“Species”

On the thread entitled “Species Kinds”, commenter phoodoo asks:

What’s the definition of a species?

A simple question but hard to answer. Talking of populations of interbreeding individuals immediately creates problems when looking at asexual organisms, especially the prokaryotes: bacteria and archaea. How to delineate a species temporally is also problematic. Allan Miller links to an excellent basic resource on defining a species and the Wikipedia entry does not shy away from the difficulties.

In case phoodoo thought his question was being ignored, I thought I’d open this thread to allow discussion without derailing the thread on “kinds”.

1,428 thoughts on ““Species”

  1. colewd,

    Which of these is evidence for ID? John’s quote appears to me to be asking about evidence for ID, not looking for problems evolution may not (or may, there’s a lot there Mr Gish) have solved.

  2. colewd:
    John Harshman,
    I have discussed this with you and others in past threads.To jog your memory I discussed 6 problems with chimps and man sharing a common ancestor.
    [list of “problems”]
    In addition the origin of the eukaryotic cell
    [ist of “problems”
    These describe two crucial evolutionary events which are mission critical to explain for UCD to be valid.

    Again, you are presenting what you think is evidence against naturalistic evolution, for which the claimed alternative is ID. This is, if anything (I think it isn’t anything but that’s irrelevant here), evidence for ID. Again, evidence for ID is not evidence against common descent. If you disagree, please explain why.

  3. Allan Miller:
    colewd,

    Which of these is evidence for ID? John’s quote appears to me to be asking about evidence for ID, not looking for problems evolution may not (or may, there’s a lot there Mr Gish) have solved.

    No, I’m not asking for evidence for ID. I’m asking for evidence against common descent. Those might be the same thing if in fact ID and common descent were mutually exclusive. But they aren’t.

  4. colewd,

    Until the common ancestor nodes are precisely defined, without assuming its own conclusion, it is a house of cards.

    Can I prove that bees descended from hummingbirds using the data? I’d say not, despite that being a conclusion I have just (for the sake of argument) assumed. Is it, then, only defensible conclusions that are assumed?

    Y’all keep saying it’s circular, or question-begging, without really defending that.

  5. John Harshman,

    Sorry, misread. This:

    I merely said that to point out that evidence for ID (if there were any) would not be evidence against common descent. I have repeatedly asked you to cite some of that evidence.

    I thought ‘that evidence’ was the first, not the second.

  6. colewd:
    John Harshman,

    It does not explain the evolution of de novo DNA sequences which are mission critical for evolution.

    Until the common ancestor nodes are precisely defined, without assuming its own conclusion, it is a house of cards.I know you agree with this because that is part of what your paper was attempting to do.

    Let me join in asking you what you mean by “precisely defined” here. What exactly do you think my paper was attempting to do? And did it succeed?

    Also, why would common descent lack explanatory power just because it doesn’t explain everything you might want to know? What de novo sequences, by the way?

    Once more I beseech you (though not in the bowels of Christ—ewww) to make a greater attempt at clarity when you post.

  7. Neil Rickert: Feel free to start such a thread.

    I’m not sure why I need to say it again but I simply have no desire to do a Bible study here or to discuss the evidence of God’s existence or the problem of evil or the reliability of the Bible or any other such thing.

    I would much rather discuss the topic at hand. It’s the resident atheists who are obsessed with that stuff.

    For some reason they feel the need to inject it into every conversation

    peace

  8. John Harshman,

    What de novo sequences, by the way?

    New DNA sequences that produce functional RNA for gene expression timing control, gene translation or other functional purposes.

  9. colewd:
    John Harshman,

    New DNA sequences that produce functional RNA for gene expression timing control, gene translation or other functional purposes.

    That still sounds very vague to me, but let me ask you: how familiar are you with the literature to affirm that has never been observed?

  10. colewd:
    John Harshman,

    New DNA sequences that produce functional RNA for gene expression timing control, gene translation or other functional purposes.

    Now I have to further ask what you mean by “new”. Are you referring to fairly long bits of DNA that appear out of nowhere? If so, can you give an example of such a bit? Note that I didn’t actually ask you for a definition of “de novo sequence”; I asked you for examples. Examples will act to clarify the definition.

    Let me remind you that I have repeatedly asked you to try very hard to achieve clarity.

  11. John Harshman,

    Let me join in asking you what you mean by “precisely defined” here. What exactly do you think my paper was attempting to do? And did it succeed?

    I thought your paper was trying to show a methodology for creating phylogenic relationships of birds. It discussed the extreme challenges and came up with a weighting system for the strength of the relationships. Overall I thought it was an outstanding paper dealing with a very challenging subject.

    The evidence I provided on the challenge of explaining the origin of man and eukaryotic cells is an argument against Universal Common Descent and not claiming common descent has never occurred. I do agree with Alan’s prior point.

    The idea of a single common ancestor is troubling to me because it takes two animals both male and female to create offspring. I assume common ancestor means a male and female who had offspring that became geographically isolated in order for speciation to occur. Do I understand this correctly?

  12. John Harshman,

    Now I have to further ask what you mean by “new”. Are you referring to fairly long bits of DNA that appear out of nowhere? If so, can you give an example of such a bit?

    the bits that code for
    -hemoglobin
    -actin
    -myosin
    -titin
    -beta catenin
    -e cadeherin
    -myc
    -cyclin d
    -hox
    -n cadeherim
    -the micro RNA’s that control placenta expression

  13. colewd: The idea of a single common ancestor is troubling to me because it takes two animals …

    It takes two animals… FML are you serious? Forget about animals. Forget about eukaryotes… forget about the bible for a second and use your fucking brain

  14. colewd:
    John Harshman,

    the bits that code for
    -hemoglobin
    -actin
    -myosin
    -titin
    -beta catenin
    -e cadeherin
    -myc
    -cyclin d
    -hox
    -n cadeherim
    -the micro RNA’s that control placenta expression

    What makes you think that any of these came out of nowhere?

  15. colewd,

    The idea of a single common ancestor is troubling to me because it takes two animals both male and female to create offspring. I assume common ancestor means a male and female who had off spring that became geographically isolated in order for speciation to occur. Do I understand this correctly?

    Once sex is established, it always takes two. But in fact if you follow gene trees, they each coalesce upon a single individual. Homozygous (identical) sequences in a diploid are reasonably inferred to have common ancestry (unless you think that’s circular …) with a single copy of the gene in one individual (it had a diploid partner, but that was lost). Heterozygous sequence too, but there has been mutation in one or both lineages.

    Each gene may coalesce on a different individual, but then you don’t just stop there. Eventually, as one ascends the family tree, one finds fewer and fewer ancestors occupying nodes at a given remove, despite the exponential doubling of nodes. At the limit, all disappear except for one.

    This applies to autosomes and the X, which has 2 copies in females. Mitochondria and the Y coalesce on singletons anyway.

    Of course when you get back to LUCA, that’s the ancestor of prokaryotes as well as eukaryotes, and sex (as we know it) does not come into it.

  16. Rereading your question, you were talking of speciation. My response was in relation to a single population. But basically you don’t need just 2 individuals for speciation. You just need to split a population and then keep them separate for long enough for hybridisation to become impossible (or, since interfertility can be a continuum of degree, sufficiently rare to not cause much gene flow).

  17. colewd:
    John Harshman,

    Better stated: their origin is very difficult to explain.

    Their origin has zero to do with common descent provided that, for all I know, evidence shows that most of the protein library is present in life across the board and emerged in the early stages of unicellular (prokaryotic?) life

  18. Just to be clear the question of common descent is a different issue than the “problem of species”.

    In a world with out common descent we would still need a way to differentiate between a wolf and a coyote. By the same token if we accept universal decent we still need to explain why a wolf is not the same species as a coyote.

    peace

  19. colewd:
    John Harshman,

    I thought your paper was trying to show a methodology for creating phylogenic relationships of birds.It discussed the extreme challenges and came up with a weighting system for the strength of the relationships.Overall I thought it was an outstanding paper dealing with a very challenging subject.

    Thanks, but you are wrong about what it was trying to show. The point was to demonstrate that some particular relationships among some birds are true. (And by “relationships” I mean actual common descent, not some vague idea of correlation, or whatever.) Any discussion of methodology was in service to that point. Not sure what you mean by “weighting system”.

    The evidence I provided on the challenge of explaining the origin of man and eukaryotic cells is an argument against Universal Common Descent and not claiming common descent has never occurred. I do agree with Alan’s prior point.

    Not sure which prior point of Alan’s you mean. But I have already explained why the origins of particular features and common descent are separate questions, and one doesn’t bear much on the other. You even appear to have acknowledged that point on occasion.

    The idea of a single common ancestor is troubling to me because it takes two animals both male and female to create offspring.I assume common ancestor means a male and female who had off spring that became geographically isolated in order for speciation to occur. Do I understand this correctly?

    No. First, the “single common ancestor” is a population or species, not an individual or pair. Second, though geographic isolation is probably a factor in most speciation, there are exceptions.

  20. colewd,

    How would you describe the speciation event that starts from a common ancestor?

    Hmmm.

    It’s important to remember that the ‘ancestor’ is a population at the branching node, but ancestry ultimately resolves to individuals in prior populations.

    Think of a speciation ‘event’ like a large capital Y in blocky 3D font. The bottom of the base is a single population that can fully interbreed. The tips of the arms are two derived populations that cannot.

    A population is always to some degree in the process of diverging, because new mutations do not get instantly mixed in. But because mating can occur, divergence is limited and the population remains approximately homogeneous, although it may still change in step (anagenesis).

    When you introduce any kind of reduction in population-wide mating, however caused, then independent divergence can start to occur (cladogenesis). This is happening around the branch of the Y, but it can be quite extended in time. Interfertility is likely to start to diminish between the two steadily. When the last interfertile individuals die, speciation is complete.

    Now, if you follow any given gene present and identical in both of the arms, its ancestor (in an individual) is likely to precede the branch of the Y by some distance.

    If you take a gene that differs between the 2 arms (there must be some; that’s what divergence is), they will also coalesce upon an individual in the ancestral population. Mutation has occurred in one or both lines, but they trace ancestry back to the same single copy.

    Individuals in both derived populations ultimately share common ancestry with individuals who lived way before the node. But the formation of the node itself is a population process.

  21. Patrick: How is that observation evil? It’s simply a fact.

    I didn’t say the observation is evil, that’s a misrepresentation of what I actually wrote. Do you care?

    Because if you don’t, please stop responding to me. Put me on ignore. If you aren’t going to post in good faith don’t post at all.

  22. Joe Felsenstein: Perhaps Mung can enlighten us.

    Ah, so you believe in miracles?

    Even young earth creationists believe that all extant live evolved from the survivors of the flood and thus share common ancestors.

  23. Mung:

    Even young earth creationists believe that all extant live evolved from the survivors of the flood and thus share common ancestors.

    Ah, so creationists can believe in common ancestry within baramins, but not in universal common ancestry. Which ID advocates can believe in.

    More traditional creationists believed in the fixity of species, which ruled out any common ancestry.

  24. Aha!

    I see colewd has been discussing “islands of function” with gpuccio at UD. Hence thé séquences coming out of nowhere. There doesn’t have to be only one needle in the haystack, colewd.

  25. dazz,

    Bill Cole on the bacteria flagellum:

    The sequential space is 4 to the 100000th power… that’s an imaginary number, that’s an infinite number

    https://youtu.be/hIy7BhVgPCs?t=6884

    Probably not the right thread to post this, but rather amusing stuff

    Too funny not to post. Thanks for the laugh.

  26. GlenDavidson: https://youtu.be/hIy7BhVgPCs?t=6884

    Probably not the right thread to post this, but rather amusing stuff

    Match that accomplishment, Darwinists, if you ever can.

    ID marches on at the same level of success as ever.

    Glen Davidson

    He was a statistics major, so he must know what he’s talking about. 4^10^5 is an infinite imaginary number, perhaps i times C. Hey, that’s IC!

  27. Allan Miller,

    It’s important to remember that the ‘ancestor’ is a population at the branching node, but ancestry ultimately resolves to individuals in prior populations.

    Think of a speciation ‘event’ like a large capital Y in blocky 3D font. The bottom of the base is a single population that can fully interbreed. The tips of the arms are two derived populations that cannot.

    Defining the common ancestor as a population helps a lot. Thanks.

  28. Alan Fox,

    I see colewd has been discussing “islands of function” with gpuccio at UD. Hence thé séquences coming out of nowhere. There doesn’t have to be only one needle in the haystack, colewd.

    If the haystack is big enough multiple needles don’t help much 🙂

  29. colewd:

    If the haystack is big enough multiple needles don’t help much

    Is colewd the same person who posts at UD as bill cole?

  30. dazz: Stop being an asshole and define/delimit species yourself if you can, or shut up

    You are an insult to indigestion.

    No, I think you are an insult to concrete and rabbits.

    Now don’t stop being an asshole and shut up.

  31. colewd:
    Alan Fox,

    If the haystack is big enough multiple needles don’t help much 🙂

    Granted theoretical protein sequence space is enormous. But if functional sequences are widespread, evolution will stumble across them. That functional sequences are rare or unique is not supported by evidence.

  32. Alan Fox,

    Are you suggesting that John knows more about posh fashion than Tolmeia, or that Tolmeia knows more about biology than John?

  33. colewd:
    If the haystack is big enough multiple needles don’t help much

    You actually don’t realize how dumb this is, do you?

  34. Alan Fox: Granted theoretical protein sequence space is enormous. But if functional sequences are widespread, evolution will stumble across them. That functional sequences are rare or unique is not supported by evidence.

    The quantity is not important. What is important is whether they are reachable in mutation sized steps.

    That is what Arrival of the Fittest is about.

    You want to argue Isolated Islands, you find a way to discredit Wagner and all the thousands of research papers that support Wagner’s thesis.

  35. Allan Miller:
    dazz,

    Beat me to it (though I was going to be kinder). Depends on the multiple, obviously!

    I was kind enough to Bill at Sandwalk, everybody was. All these recurrent questions were addressed in detail, papers were offered to him with evidence showing he is wrong. He refuses to learn, doesn’t even try to understand the arguments presented to him, like all creationists do.

  36. Dividing the living world into species is a useful way of understanding life as long as we recognize the limitations of this categorisation. Comparing individuals within a species of prokaryotes is very much different from comparing individuals in great ape species and it is vastly different than comparing the difference in humans.

    Lower organisms are slaves to the destiny of their species (or kind if you prefer). Evolution is a progression towards the freedom of the individual. Study an individual bacterium in a colony and it is, in essence, interesting only in so far as it is behaving as part of the group. A salmon hatched in some British river has its destiny mapped out before it and we can predict what that destiny will be barring any external disruptions. Defining a person as a member of the species Homo sapiens tells us very little about that person. Defining an individual bacterium as a member of the species Escherichia coli tells us all we need to know about that individual.

    What is interesting about the life of a human is his or her individual history. People can be held as slaves and so in that respect they are unfree, but they can still be free in their thinking. And that is the enduring message that can be taken from Christ. We have the potential to be free in the way that matters most. The slave who accepts his or her circumstances and truly is pleased to serve others has more meaningful freedom than the slave owner who through personal greed and selfishness thinks that others are there to do his or her bidding. The latter is a slave to his or her lower passions.

    In essence a human individual has more in common with an entire species of lower animal than an individual of that species. We may have difficulty defining what a species is but it is a good question in that it spurs us on to further questions worth thinking about.

  37. CharlieM: Dividing the living world into species is a useful way of understanding life as long as we recognize the limitations of this categorisation.

    Excellent comment, in fact the entire post is quality stuff!!!

    It’s what I’ve come to expect from you. keep it up

    peace

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