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The New and Improved Tree of Life

This is your brain on NeoDarwinism:

Old ToL


This is your brain on NeoNePlusUltraDarwinism:

NewToL

Any questions?

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26 Responses to The New and Improved Tree of Life

  1. What’s the difference between NeoDarwinism and NeoNePlusUltraDarwinism? Is it sort of like the difference between HIV and AIDS?

    If so, no thanks. :P

    BTW, how do some of you guys stick smileys into your comments?

  2. Never mind about the smileys. Apparently they don’t show up in the preview section.:D ;)

  3. That’s a tree? It looks like the freeway system in L.A.

  4. It looks like a solution to Zork.

  5. Is there any place one can get a larger version of this, this, “tree”thingy?

  6. Ahoy, Dave!
    I would have assumed that based upon your reasoned support of common descent that you wouldn’t have any problems with these representations of the inter-relatedness of organisms. Color me naive, but what’s your beef?

    Mikey Tutu

  7. Ya, it’s from Doolittle’s article in Scientific American called “uprooting the tree of life.”

  8. I think the important idea here is that early in the history of life the notion of “species” has less meaning than it does now. We think of organisms reproducing somewhat pristinely by either sexual or asexual reproduction, and so we have a picture of there being fairly discrete lines of parent-child descent. However current hypotheses about horizontal gene transfer early in life’s history imply that those lines are blurred, and that significantly different kinds of organism came about in ways that were not exclusively from parent-child reproduction.

    I think it is important to remember that the pictures we draw and the metaphors we use to understand reality are vastly simpler than reality itself. What Doolittle and others are trying to do is offer a picture and metaphor that helps us more accurately understand some new issues in the early history of life – issues that were not known when the original “tree of life” metaphor was first advanced/

  9. It is interesting that there are 7 or several times when life arose in this model. Three lines survived.

    How exactly did life arise several times and have a common genetic platform so they could exchange software?

    It was a long time before intelligently designed computers running different platforms were able to swap data, let alone software. Is this yet another level of irreducible complexity? I suppose it is another case of where “evolution is cleverer than you are”.

  10. “How exactly did life arise several times and have a common genetic platform so they could exchange software?”

    I’m not a computer guy, but it seems obvious to me that given enough time, identical versions of Windows or Vista or Mac OS will be created by different people working seperately on different planets. I don’t see why biological software should be any different.

    Country, type this : and this ) without spaces and you get a smilie. If you type this ; and this ) it’s winking. I think you can frown too, if you like.

  11. Mikey Tutu

    Does horizontal gene transfer, a mechanism known to be in operation today, invalidate common descent? If it does, I missed that memo somehow.

    My personal reasons for faith in common descent are a virtually identical genetic code shared by all living things so far examined and the law of biogenesis. These days I usually couch my definition of comnmon descent as being from one or a few common ancestors due to controversy over how many starting points there are in the New and Improved Tree of Life based upon the NeoNePlusUltraDarwinian Hypothesis.

    Keep in mind there is no theory of evolution. There are only hypotheses of evolution.

    On an unrelated note, the website one hits when clicking on your name is fine for ATBC but not for this forum. I’m all for your freedom of association and everything but for this blog it’s pretty inappropriate.

  12. Does horizontal gene transfer, a mechanism known to be in operation today, invalidate common descent? If it does, I missed that memo somehow.

    I don’t think we are seeing horizontal gene transfer. I think we are seeing bits of code reused in different programs.

    For example, I found this paragraph on Wikipedia describing what is called “inheritence” in object oriented programing

    In object-oriented programming, inheritance is a way to form new classes (instances of which are called objects) using classes that have already been defined. The new classes, known as derived classes, take over (or inherit) attributes and behaviour of the pre-existing classes, which are referred to as base classes (or ancestor classes). It is intended to help reuse of existing code with little or no modification.

    This is something that you know more about than me. But isn’t there a lot of software out there with common objects? Aren’t those common objects the product of intelligent design and not common descent?

  13. jehu:

    “I don’t think we are seeing horizontal gene transfer. I think we are seeing bits of code reused in different programs.”

    You are perfectly right! Homology in code can perfectly be explained as reutilization of the code. And you are perfectly right again, the most functional way of programming, today, is object oriented: the programmer designs the program in form of autonomous objects, which can be reutilized in the next project, and in a different context.

    HGT is an interesting mechanism, but it is well documented only in prokaryotes (bacteria and archea), while it is very doubtful that it may have any relevance in higher forms of life. As already discussed elsewhere in this blog, anyway, HGT
    can never be a source of new information, only a way to “mix it up”.

    As I see it, there are vatious possible conceptual models to explain “homology” in DNA codes, or in phenotypes:

    1) Homology is evidence of common ancestry and non-intelligent evolution: that’s the usual neo-darwinist view, and it is certainly false.

    2) It is evidence of common ancestry and of ID through modifications of the code: in this case, we can think that the designer has acted, slowly (continuosly, step by step), or in “condensed” cronological patterns (that is at certain times, more or less suddenly), to modify already existing beings, imparting new intelligent information through natural or supernatural laws (both possibilities apply). In that model, both ID and common descent are true, but unguided evolution is not. If one accepts the “slow” option, then even graduality is true.

    3)It is evidence of reutilization of the code, but not of direct modifications of already existing beings. This is more the “special creation” option: the designer has “made” each new species as a new “prototype”, creating the new information and the new “hardware” implementation at the same time, through natural or supernatural laws. In this model, ID is true, but not common descent, and homologies are only evidence of reutilization. Even graduality, in my opinion, is not easily incorporated in this framework.

    I want to say that I think we have plenty of scientific evidence to refuse option 1, but really not enough evidence to decide between 2 and 3. So, for me, at present anyone is welcome to prefer what one prefers. It is true, anyway, that once the refusal of option 1 is well espablished, it is perfectly possible, in principle and through research, to scientifically discuss the relative merits of options 2 and 3 (I insist, scientifically. Our personal phylosophical and religious views are absolutely important and valid, but should not, in any way, interfere with the scientific discussion).

  14. “It is interesting that there are 7 or several times when life arose in this model. Three lines survived.”

    That will depend very much on your definition of life. The root of the tree says ‘population of ancestral cells’, which would already be alive.

    “HGT is an interesting mechanism, but it is well documented only in prokaryotes (bacteria and archea), while it is very doubtful that it may have any relevance in higher forms of life.”

    Its certainly seen in single celled eukaryotes and there is evidence that is has occured in limitesd amounts between parasited and insects. Having said that this tree doesnt assume it does occur in higher creatures.

    “I want to say that I think we have plenty of scientific evidence to refuse option 1, but really not enough evidence to decide between 2 and 3.”

    The easiest, cheapest and quickest way to disprove 1 as a scientific option is to prove either 2 or 3.

  15. idnet wrote,

    It is interesting that there are 7 or several times when life arose in this model. Three lines survived.

    How exactly did life arise several times and have a common genetic platform so they could exchange software?

    I have the issue of Scientific American from which this picture was taken. It’s from February, 2000.

    The caption to the picture makes it clear that is trying to portray an idea, not an exact number of lineages. Among other things, the caption says,

    This “tree” also lacks a single cell at it’s root; the three major domains of life probably arose from a population of primitive cells that differed in their genes.

    So, remembering that this is a short article in a popular science magazine, the image I get is this: at the beginning of life there were entities (maybe even not properly considered organisms) which contained genetic material, and that genetic material often recombined in new ways through direct transfer as opposed to reproduction. This created such a pool of entities with different genetic makeups that grouping them into taxonomic levels would not be meaningful.

    From this pool of genetic potential arose the three main branches, although gene transfer continued to play a role, as indicated in the picture by the two well-accepted transfers that gave rise to chloroplasts and mitochondria in the eukaryotes as well as be miscellaneous and unknown other transfers.

    As time went by and organisms became more specialized and complex, the effect of gene transfer became less, so that distinct lineages as modeled in the image of a branching tree became much more the norm.

  16. What Doolittle and others are trying to do is offer a picture and metaphor that helps us more accurately understand some new issues in the early history of life – issues that were not known when the original “tree of life” metaphor was first advanced/

    The problem becomes when people start teaching a metaphor as the truth, at which point it stops being a metaphor, anyway.

    I remember being taught the classic tree of life around 7th grade. I remember thinking then it was BS — and not because of any religious sensibilities. A pretty smart little 7th grader was I.

  17. Jack Krebs:
    I think the important idea here is that early in the history of life the notion of “species” has less meaning than it does now.

    “Species” is pretty ambiguous now. If we use the breeding criteria then there are some humans that may be called a different species than other humans.

    Also there are those who seriously doubt that chloroplasts and mito arose via endosymbiosis- just ask John Davison. So far the only test is “Well they do resemble bacteria is some aspects”.

    gpuccio:
    1) Homology is evidence of common ancestry and non-intelligent evolution: that’s the usual neo-darwinist view, and it is certainly false.

    Homology and common ancestry- that would be OK if alleged homologous structures arose from homologous genes or similar developmental pathways. But we know that isn’t so. We see similar structures arise via differing pathways and via differing genes. We see similar genes give rise to differing structures.

    Gavin de Beer demonstrated that homology is a failure for Common Descent- back in the 70s and even before.

  18. Touché!

  19. Chris Hyland:

    “The easiest, cheapest and quickest way to disprove 1 as a scientific option is to prove either 2 or 3.”

    I don’t agree. Scientific theories should have at least two properties:
    a) They shoud be possible, in other words they should provide a logically reasonable model to explain facts.
    b) They should be supported, at least to some degree, by new experimental facts or new discoveries. In other words, they should be, not “proven” (a scientific theory can never be absolutely “proven” true), but rather gain credibility, and not only the plausibility of point a.

    If a theory satisfies point a but not so much point b, it can be retained and furtherly tested. But if a theory does not satisfy point a, it can and must be refused, even if no other theory is available or has been supported by evidence. Indeed, I cannot understand the reason why modern scientists seem to think that we must have an “officilal” theory for everything, as though science should be afraid of admitting that there are things, in reality, that it cannot, at present, explain, not only in the details, but in principle.
    So much said, I must add that, regarding the nature of biological information, we are more lucky than that. We have one theory, neo-darwinism, which does not satisfy points a and b. Part of the ID debate is intended only to demonstrate that neo-darwinism is not plausible, indeed it is not even possible, and that therefore it can be safely refused. We could call this part of the ID debate the “negative” part, and it is in itself sufficient to disprove neo-darwinism, even without any need to affirm a design theory.
    But, luckily, ID is more than that. The “positive” part of ID is the affirmation that a designer is a possible, legitimate, plausible and probable inference to explain biological information, an inference correctly based on the intrinsic nature of that information and on what we know of design processes. Therefore, an alternative theory exists, it perfectly satisfies point a, and in my opinion it is continuosly supported by each daily new discovery in the field of biology.
    So, to sum up: we have no reason not to refuse neo-darwinism, if we can prove that it is not possible or plausible (I intend, not in the strictly mathemathical sense, but in the physical sense). We don’t need any alternative theory to do that. ID “negative” arguments are more than sufficient at that regard. On the other hand, we have a good alternative theory, ID, which does not explain everything (it does not tell us anything about the designer, or the methods and modalities of the design implementation), but is perfectly satisfactory in explaining the “nature” and typology of biological information: designed, intelligent information. All the “positive” ID arguments support that theory, and it is at present the only plausible, satisfactory intellectual framework about the nature of biological information, and therefore it deserves the attention and respect (not necessarily the belief) of all scientists.
    One last remark: positive “ID” has not been proven true, and never will be, because no true scientific theory can be proven true. And, thanks God, it will never become a “fact”: it will always be a wonderful, elegant and useful scientific theory.

  20. jehu

    I don’t think we are seeing horizontal gene transfer. I think we are seeing bits of code reused in different programs.

    What’s in a name? That which we call a rose by any other name would smell as sweet.

    What’s the difference between genes and program code?

  21. jack krebs

    After reading your comment it occurs to me I should have titled the article The New and Confused Tree of Life. :-)

  22. Hmmm. I’m not sure what is confused about it. The article is six years old, and its purpose was, I think, to communicate some of the new ideas that were developing about this subject. Of course these ideas are incomplete and have not risen to the level of accepted theory, so perhaps they are “confusing” in that sense.

  23. Mikey Tutu

    re; touche

    I about fell out of my chair laughing when I saw your recent artwork. The aliens are from Futurama, right? I was almost certain they were but I couldn’t find them in the wiki list of Futurama recurring alien characters.

  24. DaveScott,

    What’s in a name? That which we call a rose by any other name would smell as sweet.

    Well I don’t think the information was transferred horizontally. I think that from the beginning the programmer used the same objects in different configurations in different organisms.

    What’s the difference between genes and program code?

    IMO genes are a programed code, an amazingly sophisticated and efficient code.

  25. Maybe it is a concession to the design idea.

    Notice the similarity to the diagram with these printouts and maps of old atari 2600 source code.

    http://benfry.com/distellamap/

  26. Rennie,

    Well those are single program diagrams so it doesn’t really compare. If you tried to arrange those programs in a phylogenic tree, now that would be interesting!

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