretical other pairings that could exist, and [there’s] the otherwise curious observation that methylUridine is the DNA base in every organism known – again, convergence?

  10. Venter is wrong, stating his conclusion far too broadly. I note that J-Mac is terribly impressed by Venter’s reputation and credentials since J-Mac wants to cite Venter as disproving the notion of an evolutionary tree. The minute Venter agrees with evolutionary biologists, J-Mac will simply lump him in with them and have a much less respectful description.

    Venter’s argument has much more validity in the prokaryotes (Bacteria and Archaea) and is mostly wrong in the Eukaryotes. Even in the prokaryotes, although on a scale of hundreds of millions or billions of years there is much horizontal gene transfer, most reproductions do not involve any HGT.

    There are violations of the tree in Eukayotes, such as hybridization, but they are rare enough to make a treelike phylogeny largely true. This can be confirmed by comparing phylogenies for different loci, and lots of that has been done.

  11. Actually, worth looking at Sandwalk also to observe the work of one ‘John Witton’. Powerful fond of ellipses, he was …

  12. Joe Felsenstein: J-Mac is terribly impressed by Venter’s reputation

    Shouldn’t I be? Unlike many speculative, big mouths here he is an experimental scientist

    Unless you performed some experiments that prove him wrong…
    or you gathered more then 60 million unique genes sets like he did…

    After your unfounded claim that 10 billion species are evolving and transitioning into other species I think I’m going to stick to Venter…for now…

  13. Allan Miller:
    Actually, worth looking at Sandwalk also to observe the work of one ‘John Witton’. Powerful fond of ellipses, he was …

    This must be the best evidence for common descent you will ever find …lol

  14. J-Mac: Shouldn’t I be? Unlike many speculative, big mouths here he is an experimental scientist

    The criticism of Venter isn’t that he’s not an experimental scientist, the criticism is that his conclusions extend far beyond what his experimental results support.

  15. Flint: The criticism of Venter isn’t that he’s not an experimental scientist, the criticism is that his conclusions extend far beyond what his experimental results support.

    O’RLY?
    Criticism based on what? “…I don’t like what Venter is saying..” kinda criticism? It’s noted… I get it…;-)

  16. Rumraket:
    This J-mac guy is my new favorite creationist.

    Keep going J-mac, by Christmas you’re sure to have made the whole rotten edifice come crashing down. This is where it all began, the collapse of Darwinism. And you’ll be the guy who did it.

    I hope you mean it? 😉

  17. Rumraket:
    So J-mac in the previous thread thinks there’s no way to falsify evolution, but in this thread he thinks Craig Venter’s research has falsified it.

    there is no tree of life and the search for an alternative is nowhere to be found…. you interpret what that means…;-)

  18. The OP opens:

    There is probably no one in the world of biology today as respected as Craig Venter.

    Thank heavens I didn’t have anything in my mouth when I read that opening. Full-on spit take.
    As others have noted, Venter is wrong. What he says about pH 12 is obviously irrelevant, and what he says about the genetic codes is extremely misleading, as anyone who has read the A Prediction Tested thread here knows. He is exaggerating for (self-aggrandizing) rhetorical effect. The irony being, as Joe noted, that the moment he says something that J-Mac disagrees with then he’ll revert to being just another lying scientist.
    My opinion of Venter is up there with my opinion of Mullis. 😉 By way of contrast, John Sulston is awesome, and you should hear him on the subject of Venter.
    This selective credentialism is fascinating.
    E4link

  19. J-Mac: O’RLY?
    Criticism based on what? “…I don’t like what Venter is saying..” kinda criticism? It’s noted… I get it…;-)

    It’s not that people “don’t like” what he’s saying. It’s not even that people disagree with what he’s saying. It’s that his claims, whether right or wrong, exceed what his experimental evidence supports.

    It seems that it’s much easier for a scientist to find what he wants or needs in his results, rather than what’s actually there. Not all confirmation bias is deliberate, or even conscious. Countless hours, for example, have gone into investigating exactly why men are smarter than women, whites are smarter than blacks, Germans are smarter than the French, and so on (and on, and on). And during these investigations, it never occurred to anyone to wonder if their presumption was actually true. That was taken for granted. Even by Darwin, who wrote that men evolved to be superior to women.

  20. Joe Felsenstein:
    Venter is wrong, stating his conclusion far too broadly.I note that J-Mac is terribly impressed by Venter’s reputation and credentials since J-Mac wants to cite Venter as disproving the notion of an evolutionary tree.The minute Venter agrees with evolutionary biologists, J-Mac will simply lump him in with them and have a much less respectful description.

    Venter’s argument has much more validity in the prokaryotes (Bacteria and Archaea) and is mostly wrong in the Eukaryotes.Even in the prokaryotes, although on a scale of hundreds of millions or billions of years there is much horizontal gene transfer, most reproductions do not involve any HGT.

    There are violations of the tree in Eukayotes, such as hybridization, but they are rare enough to make a treelike phylogeny largely true.This can be confirmed by comparing phylogenies for different loci, and lots of that has been done.

    You are gettin old or you have selective memory?
    I’m also impressed with W. Ford Doolittle and his Uprooting the Tree of Life
    http://labs.icb.ufmg.br/lbem/aulas/grad/evol/treeoflife-complexcells.pdf

    As well as Eric Baptese “We have no evidence at all that the tree of life is a reality,” (Eric Bapteste), an evolutionary biologist at the Pierre and Marie Curie University in Paris.
    Time to move from your old, outdated views…science moves on…unlike you… 😉

  21. Flint,

    What’s you contribution to the OP? If you don’t mind me asking… You don’t like it? I got the idea the first time you commented…you don’t have to repeat the same thing using different words…Again; I get it…

  22. Interestingly, IQ tests have been tweaked from the earliest versions, on the assumption that men and women should score equally. No such tweaking has been done for race, nationality, or economic status.

  23. J-Mac:
    Flint,

    What’s you contribution to the OP? If you don’t mind me asking… You don’t like it? I got the idea the first time you commented…you don’t have to repeat the same thing using different words…Again; I get it…

    You say you get it, but I haven’t seen any further indication that this is true, and plenty of indication that it is not. To quote William Benetta, “In all of these efforts, the creationists make abundant use of a simple tactic: They lie. They lie continually, they lie prodigiously, and they lie because they must.” His description of your efforts could not be improved.

  24. petrushka:
    Interestingly, IQ tests have been tweaked from the earliest versions, on the assumption that men and women should score equally. No such tweaking has been done for race, nationality, or economic status.

    And I’m guessing that, properly done, these tweaks could successfully eliminate all of these undesirable inequalities. Maybe it will prove more difficult to eliminate the effect of IQ (as measured by tests) improving with practice.

  25. J-Mac:

    Flint,
    Give me one reason why I should continue to wasting time conversing with you?

    Here’s one: Your incompetence amuses us.

  26. J-Mac: I’m also impressed with W. Ford Doolittle and his Uprooting the Tree of Life

    Does this “impressed” feeling also extend to Dr. Doolittle’s views on endosymbiosis and on junk DNA, I wonder?
    Or are you, as Joe predicted, only impressed with scientists when you think that they are agreeing with you?

  27. DNA_Jock: Does this “impressed” feeling also extend to Dr. Doolittle’s views on endosymbiosis and on junk DNA, I wonder?
    Or are you, as Joe predicted, only impressed with scientists when you think that they are agreeing with you?

    Read my Mystery #6 and stop wasting my time!

  28. https://answersingenesis.org/biology/microbiology/information-processing-differences-between-bacteria-and-eukarya/

    More and more studies have demonstrated that even the most phylogenetically favorable biological sequences refuse to fit into one single tree; they typically end up a forest, although often they are not presented that way (Ebersberger et al. 2007; Puigbo, Wolf, and Koonin 2009; Rochette, Brochier-Armanet, and Gouy 2014). For example, early last year, Rochette and colleagues reported a thorough phylogenomic analysis of eukaryotic proteins that have prokaryotic homologs (Rochette, Brochier-Armanet, and Gouy 2014). They identified 475 such protein families in which eukarya are monophyletic from 234,892 protein families from 820 bacteria, 62 archaea, and 64 eukarya. Since 65 of these 475 families contain two to four Last Eukaryote Common Ancestor (LECA) clades, defined as clusters of homologs composed of proteins from bacteria and/or archaea and two groups of eukarya, a total of 554 LECA clades were obtained. To reduce the size of the trees and the taxonomic biases, they selected 144 bacterial and 39 archaeal genomes. For each LECA clade, ten eukaryotic organisms were selected. The authors then reconstructed the phylogenetic trees and found that 434 (78%) of the 554 LECA clades remained monophyletic for eukarya with more than 50% nonparametric bootstrap support (Fig. 1A). Therefore, 311 (~42%) out of the 744 phylogenetic trees generated show that eukaryotes are not monophyletic (191 in the initial phylogenetic construction, 120 in the reconstruction with the reduced data set). Based on extended topological criteria called configurations, Rochette and colleagues concluded that 56% (243) of the 434 (probably 433, see note in the legend of Fig. 1) LECA clades have bacterial origin, 28% (121) archaeal origin, 0.7% (3) “three-domain” configuration (Archaea, Bacteria, and Eukarya all monophyletic), and 15% (67) have tangled phylogeny (Archaea and Bacteria appeared mixed) (Rochette, Brochier-Armanet, and Gouy 2014) (Fig. 1B). Furthermore, of the 243 LECA clades with bacterial origin, only 44 (18%) could be traced to a specific bacteria phylum (41 to Alphaproteobacteria, two to Cyanobacteria, and one to Verrucomicrobiae) (Fig. 1C). Note that the authors found that the “trees were extremely heterogeneous in terms of species content, number of paralogs per genome, branching patterns, as well as in terms of branch length and bootstrap support distributions among branches.” In fact, no two trees were the same. This echoes the conclusion of an earlier study by Puigbo and colleagues, who found that no two trees in their 102 nearly universal trees were the same (Puigbo, Wolf, and Koonin 2009). Thus, even with the most extreme data filtering, no single consensus tree could be obtained in either of these studies.

  29. J-Mac: there is no tree of life and the search for an alternative is nowhere to be found…. you interpret what that means…;-)

    If it troubles you that something about evolution is not strictly true, then I’ll point out that:

    Boyle’s law is false;
    Kepler’s laws are false;

    They are false, but they make very good predictions.

    Scientific theories are idealizations. They are not expected to be literally true. Most scientists understand this. Maybe take a look at Nancy Cartwright’s book “How the laws of physics lie”.

  30. DNA_Jock:
    J-Mac,

    So that’s a “No” then. Proving Joe correct. Thank you for your honesty.

    So, now you’ve proven you didn’t read my Mystery # 6! So you are trolling.
    Welcome to ignore! 😉
    ciao DNA_Sock!

  31. I find it useful at times like this to recall that the only real issue is whether humans are related to apes by common descent. Cousins.

    Everything else is window dressing.

  32. J-Mac:
    Neil Rickert,

    Oh yeah? What do you expect me to do? Cry?
    Grow up! This is not the first and the last time “you got slapped around”…
    You can bet on it…

    “The first or the last time” by the way.

  33. J-Mac: So, now you’ve proven you didn’t read my Mystery # 6! So you are trolling.
    Welcome to ignore!
    ciao DNA_Sock!

    Just think (kidding, of course) — if you put everyone who laughs at you on ignore, you can create your very own personal echo chamber. And then you’ll no longer have to pretend to think about your posts, since those in your chamber won’t care anyway.

  34. petrushka:
    I find it useful at times like this to recall that the only real issue is whether humans are related to apes by common descent. Cousins.

    Everything else is window dressing.

    ??? Since when did humans STOP being apes? Last I noticed, humans fell smack in the middle of the ape clade.

  35. J-Mac: You are gettin old or you have selective memory?
    I’m also impressed with W. Ford Doolittle and his Uprooting the Tree of Life
    http://labs.icb.ufmg.br/lbem/aulas/grad/evol/treeoflife-complexcells.pdf

    As well as Eric Baptese “We have no evidence at all that the tree of life is a reality,” (Eric Bapteste), an evolutionary biologist at the Pierre and Marie Curie University in Paris.
    Time to move from your old, outdated views…science moves on…unlike you…

    Yawn. I am well aware of the views of all these folks, having been around to meet all of them and hear the views of most. Ford Doolittle is a friend, so is Charlie Kurland, I’ve met Venter years ago and I think Eric Bapteste too. The prevalence of horizontal gene transfer in the Bacteria and Archaea is widely known.

    If you are impressed by Ford’s 2000 Scientific American article, then what about this passage from near the end of it, which you must have missed:

    What would a truer model look like? At the top, treelike branching
    would continue to be apt for multicellular animals, plants and fungi.

    So Doolittle is not calling into question the trees of, say, apes and humans, or most of the trees of animals that have been discussed in TSZ.

    Suddenly less impressed? I thought so.

  36. Joe, to J-Mac:

    If you are impressed by Ford’s 2000 Scientific American article, then what about this passage from near the end of it, which you must have missed:

    What would a truer model look like? At the top, treelike branching
    would continue to be apt for multicellular animals, plants and fungi.

    So Doolittle is not calling into question the trees of, say, apes and humans, or most of the trees of animals that have been discussed in TSZ.

    J-Mac,

    I know this hasn’t sunk in yet, but to deny common descent isn’t merely dumb — it’s at a flat-earth, roll-your-eyes, Sal Cordova level of stupidity.

    It’s something to be ashamed of and something to fix immediately if you have even the slightest concern for truth.

  37. Just to note that there are two somewhat separate issues here: whether there was a single LUCA, and the extent to which HGT confounds the tree/bush/pumpkin that sprouts from this individual or set of individuals.

    It does make me laugh when people say it’s-not-a-tree-it’s-a-bush though. Ever seen a bush?

    Then Sal joins in with his ‘it’s an orchard’, or ‘it’s a forest’ – concepts, to the extent that they are appropriate (not very), prompted by phylogenetic analysis, a method Sal does not think actually has any validity. Like the selective puffing of pet experts, the selective application of invalid methods always gives me a giggle.

Leave a Reply