Living the Scientific Life (Scientist, Interrupted)

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Two nectar-feeding birds from Hawai’i, the kioea (brown-streaked, in middle) and an o’o species (lower left), looked so much like nectar specialists from the western Pacific (two species on right) that taxonomists put them all in the same honeyeater family, the Meliphagidae. All the Hawaiian birds are unfortunately extinct, but DNA evidence shows that their resemblance resulted from convergent evolution, because the Hawaiian birds were actually much closer to birds from the Americas, such as Bohemian Waxwings (upper left).

Image: John Anderton.

ResearchBlogging.org

Every once in awhile, I will read a scientific paper that astonishes and delights me so much that I can hardly wait to tell you all about it. Such is the situation with a newly published paper about the Hawai’ian Honeyeaters. In short, due to the remarkable power of convergent evolution, Hawai’ian Honeyeaters have thoroughly deceived taxonomists and ornithologists as to their true origin and identity for more than 200 years.


Like an artist molding a lump of clay into a specific shape to meet her demands, so nature operates through natural selection to take advantage of naturally-occurring genetic variation throughout the generations to alter the physiology, morphology and behavior of living beings to meet ecological demands. Bold mutations can result in dramatic changes, while subtle genetic variations result in smaller, sometimes hidden, shifts — but only if these changes are adaptive, only if they provide the owner of those genes with a special “edge” that allows them to attract more and fitter mates, and to produce more and fitter offspring who then pass on these adaptive genes to future generations.

“It’s like we had this animal we always thought was a dog, and it’s turned out to be a mongoose,” reports one of my scientific colleagues, Robert Fleischer, of the Smithsonian Institution in Washington, D.C. Fleischer was the lead author of this study.

The Hawai’ian birds’ striking resemblance to the Honeyeaters of New Guinea and Australia demonstrates how evolution within different lineages can cause dissimilar species to converge on similar body plans and forms to meet the demands of similar “jobs”.

Figure 1. Tongues of Meliphagids, Moho, and Relatives of Moho and Chaetoptila
Shown are illustrations of tongues of meliphagids (A-D), two species of Moho (E and F), and relatives of Moho and Chaetoptila on the basis of our results (G and H). This suggests convergence of the tongues of Moho from ancestral tongues like (G) and (H) to tongues like (A)-(D). The following are shown: (A), Meliphaga fasciogularis; (B) Myzomela sclateri; (C), Anthornis melanura; (D), Philemon buceroides; (E), Moho nobilis; (F), Moho braccatus; (G), Dulus dominicus; and (H), Phainopepla nitens. Illustrations (A), (C), and (E) are from Dorst [21]; (B) is from Scharnke [22]; (D) and (H) are from Beecher [23]; (F) is from Gadow [24]; and (G) is from Gardner [25]. Tongue illustrations are reproduced with permission from the British Ornithologists’ Union, American Ornithologists’ Union, Société Ornithologique de France, and the Journal of Ornithology.
DOI: 10.1016/j.cub.2008.10.051.

The Honeyeaters are — were — all classified into the same taxonomic family, Meliphagidae, based on several shared characters. First, they specialize in consuming a sugary diet of nectar so they have long tubular or semi-tubular tongues with a brush on the tip, which evolved for gathering nectar from flowers (figure 1); their beaks curve downwards (figure 2); they have an operculum over their nares to protect their nasal cavity from pollen; and all these species function in ecologically important roles as pollinators and as dispersers of seeds. Other characters that these birds share are long legs and strong, perching feet; and remarkable similarities in plumage color and pattern (figure 2), behavior — and even in song.

Figure 2. Illustrations of Three of the Five Species of Hawaiian ”Honeyeaters” and Three Representative Meliphagid Honeyeaters
The three Hawaiian taxa represent the three primary morphological types found in Hawaiian ”honeyeaters” (Mohoidae: [A], Moho nobilis; [C], Chaetoptila angustipluma; and [E], Moho braccatus). The three meliphagids include one from New Zealand ([B], Prosthemadera novaeseelandiae), one from Australia ([D], Anthochaera carunculata), and one from Samoa ([F], Gymnomyza samoensis). Paintings are by John Anderton and are used by the authors with permission. [larger view].
DOI: 10.1016/j.cub.2008.10.051.

“The similarities between these two groups of nectar-feeding birds in bill and tongue structure, plumage and behavior result not from relatedness, but from the process of convergent evolution — the evolution of similar traits in distantly related taxa because of common selective pressures,” Fleischer points out.

To do this work, the team sequenced and pieced together as much as 1923 basepairs (bp) of nuclear (chromosomal) DNA and 717 bp of mitochondrial DNA from multiple specimens of Hawai’ian “Honeyeaters” in the genera, Moho and Chaetoptila. When they analyzed their data alongside DNA data for other Meliphagids, they discovered that the Hawai’ian birds formed a cohesive group, but astonishingly, the Hawai’ian group was nowhere near the Honeyeaters of New Guinea and Australia (figure 3);

Figure 3. Phylogeny Reconstructions for Hawaiian Mohoids and Outgroups with Different Data Partitions
(A) Section of a ML tree constructed from up to 717 nucleotide sites of mtDNA sequence for the five species of Mohoidae and 43 additional songbird taxa. The tree shows strong support for monophyly of the Mohoidae and also supports placement of the Mohoidae within the waxwing and silky flycatcher clade and Passerida. Relationships among species within the Mohoidae are not well resolved. Bayesian posterior probabilities and ML bootstrap support values are provided at relevant nodes.
(B) Schematic of a phylogenetic tree constructed with Bayesian inference from 190 sequences of up to 1544 bp of the RAG-1 gene [9, 19]. Taxa are merged into triangles indicating major, supported clades that generally match the topology found by Barker et al. [9] with a larger data set. Sequences from Moho nobilis and Moho bishopi fall within the red clade, rather than, as expected, within the basal honeyeater clade (dark blue); the expanded clade shown at upper right reveals the position of these taxa within the clade containing waxwings, silky flycatchers, and the palm chat. This tree includes only the two Moho species for which more than 1000 bp of RAG-1 sequence was obtainable. Shorter RAG-1 sequences of Chaetoptila angustipluma and Moho apicalis are nearly identical to these sequences of Moho in sections of overlap, and thus support these results.
(C) Maximum likelihood phylogram constructed from analysis of up to 421 nucleotide sites of b-fibrinogen introns 5 and 7 combined. At nodes are Bayesian posterior probabilities and ML bootstrap values (100 repetitions). The sequence data set for this tree was limited to outgroup species for which sequences of both genes were available, but analyses with considerably larger numbers of taxa (115 and 189 sequences) for each gene separately produced the same results. [larger view].
DOI: 10.1016/j.cub.2008.10.051.

Surprisingly, the Hawai’ian “Honeyeaters’” closest mainland relatives are the silky flycatchers (the waxwings and Phainopepla) of North America! This finding is in agreement with a controversial prediction made by the famous ornithologist and island biogeographer, Ernst Mayr; that all or nearly all endemic Hawai’ian birds were of North American origin.

Fleischer and his colleagues also used their DNA data to estimate that the Moho and the silky flycatchers diverged between roughly 14 and 17 million years ago. This is a significant period of time for evolution to occur, so the strong resemblance between the Meliphagid Honeyeaters of New Guinea and Australia with those “Honeyeaters” of Hawai’i is plausible, even while it remains remarkable. Further, their DNA-based estimate of the divergence time suggests that the “Honeyeaters” are the oldest lineage found on the Hawai’ian island chain — a time that also coincides nicely with the estimated arrival of the first bird-pollinated plants.

As a result of the deep divergence between the two “Honeyeater” groups, Fleischer and his colleagues proposed that the five Hawai’ian Honeyeaters be placed into their own taxonomic group. They also proposed that this group be elevated to the status of family — a very rare occurrence in modern times. They christened the Hawai’ian “Honeyeaters” the Mohoidae — “Moho” in honor of the most species-rich genus, Moho, and “-idae”, a Latin suffix that denotes a taxonomic family.

“This was something that we were not expecting at all,” remarked a surprised Fleischer. “It’s a great example of how much we can learn about systematics and evolution by applying new technologies like ancient DNA analysis to old museum specimens.”

Why do I think this paper is amazing? First, this work brilliantly reveals the astonishing power of convergent evolution, which made disparate bird groups look, sound and behave so similarly that no one ever had any reason to question their taxonomic placement as each other’s closest relatives in the avian tree of life. Indeed, without the DNA data, no one would ever have been able to recognize or correctly identify the closest relatives of the Mohoidae at all. Second, these data show that the avian colonization of the Hawai’ian islands occurred from the mainland of North America, as Mayr hypothezised — not from the islands of the western Pacific, as many taxonomists erroneously thought, based on the deceptively similar AustraloPapuan Honeyeaters.

According to Fleischer, all five Mohoidae were medium-sized songbirds with slender, slightly downward curved bills with unique scroll-edged and fringed tongues, making them very specialized nectar-feeding birds. They inhabited undisturbed forests on most of the larger Hawaiian islands.

Tragically, all of the members of this newly described family are extinct. The Kioea disappeared first, in 1850, and then the four O’os soon followed that species into oblivion until only the lonely Kauai O’o, Moho braccatus, remained in the Alakai Swamp [short film of this species]. That species was last seen in 1987. All five species of Mohoidae disappeared due to human factors: destruction of their habitats, hunting for feather art, the introduction of predators such as rats, mongoose, pigs and domestic cats, and the introduction of avian diseases, particularly malaria, to the islands.

Thus, even before it was named, the newly christened Mohoidae became the only bird family to become extinct within the last hundred years.

Sources:

R Fleischer, H James, S Olson (2008). Convergent Evolution of Hawaiian and Australo-Pacific Honeyeaters from Distant Songbird Ancestors. Current Biology DOI: 10.1016/j.cub.2008.10.051.

ScienceNews (quotes).

Comments

  1. #1 Bob O'H
    December 16, 2008

    I see you couldn’t resist sneaking a waxwing in there. :-)

    I was confused by your final sentence, thinking that you meant there had been no survivor in the last 100 years. So I did a quick search to check, and found a short clip of the Kauai o’o. Depressing that all that’s left of the species is a few skins and a short bit of tape.

  2. #2 sara
    December 16, 2008
  3. #3 Nuytsia
    December 16, 2008

    Very cool. Been reading this with Anthochaera paradoxa calling outside my window.
    Sweet. :-)

  4. #4 AnthonyK
    December 16, 2008

    This is a remarkable and beautiful piece of research, a story, elucidated by DNA (and the biologists who researched it), especially as it contains that clear indication of evolution – extinction. Even I, a non-scientist, find that I can follow the cladogram and deduce that, for example, the species concerned are in fact at least as distantly related as either are to crows.
    I also note that these DNA analyses seem to be creationist-proof. How could anyone discredit this research?
    Well done on this post, it is a model of scientific clarity.

  5. #5 "GrrlScientist"
    December 16, 2008

    bob — i fixed the final sentence, hopefully, that clarifies things, and I added a link to the video you so kindly found. thanks!

    thanks, Nuytsia and Anthony.

    I also note that these DNA analyses seem to be creationist-proof. How could anyone discredit this research?

    it will be interesting to see how the religious wingnuts deny this research, anthony. but similar to alcoholics and crackheads, i am sure they’ll think of some sort of elaborate denial to support their silly little fanatasy lives.

  6. #6 AnthonyK
    December 16, 2008

    It seems unbearably poignant that all that exists of this family is a few specimens in museums and 10 seconds of film. Still, this is much much more than we have of most extinct animals.

  7. #7 Sheri Williamson
    December 16, 2008

    Not to imply that beauty should be the main criterion by which we measure our losses to extinction, but the illustration of the Hawai’i ‘O’o makes me sick with grief.

    There’s a Caribbean species from the same lineage that seems to be on its way to convergence with the honeyeaters. The streaky brown Palmchat (tongue G in Fig. 1 and Dulus dominica [sic] in Fig. 3) looks much more like the poor lost Kioea and its western Pacific doppleganger(s) than its waxwing/silky-flycatcher relatives. Thankfully, it doesn’t appear to be in any danger of extinction.

  8. #8 Ronald Orenstein
    December 16, 2008

    Thanks, Devorah, for drawing our attention to this remarkable study. There are a number of interesting things about it besides the result:

    1. The waxwings seem to be part of a broader radiation than anyone thought; another recent paper places the Sulawesi “whistler” Hylocitrea within this group (see Molecular Phylogenetics and Evolution 49 (3), December 2008, Pages 1036-1040).

    2. I wonder if there are any similarities between the Mohoids and their new ancestors that we now might notice (compare the tail of some Moho spp to that of the Long-tailed Silky-Flycatcher, for example?

    3. Now that Moho and Chaitoptila are seen to be derived from Northern Hemisphere birds, that leaves only one songbird in Hawai’i regarded as clearly Australasian: the ‘Elepaio (Chasiempsis sandvicensis). I wonder if it is really a monarch, as has always been thought (though a recent DNA study mentioned on this blog suggests that it is…); although the Millerbird (Acrocephalus familiaris) may also have been derived from Pacific Island, rather than Asian, ancestors.

    4. Isn’t it amazing that we can get DNA from birds extinct since the early 19ht Century? Maybe someone will do the same for other lost birds like the “starlings” of Mauritius?

    5. And isn’t it disgusting that every one of these wonderful birds, once common and striking members of the Hawai’ian avifauna, is now extinct?

  9. #9 Nathan Myers
    December 16, 2008

    Ronald: Extinction itself was not believed possible until
    after most of these were gone.

    My father still says “who needs polar bears anyway?” My answer is, how much coal does a canary mine?

  10. #10 RecessionCone
    December 16, 2008

    There’s no reason to insult creationists here. Hopefully we can learn to disagree with them without comparing them to crackheads.

    Tolerance: it’s a beautiful thing.

  11. #11 Loren Coleman
    December 16, 2008

    Excellent posting.

    This all reminds me of the secret kinship of falcons and parrots that was acknowledged in 2008, as per here.
    :-)

  12. #12 WingNut
    December 16, 2008

    …similar to alcoholics and crackheads, i am sure they’ll think of some sort of elaborate denial to support their silly little fanatasy lives

    …meanwhile scientists just get stuff wrong again and again until one day millions of years later they figure it out; that is, until they figure it out better. But anyone who doubts them is stupid, right?

  13. #13 Crackpot Christian
    December 16, 2008

    Tolerance is a beautiful thing :) I am a young earther and this is well researched and of course DNA can trace linearage. Not sure it proves evolution though, a bird is still a bird, changes in a species and natural selection fit our model too. Do you still think we deny natural selection and/or speciation (changes is a species). Our models differ or should only differ, in that creationist believe each species has a common ancestor, you believe all creatures have one common ancestor.

  14. #14 Joseph Colton
    December 16, 2008

    Programmers reuse good code. I see no reason to believe the God has to create everything from scratch. I am often amused that so many people from the scientific world think that God cannot reuse code. If I were a God, and I were to create a world, I would build up the world by establishing what is needed, then building upon it by process of slow evolution.

    Scientists can learn a lot from scripture, if you do not take the creation as literally seven days instead of creation periods, then I think you will find that scientists are actually verifying the bible.

  15. #15 AnthonyK
    December 16, 2008

    Ah, creationists, creationists. Listen, if you’re a religious person then obviously God created the world. Since no one can prove that God or Gods don’t exist we are left with the current scientific/rationalist position – that if he does exist then he created life over billions of years, and evolution was his method.
    I know that all too unfortunately so many Christians in the US have been told to doubt this, and it has become an article of apologetics that evolution is wrong, but really, unfortunately your position is 100% hogwash – well 95% hogwash and 5% wishful thinking. The DNA evidence alone on this and every other animal/plant we have studied shows this. Why don’t you just accept it? It makes no difference to Jesus, and it makes no difference to you. The universe is a fantastically complex and wonderful creation, why must you insist on debasing all that we know until it’s no more than a fairy tale?

  16. #16 John Walters
    December 16, 2008

    I started birding while living in Hawaii, back in 1976. At that time the ‘O’o'a’a (Kaua’i ‘O’o, Moho braccatus) was still living in the ‘Alakai swamp on Kaua’i. Never had a chance to see it (very few people did), but I did have an opportunity once to visit the bird collection at the Bishop Museum and handle a specimen of the ‘Ula-ai-Hawane (Ciridops anna), an extinct species of Hawaiian honeycreeper from the Big Island. Only five specimens were collected before its extinction in the 1890s. It was almost a religious experience–a bird we almost never knew.

  17. #17 Don Codling
    December 16, 2008

    I chanced on this thread through my wife’s keen interest in birding, and read it with great interest … and greater perplexity. What is described is a fascinating piece of scientific detective work. An earlier scientific theory was shown to be flawed, and had to be discarded.

    But what on earth does this have to do with the disagreement between creationists and evolutionists? Creationists believe it happened by design; evolutionists believe it happened by random changes. Somebody please show me a logical argument that this research proves anything about either.

    Please take away the blind prejudices and show me some logic.

  18. #18 bartelby
    December 16, 2008

    I’m not a biologist or an historian if science either, but I sense an echo here of a somewhat less rank scientific heresy than creationism. Lamarck’s theory that changes acquired during an organism’s lifetime are somehow transferred into genetic information and passed on to the offspring is as discredited scientifically as the theory of phlogiston. But here we have “convergent evolution” turning waxwings into honey eaters functionally while the birds retain their genetic identity as waxwings. Passing strange!

  19. #19 Ravilyn Sanders
    December 16, 2008

    Don Codling said in #17
    evolutionists believe it happened by random changes.

    Don, you should first drop your prejudice and spin before asking others to drop their prejudice. Evolutionist is loaded term being used by creationists for propaganda. 99.999% of the biologists and scientists accept evolution, there is no need to coin a term called Evolutionist. Call them simply biologists or scientists. Second they don’t believe it happened by random changes. The real Natural Selection, Sexual selection and genetic drift are the main causes for speciation and evolution, not random changes.

  20. #20 Blind Squirrel FCD
    December 16, 2008

    #10,12,&14 You are quite correct to object to the unfair comparison between alcoholics and crackheads and creationists. Alcoholics and crackheads do not need to deny anywhere near the amount of reality as a creationists does to maintain homeostasis.

  21. #21 AnthonyK
    December 16, 2008

    Strange indeed. Convergent evolution – look this up – is fascinating, and this is a great example of it. The difference between this and Larakism is that Lamark proposed, effectively, that traits acquired, or learned, during the lifetime of an organism could be coded in its DNA and then passed on to its offspring. It is, in many ways, a tempting hypothesis – but is alas, wrong (even though Darwin thought that it contributed to evolution).
    Convergent evolution, on the other hand, is the surprising observation that different animals in the same sort of envioronment can share many characteristics – especially appearance and behaviour – but that these arise from the genome and are only passed on through natural selection. See, for example, the overlap between marsupials (in Australia and New Zealand) and placental mammals elsewhere.
    I think that this is a particularly beautiful, and poignant example of many things, not least of which is the exquisite way natural selection and genetic drift produce the glory of nature.

  22. #22 Sheri Williamson
    December 16, 2008

    AnthonyK @ #21: You might say that Lamarck has been partially vindicated by the discovery of transgenerational epigenetic inheritance.

  23. #23 AnthonyK
    December 16, 2008

    Do you know, that was on the tip of my tongue…

  24. #24 vince
    December 16, 2008

    “Programmers reuse good code. I see no reason to believe the God has to create everything from scratch”

    if you study genetics, you see a lot of reused stuff. A lot of single celled organisms still use similar biochemical pathways to humans

  25. #25 Herbys
    December 16, 2008

    @#12:
    Science, by definition, never settles something as absolute truth, and you are right in that science is always changing.
    But this change is CONVERGENT. New theories very, very rarely change significantly what has been “known” in the past. New discoveries often refine, or slightly alter what has been “known”. Newtonian laws didn’t got invalidated by Relativity. Relativity just added more precision in areas that were well beyond testing and understanding when Newton discovered the former laws. And you should be able to recognize that when Relativity was proposed, it was done in opposition to current observation: it predicted things that countered common sense, but made predictions that could be verified many years later.
    It is likely that evolution will be refined in many years. But the chances of us some day finding that the earth was created five thousand years ago, that species do not evolve, that there’s no natural selection and that all beings have been “designed” as they are, are dim, and there’s not a single precedent in science having ever been that wrong.
    And no, scientists didn’t think the earth was flat before Columbus, those were clergymen, scientists knew since the times of ancient Greece that the earth was round, and even knew its diameter. So don’t come with that as a counterpoint as you were about to do.

  26. #26 Keep your pants on
    December 16, 2008

    Are there branch lengths for the red clade of interest? If the base is long one could easily envision this result as long branch artifact. Note carefully that 1) these are Bayesian support values (notorious for perhaps being exaggerated) and 2) that the backbone nodes are *very* weakly supported, with only one node between the two clades really well supported (92). Results like this are flashy, but one can relatively easily envision them being overturned with new and more extensive data. While it looks like this particular result will probably hold results of this type are *not* the be-all and end-all.

  27. #27 Christopher Taylor
    December 17, 2008

    Nice. I thought this was worth adding my own take on it.

    #26 – True, a lot of the higher clades aren’t strongly supported, but that uniting Moho and Chaetoptila specifically with bombycillids is. The overall tree is similar to that found in other studies such as Barker et al. (2004) (except for some of the relationships within Passerida), and while I can’t recall the details off the top of my head, I believe there’s also some indel characters that support Passerida, though I don’t know if those would be testable for mohoids in particular.

    I expect that the inclusion of ancient DNA will almost inevitably tend to pull down support in a tree – ancient DNA is (unsurprisingly) generally fragmented and not available in the same quantities as that taken from live specimens.

  28. #28 Bob O'H
    December 17, 2008

    Crackpot Christian @13 –

    Not sure it proves evolution though, a bird is still a bird, changes in a species and natural selection fit our model too.

    Eh? This work is about change between species – processes of speciation and adaptation, how one group of species can evolve to be similar to another.

    Now, you could claim that this is change within a baramin, but would you really claim that fairy wrens and nuthatches are in the same baramin (look at Fig. 3b)? It’s difficult to see how a design model would explain this.

  29. #29 Corey Barcus
    December 17, 2008

    Readers might like to know that a major geologic event was taking place in North America at this time 14-17 mya; the formation of a large igneous province in Washington and Oregon. Furthermore, it is quite possible that an impact initiated these events as well as formed the Yellowstone hotspot (which created the Snake River Plain).

    http://en.wikipedia.org/wiki/Columbia_River_Basalt_Group

  30. #30 BioinfoTools
    December 17, 2008

    21 writes: “See, for example, the overlap between marsupials (in Australia and New Zealand)”

    There are no (present-day) marsupials native to New Zealand. There are in Australia and Indonesia. Furthermore, the only land mammals native to New Zealand are bats. (There is apparently some argument as to if there were mammals in past, as shown by the fossil record, but this is getting away from what I know well.)

    I would add that it may help to remember that different alterations of the regulatory regions of genes can achieve similar outcomes, and in this way similar “forms” can arise from independent genetic alterations (not just the recurrence of the identical genetic alterations). Just because the “body forms” are related does not mean that the underlying genetic changes encoding the related forms are the same.

  31. #31 BioinfoTools
    December 17, 2008

    I should add that my last paragraph in post 30 was a general comment about convergence, not about the particular data used in this study.

  32. #32 Tom Hammer
    December 17, 2008

    Tolerance and creationism?

    Now that’s some comedy right there.

  33. #33 Tony Hammer
    December 17, 2008

    Tolerance and creationism?

    Now that’s some comedy right there.

    And science doesn’t run on tolerance. It runs on data. Creationists ain’t got none.

  34. #34 Bob
    December 17, 2008

    You are so right. There is no need to insult creationists. Once you refer to them as creationists – they have already been insulted as much as is possible. You could call them moronic creationists, but that would be oxymoronic!

  35. #35 AnthonyK
    December 17, 2008

    #30 – I stand corrected, but I’ve also learned something. Making mistakes where science is concerned can often be far more instructive than getting it right.

  36. #36 David Marjanovi?
    December 17, 2008

    I actually wonder how similar mohos and honeyeaters really are, especially under the skin. Now that people are aware that mohos aren’t honeyeaters, maybe they’ll find some anatomical differences. Are any skeletons of mohos preserved?

    Thus, even before it was named, the newly christened Mohoidae became the only bird family to become extinct in the last hundred years.

    Don’t ascribe so much significance to that word. “Family” is not defined; anything is a family when I say it is a family. If I want to turn Mohoidae into a subfamily of waxwings, or alternatively into a superfamily with separate families for Moho and Chaetoptila, nobody can stop me — even though, in turn, nobody is forced to accept my change. If you don’t believe me, read the International Code of Zoological Nomenclature.

    ————————————————–

    Programmers reuse good code. I see no reason to believe the God has to create everything from scratch. I am often amused that so many people from the scientific world think that God cannot reuse code. If I were a God, and I were to create a world, I would build up the world by establishing what is needed, then building upon it by process of slow evolution.

    But why, then, are the similarities between all species arranged in a tree-shape? Why are there intermediates between humans and monkeys, but none between humans and bees or humans and strawberries? Why are there intermediates between whales and hippos but not whales and whale sharks?

    This is something we wouldn’t expect from an intelligent designer, but it is exactly what we’d expect from evolution from a single common ancestor.

    The same, incidentally, holds for stupid design. Whose bright idea was it to use DNA as the material of heredity — in all known life without exception, mind you –, when DNA falls apart when stored in water? We spend lots of energy to constantly repair it. It doesn’t have to be that way, see here for example. The simplest hypothesis is that it wasn’t an idea in the first place; it was just the most easily attainable solution, so it evolved first, and now we’re stuck with it.

    Scientists can learn a lot from scripture, if you do not take the creation as literally seven days instead of creation periods, then I think you will find that scientists are actually verifying the bible.

    So you don’t even know that the first whales appeared 100 million years after the first birds, which appeared around 200 million years after the first terrestrial animals, which in turn appeared several tens of millions of years after the first “fishes” even under the most restrictive definition of “fish”? This directly contradicts Genesis 1:20-25, which has fish, whales and birds being created on the 5th day and land animals on the 6th.

    And I haven’t even mentioned the contradictions between Gen 1:1-2:3 on the one hand and Gen 2:4b onwards on the other…

    You have a lot to learn.

  37. #37 David Marjanovi?
    December 17, 2008

    Actually, Gen 1:20-22 doesn’t mention “fish” at all, it mentions “great whales” and otherwise it just talks vaguely about creatures that move, live, and are brought forth by the waters. If that means all aquatic animals, let alone all aquatic living beings, are supposed to have been created at the same time, then that’s even worse than explained in my previous comment!

    But then, what do we expect of a slight adaptation of this here.

  38. #38 Lisa
    December 17, 2008

    I’d love to see a post that explains in more detail how these types of analysis are done. As a non-scientist, I can get the basics from the chart, but how do they calculate those values? What exactly IS a Bayesian consensus tree and why is it reliable? What are “Bayesian posterior probabilities” and “ML bootstrap values”? Can these questions even be answered in a simple way?

  39. #39 AnthonyK
    December 17, 2008

    Dear Lisa, I’m not a scientist either (well a chemistry degree 30 years ago doesn’t really count) so I can’t explain these terms. The problem is, as with so much of science, that they are complicated, and that to understand them would probably take hours and involve a lot of introductory stuff on cladistics and taxonomy. Bayesian inference is a measure of probability (see wikipedia) but even that explanation is too complicated for me to get more than a general gist of it.
    Can anyone put it in a single paragraph?

  40. #40 Bob O'H
    December 17, 2008

    Lisa – AnthonyK is right, it is messy and complicated. So, I hope I’ll at least get points for trying…

    The trees have been fitted to the data – in essence, there is a model for how the sequences evolve on a tree, and a model for how the trees evolve. These both contain a bunch of parameters (e.g. controlling the mutation rate, and the rate of branching). Fitting the models means estimating these parameters, as well as the likely trees. There are two ways of doing it that were used here: Maximum Likelihood (ML), and Bayesian.

    The Maximum Likelihood method maximizes the likelihood, i.e. it finds the parameters (and the tree) that are most likely to have given the data. The Bayesian method also uses the likelihood, but in a rather different way, one which gives a “posterior distribution” of the parameters and the tree, i.e. a probability for each tree and for the parameters (there is a cost of this, and there have been huge debates about the details). So both can produce a most likely tree, for slightly different meanings of “most likely”. This is the consensus tree.

    Of course, we don’t know how reliable the tree is: it could be that the data only support one tree, or it could be that there are lots of very different trees that are almost as likely. So we want some way of assigning support to the tree, or to different branches of the tree (often the most likely trees will be almost the same, with only one or two branches different). So, we can apply a measure to each branch of the tree, and ask how often that branch appears in all the likely trees. The Bayesian method produces these measures anyway: these are the Bayesian posterior probabilities. The ML method uses a very different approach, called bootstrapping, which relies on re-sampling the data lots of times and fitting a new trees to each re-sampled data set. The “ML bootstrap values” are the proportion of times that that particular branch appears in the tree.

    Basically, both the posterior probabilities and bootstrap values show how reliable that branch is, but they differ in the details. A larger value is better.

  41. #41 random programmer
    December 17, 2008

    “Programmers reuse good code. I see no reason to believe the God has to create everything from scratch”

    If God is a programmer, he deserves to be fired.

    You could try to explain away DNA evidence by saying God reused code. But if so, why did he forget what he’s already done and start from scratch in cases like this (convergent evolution)?

    Not to mention all the junk in DNA. Duplicated code (God’s a cut-n-paste monkey?), code that doesn’t actually do anything, dead code everywhere, no comments, code that was just slapped from random viruses, etc. I’d hate to have to maintain that mess. Maybe God outsourced the project to Brahma?

  42. #42 Don Codling
    December 17, 2008

    Ravilyn Sanders said in #19
    “Don, you should first drop your prejudice and spin before asking others to drop their prejudice.”

    For a start, I didn’t ask anybody to drop their prejudice. I asked someone to show me logically how the research on honey eaters supports either creation or evolution. Further, his statement re: randomness parses to “They don’t believe it happens by random changes; random changes are the main cause …” i.e., it is self contradictory. From Wikapedia: “In population genetics, genetic drift is the accumulation of random events that change the makeup of a gene pool slightly”. Note the word “random” in the middle.

    I’m still looking for a logical explanation of how this research points either to evolution or creation.

  43. #43 AnthonyK
    December 17, 2008

    The research on honeyeaters supports convergent evolution. This comes, and is part of, the “tree of life” and common descent. It’s as simple as that. No support for creationism at all – but then, there is none.
    There is a random component to evolution, but evolution is not based on random chance. Pick a good biology book. There are plenty of them around. These will provide the other evidence for evolution, which is overwhelming. But then you aren’t after evidence, are you?

  44. #44 DeafScientist
    December 17, 2008

    By their nature, phylogenetic trees are evidence for evolution because they show that divergence from common descent is consistent with the observed changes.

    Another recently reported example of convergent evolution in the same region of the world is the wonderfully named Lord Howe Island Tree Lobster: http://www.abc.net.au/science/articles/2008/12/17/2447999.htm?site=science&topic=latest http://membracid.wordpress.com/2008/12/17/tree-lobsters/

  45. #45 Don Codling
    December 18, 2008

    Affirming that the research on Honey Eaters supports evolution versus creation does not make it so. What I read is compatible with the views both of evolutionists & creationists. It does not particularly affirm either, that I can see. Yet a variety of people commenting insist that this proves the evolutionary theory (or at least some part of it), & disproves creation. So I asked someone, anyone, to explain logically how it does that. The response was a fair bit of abuse & a flat affirmation that it’s so. It sounds to me like a classic blind faith statement, the kind that holds to its position without concern for evidence one way or another.

    For the record, I have read a fair number of books by evolutionists & creationists. I grew up accepting evolution as the way God put the living world together. I studied Math & Physics in university, there learning formal logical thinking & the scientific method. Later, I was treated to a lecture on why Christians had to accept the “fact” of evolution. As a scientist, red lights began flashing when a scientific theory, however widely accepted, was called a fact. The science I was offered in support of this view was so rotten that I was moved to re-examine what I had always accepted. I became a skeptic regarding evolution because the evidence appears to be full of contradictions to the theory, is arguably based at critical points on circular reasoning, & is blatantly contrary to at least one fundamental biological law, Pasteur’s theory of biogenesis.

    I’m open to evidence, but not to blind affirmations & abusive language. Personally, my view is that abusive language is a cover for inability to support one’s view.

    If you want to talk reading, which is off the topic of my request for a logical explanation of how this particular research is anti-Creationist, I’d suggest two books as required reading if you are going to discuss this scientifically & reasonably.

    The first is G.A. Kerkut’s monograph, “Implications of evolution”. Kerkut writes as a zoologist (I think that was his field) who accepted the theory of evolution, but was frustrated with students who accepted it by blind faith (my words), who were totally unaware of the problems the theory had to face, & the serious arguments against it. He had to rub their noses in the fact that as a scientific theory, it had issues, & to be scientific you need to deal with those issues. The first two & last two chapters are readily accessible to the non-specialist. I at least found it heavy going when he got into the minute zoological details in the rest of the monograph.

    The second is Michael Behe’s “Darwin’s black box”. Behe is a microbiologist, who argues that modern understanding of the intricacies of cellular activity preclude anything but design for the origins of the cell. The cell had to come together in one package, because if it had developed by small changes, it would have self-destructed many times along the way.

    But I’m not asking you, at this point, to challenge the roots of your faith. I’m simply asking you to show logically how this particular research argues for evolution versus creation. A lot of you insist that’s the case. If you’re right, you should be able to show it. If you can’t show it using good logic, you are operating on blind faith in that affirmation.

  46. #46 Lisa
    December 19, 2008

    Thanks, Bob and Anthony. That makes it at least a little clearer. I guess for the rest I’ll have to read up on Taxonomic Methodology… or just accept that “MATH” is the answer! :)

  47. #47 DeafScientist
    December 19, 2008

    Lisa,

    Look for ‘phylogeny’ or ‘phylogenetics’, searching for ‘taxonmy’ will give you a lot about naming things! Some introductory books on evolution might have a chapter on it too.

  48. #48 DeafScientist
    December 19, 2008

    Opps. ‘taxonomy’, not ‘taxonmy’: left out an ‘o’, sorry.

  49. #49 DeafScientist
    December 19, 2008

    Don:

    The book you are referring to was published in 1960. It predates molecular phylogenetics (what is used to make the evolutionary trees in article above), never mind molecular biology and modern genetics. For example, the early methods for “rapid” (for their day) DNA sequencing were not developed until the 1970s.

    To cut a very long story short, try read more modern works by people that support evolution. You can’t expect to get an understanding of the current support for evolution by reading dated works or works by people like Behe who want to dismiss evolution by what means that they can. (In particular, a common problem with the arguments put forward by creationists attacking evolution is that they skip over what doesn’t suit them or re-phrase things out of their original meaning. The up-shot is that a reader cannot get any real understanding of evolution from them: too much is missing. You need to read those supporting evolution in their own words.)

    If you understand mathematics, you should understand my earlier point (see post 44). If you don’t, there are plenty of texts covering this for those will a formal training in mathematics. Lisa is setting a good example, by the way ;-)

    All, Lisa especially:

    I was being very harsh on taxonomists! That’s what I get for writing in a hurry before taking a holiday… naughty of me… Modern taxonomy involves a lot of phylogenetics, not just “naming things”. The thing that I meant was that for an internet search, I suspected that the words ‘phylogenetics’, etc., would be more likely to find what you want than ‘taxonomy’.

    I’d help with a search myself, or a brief explanation, but I’m short of time. But here’s a rushed shot at it. In broad essence, phylogenetics first takes some features that are chosen to represent the “nature” (characteristics) of the species. These need to be carefully chosen. In the case of using DNA sequences, these are the base sequence of the DNA sequences. It then asks the question “are the observed characteristics consistent with a tree representing descent from a common ancestor?” (Or not.) There are many different mathematical methods used (people compete to try do better!), but broadly speaking they all compare the chosen characteristics of each species with every other species, and from these comparisons attempt to construct a tree relating the species by descent. Note this is not always going to work: if the characteristics aren’t consistent with evolution by common descent, you won’t be able to build a reliable tree. Alternatively, if a reliable tree can be constructed it is consistent with evolution by descent (and hence evidence for evolution by common descent). The “reliability” of the tree is important, especially as these methods are essentially statistical: they give the likelihood that particular tree shown could be true given the input data. A general approach is to test the “robustness” of the tree. A tree is robust if slight changes to the input data would not alter the tree (much). We could, for example, run the computation of the trees many times, each time slightly altering the input data and compare the trees that result (this is roughly the bootstrapping process Bob refers to). Branches of the tree that are usually or always present would be considered reliable; branches that differ between the different trees too often would be considered unreliable. The numbers next to the branches indicate how reliable they are. I think I’d better stop prattling on! :-) Excuse me if I’m repeating Bob, but I know from my own experience that hearing the same message in others’ words can sometimes help.

    It may be worth looking at this book: http://en.wikipedia.org/wiki/The_Ancestor's_Tale I’ve never read it, but it might be worth checking out. I doubt it explains phylogenetics itself, but it may give an impression of the larger picture.

  50. #50 AnthonyK
    December 19, 2008

    Don, your doubts about evolution are not shared by those who know about it in detail. It is possible, I suppose that virtually 100% of biologists wordwide (heck, virtually 100% of all scientists wordwide) are wrong, and the religious people are all right, but this is not likely. However, science is highly competitive, and even one scientist with the correct idea could change our perception of the natural world by using the scientific method to make a prediction which would be true is evolution was wholly or partly false. Such a scientist would expect to receive a Nobel prize for his or her work – the greatest reward any scientist could receive for a life’s endeavour.
    However, such an explanation would have to explain the appearance of, say, common descent, while proposing a new idea/mechanism which superceded it. There is, as we speak, no such hypothesis.
    Common descent would be easy to falsify in principle. All that is needed would be to find an organism showing a DNA sequence which could not be explained by the tree of life model. An example would be a coding sequence which we shared with, say, elephants, which we did not share with chimpanzees. This would seriously weaken the whole idea of evolution as we understand it, if not destroy the idea completely. No such sequence has been discovered despite the most detailed possible scrutiny.
    You may respond that any such discovery would be covered up, but that would be to deeply misunderstand the actual process of scientific enquiry, and the motivations of scientists themselves.
    The position of religious deniers of evolution is different. With such people (and you are apparently not one of them, from your post) the position is quite simple – they do not believe in evolution because the real and imagined consequences of it being true are unacceptable – we’re not monkeys, random changes, in God’s image, morality, bible, atheist conspiracy etc. They do not believe in evolution because they don’t believe in it, in other words.
    Deafscientist and I (and of course Grrlscientist!) have tried to show you how the poor, doomed, Hawiaan honeyeater is an example of just the kind of nested phylogenetic tree which is a consequence of common descent, but you can’t accept this. So what can you do? May I suggest that you try to pursue research of your own (warning – science is difficult, see the discussion of Bayesian inference above!).
    Dawkins “An ancestor’s tale” is good.
    But further beware – evolution denial is now fully a part of Christian apologetics (this includes Behe’s book) and the anti-evolution stuff is full of nonsense, incomprehension, and downright lies by people who want to twist the truth to their own religious agenda.
    For the many scientists who do have faith, evolution, in all its glory and wonder, is evidence for God’s creation, and especially for His ability to inspire human curiosity and knowledge.
    Why not go to your nearest university, seek out the faculty of biology, and ask someone to explain it all to you. No doubt a volunteer will gladly appear.
    But once again beware, because the experience of talking about evolution with religious skeptics is often not a happy one – most people with these views (and you say you are not one of them) have been taught to be closed minded, and most enquiries are nothing more than proselytizing a supremely ignorant attitude. Creationists routinely profess an attitude of seeking after truth, whereas their real motivations are promoting their own worldview.
    I hope this has been helpful, but it will only be so if you are prepared to ask yourself the question did all life on this planet develop by means of evolution (NB evolution is not about how life arose in the first place, merely how it developed once present) and what evidence do scientists have to support it? Why, if ther really is some flaw in it, is it effectively universally accepted amongst experts?
    Your query will only be successfully answered if you are prepared to accept the possibility that the answer, so far as we know it, is, without doubt, yes.

  51. #51 Bob O'H
    December 19, 2008

    Lisa (and anyone else) –
    John Wilkins curates a list of blog posts he calls “Basic Concepts in Science“, which might be of interest. I couldn’t see anything answering exactly what you were asking, but there’s still plenty of interesting stuff there.

    DeafScientist – thanks for adding your explanation. It covered the bits I didn’t very nicely.

  52. #52 Codling
    December 19, 2008

    I have apparently misled you, DeafScientist. I did not recommend Kerkut as an example of an argument for evolution. In fact, if I remember correctly (it’s been 30 years), he did not present an argument for evolution, but just discussed some of its implications in his field. I cited the book because he took advantage of his writing for a polite “rant” about students & scientists who accept the theory blindly, ignoring or simply writing off those who challenge it (& I agree whole heartedly that there are a lot of challengers who should be written off, & likely ignored). I cited his book because he is (or was) an evolutionist who challenged other evolutionists against the kind of off handed dismissal of opposition that is all too evident in this thread. There is nothing of science in that – just blind faith. It’s just as much a religion as the Christianity that many of them are rejecting.

    You wrote, “In particular, a common problem with the arguments put forward by creationists attacking evolution is that they skip over what doesn’t suit them”. I agree, in general. Unfortunately, I also find the same true of evolutionists. Both groups are better at poking holes in the other’s theories than in answering the challenges to their own.

    Have you read “Darwin’s black box”? If you have, I’d like to know where you find fault in his argument. If you haven’t, your dismissal of him is based on ignorance, isn’t it? My reading of it did not reveal a person who wants “to dismiss evolution by what means that they can”. Rather he presented a narrow, clearly expressed, technically supported argument that processes in cells are so “irreducibly complex” that they could not develop gradually. Therefore, he concluded, there must be a designer. He did not deal with the theory of evolution directly. He did not claim it all had to have been put together on day 1. Have you read it? If you have not, please do, before you criticize him. If you have, please substantiate your criticism by showing the errors you perceive in it.

    To pick up your earlier post, while I understand mathematics, I don’t understand why “phylogenetic trees are evidence for evolution because they show that divergence from common descent is consistent with the observed changes.” Can you be more explicit? In my understanding, they are simply our best theory about the way various creatures are related. They do not prove that relationship, but express it as best we can work it out. Because DNA is more fundamental than shape or colour, the tree is being revised on the basis of DNA evidence. But that says little or nothing about the theory of evolution. It just redirects our understanding of how things may have evolved.

  53. #53 AnthonyK
    December 19, 2008

    Yawn. Same dumn arguments, same fake questions, ignoring any answers. Just as well gravitation, like evolution, doesn’t depend on your “understanding” of it, Mr Codling, or you would long ago have floated off into space.

  54. #54 Don Codling
    December 19, 2008

    Thank you for a polite & thoughtful response, AnthonyK. Regrettably, my perceptions are somewhat different than yours.

    In the first place, after 12 years of formal university education, I automatically doubt any argument that begins: “Scholars agree”, or anything like it. Let me share Codling’s basic principle of academia: Scholars disagree. You repeatedly referred to the idea that virtually 100% of experts support the theory of evolution. I would doubt that claim in principle, until it was thoroughly demonstrated. In this case, I deny it, based on my own experience.

    A few years ago I read an excellent historical study of this controversy. Unfortunately, I did not get it into my database, & I remember neither author nor title. The author supported an evolutionary view, but made a real effort to deal with the controversy in an even-handed way. Needless to state, he devoted a fair section to Stephen Gould. In doing that he commented on Gould’s perplexity with one of his best students, who did not accept the theory of evolution. Gould did not consider him ignorant, or inexpert, but they disagreed on that point.

    There are a host of scientists who have studied & rejected the theory of evolution. Unfortunately, the spokesmen for the majority usually deny that their opponents are real scientists, because “after all, real scientists accept evolution”. It is easy to get 100% if you exclude from your group anyone who disagrees. But it’s a meaningless 100%.

    You wrote regarding possible evidence discrediting evolutionary theory: “You may respond that any such discovery would be covered up, but that would be to deeply misunderstand the actual process of scientific enquiry, and the motivations of scientists themselves.” Actually, I don’t respond that such a discovery would be covered up, usually. Instead, it would be written off as insignificant. An example is in the article, “Amino acid compositions of Lamprey fibrinogen” Biochimica et biophysica acta, #453:2 (December 22, 1976), Pages 439-452. The authors presented their test, that the theory of evolution predicts that Lamprey Eel blood structures should be primitive compared to human structures, because Lampreys are evolutionary primitives. Their tests showed the contrary. Did it discredit their evolutionary theory? Not in the least. Just an anomaly.

    You wrote of religious deniers of evolution: “they do not believe in evolution because the real and imagined consequences of it being true are unacceptable”. You are right about many. Unfortunately, my discussions with & reading of most who are not theistic evolutionists leads to a similar conclusion. They believe in evolution because the real & imagined consequences of it not being true are unacceptable. In other words, it has become their religion, & they cannot allow even a question to be raised against it. Therefore they insist that any challenge is not on the basis of science, but of religion.

    I’m willing to consider seriously the possibility that life developed by something we could describe as an evolutionary process. I believed that once; I could again. (Presently I’m not prepared to affirm any process as well supported.) But I’m looking for evidence, not faith assertions. Changing the place of Hawaiian Honey-Eaters in the accepted phylogenetic tree is not evidence of evolution, but merely a shift in our understanding of what they are related to. Perhaps I should note that a phylogenetic tree can just as readily be a description of the results of the most radical 6-day creation as of evolution. It’s an organizational chart of things that show similarities. Every Christian creationist believes that God is inherently orderly, after all. It was that understanding that led to the development of modern science on Christian territory.

    So I come back from this excursus to my original question. You seem to believe that this discovery supports evolution & opposes creation. Please show that logically. So far all I have received is affirmations that it is the case.

  55. #55 Speare
    December 19, 2008

    May I just say how very disappointed I am that the first rude and insulting comment in this column, and virtually all the rude and insulting ones after it, came from scientists or others supporting evolution, while virtually all of the creation supporters contributing to the discussion maintained at least some veneer of courtesy and rational discussion?

    While I share the general impatience with fundamentalist creationism, you all are really setting a very poor example of rational discussion with the gratuitous insults.

  56. #56 AnthonyK
    December 19, 2008

    Well creationism (the bits that deny evolution – no one can prove or disprove a creator) is dangerous to the public acceptance and understanding of science. Most of these forums get infested with internet trolls (not that Mr Codling necessarily is one) who ask the same question over and over, and then use the post as an excuse to put forward ignorant, and increasingly religious views.
    I noted at the top of the post that I couldn’t see how creationists could deny this beautiful piece of evidence, and I now know, sort of. What pisses me off is that when I ask someone about a subject that I don’t understand, I don’t quarrel with their opinion; commentators on evolution show no such scruples.
    And then, (which is why, mildly satisfied with the interchanges I’ve had I’ll now leave) you get the cruncher:
    Science (evolution) = religion.
    No, simply wrong,
    Or are prayers so improved over the last 1000 years that they can make magic pictures on a box in your room by faith alone?
    Bye now, and be good:)

  57. #57 DeafScientist
    December 19, 2008

    Don: I’m not going to continue this as your unconstructive approach “demanding” that others “explain for you”, asking that others to do what you won’t yourself, etc., etc., is all too familiar for me to waste my holiday time on. I’ve already given you a direction that would help you understand, it’s over to you to take it.

    (I’m still happy to help people like Lisa who are prepared to make an effort.)

    But, a few very quick points:

    (1) Just to remind you: the label “evolutionist” is framing device to create to create a group that doesn’t really exist (see post 19). (2) Your extended reference to “poking holes” is places a meaning on my words that I didn’t write: I wrote about creation “scientists” avoiding or misrepresenting evidence that doesn’t suit them and that it follows from that, that you need read the original works in order to get an (honest) understanding of evolution. (3) Creationism and ID don’t have a theory. At best they have an unsubstantiated hypothesis.

    “To pick up your earlier post …”, “Can you be more explicit?”, etc. The textbooks I referred to are there for a reason: for people who want to learn to use them. Nothing is stopping you making a little effort yourself ;-)

    Speare: smearing people with a broad brush isn’t constructive. Some might even see you as doing the thing you object to ;-) Just food for thought.

  58. #58 Bob O'H
    December 20, 2008

    You repeatedly referred to the idea that virtually 100% of experts support the theory of evolution. I would doubt that claim in principle, until it was thoroughly demonstrated.

    Have a look at the Disco Institute’s Descent from Darwin list. It has about 600 signatories. Then check to see how many are biologists – only a minority (about 170, depending on how you cut the cake. I’ve excluded medicine). Just to give you some idea, the last ESEB (European Society for Evolutionary Biology) meeting had over 1000 attendees, mostly from Europe. I gather the US version is even bigger. Of course, only a small minority of biologists go to these meeting. So if the DI can only manage a couple of hundred biologists, it really is a small minority.

    The authors presented their test, that the theory of evolution predicts that Lamprey Eel blood structures should be primitive compared to human structures, because Lampreys are evolutionary primitives. Their tests showed the contrary. Did it discredit their evolutionary theory? Not in the least. Just an anomaly.

    Not even that. Their argument (at least from the abstract) is wrong. Humans and lamprey lineages separated a long time ago. In that time, there ave been plenty of opportunities for evolution to occur in both lineages, so the notion that lamprey have to be more primitive is nonsense.

    Perhaps I should note that a phylogenetic tree can just as readily be a description of the results of the most radical 6-day creation as of evolution. It’s an organizational chart of things that show similarities. Every Christian creationist believes that God is inherently orderly, after all.

    So what’s with the fossils? Was God just messing around with the pleistocene?

    Changing the place of Hawaiian Honey-Eaters in the accepted phylogenetic tree is not evidence of evolution, but merely a shift in our understanding of what they are related to.

    No, it is evidence.

    What? You want more?

    The old idea was that there was one group of honeyeaters. Hence, we would expect them to group together in a phylogenetic tree. But we don’t see that. Instead, we see two distinct groups, and the two groups split according to where they live. Now, this makes sense from an evolutionary point of view: in both lineages the groups adapted to the honeyeater way of life, and then speciated. It’s fascinating that they are so similar, but if we look closer, we see that they are distinct at the DNA level: something that fits the evolutionary story, and supports it quite nicely.

    We can even be predictive: I predict there will be differences in the way the adaptations came about: different genes might be involved, or the same gene but with different mutations. This would fit an evolutionary explanation, because mutations are random and there is more than one route to the same set of adaptations, it’s unlikely that different lineages will take the same route.

    The data are also difficult to explain under a special creation model: why would the two groups separate so nicely geographically, if they didn’t each derive from a common ancestor? Why would a designer build them that way, if they are doing the same job in each location? I can’t see any other explanation than history for the DNA data. Do you have a better one (other than a simple “God wanted it this way” – that’s really no explanation at all)?

  59. #59 DeafScientist
    December 20, 2008

    Two points in the interest of clarity:

    1. My last post (post 57) was written in response to post 52, not post 54, which I had not seen at the time of writing.

    2. Don writes in post 54: It’s an organizational chart of things that show similarities. This is incorrect, mathematically incorrect at that.

    Phylogenetic trees do not represent similarities as Don suggests, they represent related ancestry. Phylogenetic methods attempt to construct the best tree representing descent from a common ancestor for the data. It is modelling an ancestry (evolutionary) process, not clustering similarities. It may seem a subtle difference to those new to phylogeny, but it is important and confusing it similarity with ancestry shows a lack of understanding.

    As a simple example, it is possible for two species that are very similar when compared to one-on-one to end up in quite separate branches of the tree. This would not be the case for a method that only clustered similarities.

    A difference is that the phylogentic methods try to determine the most likely series of changes in the DNA sequences from an ancestral sequence that would explain the differences observed.

    I would add that while the conclusions drawn from the work refer to groups or clusters, the phylogenetics methods work on constructing ancestry trees, not clustering trees.

    PS: In my previous post, ‘is places’ should read ‘is placing’.

  60. #60 Codling
    December 20, 2008

    Well! At last! Someone who actually makes a reasonable attempt to answer the original simple question (and even some of the later questions). My thanks to Bob O’H (#58).

    That doesn’t mean I’m convinced, but it’s nice to see some rational argument that I can consider and interact with.

    Regarding the minority status of creationist scientists, I am not denying they are a small minority – but the descriptions I reacted to were claims that 99.9% of biologists are not creationists. That small minority is a persecuted minority. In our enlightened, freedom loving culture, with its strong emphasis on academic freedom, a highly knowledgeable and skilled teacher in biological science can lose his or her job if it becomes known that he or she is creationist. Surprise. Many of them hide their light.

    Re: the Biophysica etc article, I have no argument with your declaration that their premise was in error. But please remember I did not cite this as evidence of the failure of the theory of evolution, but as evidence of the attitude of evolutionists (at least some of them), which is to claim that any flaw that appears is insignificant to the theory.

    The six day creationists have their own interpretations of the fossil records. Since, contrary to DeafScientist, the phylogenetic tree is based on what are considered to be the most significant similarities (though it is certainly intended by evolutionists to represent descent) the fossils do not take away the reality that six day creationists can see that tree as a description of the results of God’s creation according to their views.

    That the discovery regarding the Honey Eaters made sense from an evolutionary point of view, I already knew. That is not intended as a complaint against your explanation, by the way; I appreciated that. But the key paragraph for me was the last paragraph, your explanation why you see it going against a creationist view. Am I correct in summing it up by saying that your fundamental question against special creation is “Why?” Why would God do it this way?

    If I have that right, it goes a long way to explain the difference between our outlooks, because my fundamental question is “How?” How could the things we observe come about? I think the “Why?” question takes us out of the realms of science. But that’s another discussion. Thanks for answering my question. It gives me something to think about, to chew over.

  61. #61 Bob O'H
    December 20, 2008

    But please remember I did not cite this as evidence of the failure of the theory of evolution, but as evidence of the attitude of evolutionists (at least some of them), which is to claim that any flaw that appears is insignificant to the theory.

    I hope you’re now aware that it simply doesn’t show a flaw in the theory, just in the understanding of it by the authors.

    Am I correct in summing it up by saying that your fundamental question against special creation is “Why?” Why would God do it this way?

    More or less, yes. As a scientist, this is what I’m interested in – why is the natural world the way it is? If creationism isn’t going to give me an answer, then I’ll prefer to use an approach that does give me answers. I want to understand the natural world, and I don’t find “goddidit” very useful.

    The point is that the honeyeater data are perfectly explicable by evolutionary theory, but seem a puzzle for a creationist account of nature. If creationism can’t explain the data, then it isn’t good for creationist theory: it simply isn’t explaining the natural world.

  62. #62 DeafScientist
    December 20, 2008

    Don,

    I reacted to were claims that 99.9% of biologists are not creationists. That small minority is a persecuted minority. There is a logical leap, the second point does not follow from the first. Just because someone is in a minority does not automatically mean that they are persecuted. I am not going to respond further as I’ve seen this red herring played before (troll bait, etc.) The first point is almost certainly correct as a simple fact, which I take that you have conceded.

    Since, contrary to DeafScientist, the phylogenetic tree is based on what are considered to be the most significant similarities (though it is certainly intended by evolutionists to represent descent)

    Contrary to you, I did not make this claim. Again you show you do not understand or, perhaps, that you intend to misrepresent the science or me. I did not say that phylogenetic trees are not based on similarities, I wrote that they do more than that.

    I feel I must now ask directly: please read a textbook on the subject to learn how these methods actually work before making further statements about them. It is quite clear you do not understand phylogenetics and continually misrepresent what these methods show. I would give you the benefit of the doubt and consider it ignorance, but it does look increasing like deliberate ignorance or intentional misrepresention. Again I will point out that, nothing is stopping you from learning it and presenting it correctly and honestly, but yourself.

    I note you continue using the term ‘evolutionist’ after you have been politely asked not to use it. It is tanamount to continue to use “black”, “coconut”, etc., after being asked not to.

    You seem to be asking people to present negative material against creationism. You should first present a positive statement of what creationism is, so that people might have something to address. At this point we don’t have anything to address, other than an assumed and rather vague “goddit”. (Vague as in over what time, how, etc.) As such there is no positive statement of what it is that people are supposed to address. Where is the positive argument that you want people to consider as an alternative?

    With that in mind, in terms of being against a creationist view: in convergent evolution similar phenotypes (“designs” to creationists) are descended from more than one independent event (the independent speciation events giving rise to the similar phenotypes); creationism as per the creation myth would have it derived from just one event (the “god did it” event).

    The different groups of similar organisms are very clearly originating from at least two independent events as the data shows, not one event as creationism would have it.

    Unless, of course, you want to wriggle around and re-define creationism to suit. But that brings us back to the need for you to define, positively, and precisely, what this alternative “creationism” actually is or people won’t really be able to help you.

  63. #63 Codling
    December 20, 2008

    To Bob O’H, #61
    I half expected your response, Bob. As I was driving home tonight, I realized I had been too general in my comment on “Why” questions. Not all of them are departures from science, as I suggested. Your response confirmed my thoughts. When the “Why” question asks, “What is the cause of this event?”, it is certainly scientific. When it asks, “What is the motivation of this action?” it usually departs from science. I’m probably still not specific enough, but I’m going to have to think it out much more carefully before I try to do better.

    Regarding the particular question you asked, you directed it to the ultimate cause, if I’m not mistaken. For me, at least, “a bunch of random changes happened to come up with this” is far less satisfying than “God arranged it so” as an ultimate cause.

    If your question is not directed at the ultimate cause, then most creationist scientists I have read or had contact with would be right there beside you trying to determine why, what factors led to this presumed development. Certainly none that I have read would have any problems with differences evolving within a bird family. In other words, I think you should be putting “God did it” over against “Chance did it”, instead of over against processes and causes which we can test and measure. Probably you won’t agree, but that’s OK.

  64. #64 DeafScientist
    December 20, 2008

    For me, at least, “a bunch of random changes happened to come up with this” is far less satisfying than “God arranged it so” as an ultimate cause.

    Whether any solution is personally more appealing to anyone (or not) is besides the point. What matters is that the solution provides the best understanding we have of the world around us, based on the available evidence. For you to suggest that this would even matter, suggests that for you “what you would like to be true” matters more to you than what happens to be supported by how things happens (that is, evidence).

    To me this cuts to the chase: you would like “G-d did it” to be true, regardless of what evidence might or might not say. But what you would like is besides the point.

    Alot of scientific solutions aren’t “naturally appealing” or “intuitive”. (As someone who claims to know physics, you should know this more than most.)

  65. #65 Don Codling
    December 20, 2008

    DeafScientist, please read what I say, not what you expect me to be saying.

    I did not conced that “99.9% of biologists are not creationists”. I agreed that creationist biologists are a minority. My statement “That small minority is a persecuted minority” does not contain a logical leap because it does not present a conclusion from logic. It is a statement of observed fact, a premise for the rest of the argument. I never suggested that a minority is automatically persecuted; I affirmed that this minority is persecuted.

    Regarding phylogenetic trees, you wrote “Don writes in post 54: It’s an organizational chart of things that show similarities. This is incorrect, mathematically incorrect at that.
    Phylogenetic trees do not represent similarities as Don suggests, they represent related ancestry. Phylogenetic methods attempt to construct the best tree representing descent from a common ancestor for the data. It is modelling an ancestry (evolutionary) process, not clustering similarities.” Now you claim, “I did not say that phylogenetic trees are not based on similarities, I wrote that they do more than that.” I think you are contradicting yourself, as well as totally misunderstanding me.

    DeafScientist wrote: “I note you continue using the term ‘evolutionist’ after you have been politely asked not to use it. It is tanamount to continue to use “black”, “coconut”, etc., after being asked not to.” If a white supremacist told me, “Call people like me human beings, but others should be called negroid, mongolian, etc” I’d ignore him. Why? He’s asking me to accept his twisted viewpoint by the language I use. You think I should not use evolutionist, but scientist. However, you do not hesitate to call those who disagree with your view creationists. In other words, you want to define the language in such a way that you are considered a scientist and your opponents are not. Dream on. If you want to give me words for both parties that are not loaded, biassed, I’ll gladly use them, but don’t try to define the debate in your favour.

    You asked for a definition of my view. You asked for it, I only entered this to raise one question which Bob O’H answered, after many others dodged it. As I assume you know, there are as many creationist views as there are evolutionary views. My view? I believe that God created life as well as all else. Every evidence we have speaks against spontaneous generation of life. Beyond that I’m a skeptic.

    I’m probably more open than I was 15 years ago to the idea that God shaped the life he created by an evolutionary process, but I find no compelling evidence that pushes me to accept any of the alternatives. I am very turned off by the fact that all parties tend to answer challenges that their theory does not seem to account for either by pointing to similar flaws in their opponent’s theory or by claiming that scientific “consensus” supports them or by denying the legitimacy of their opponent as a scientist. Regarding consensus, let me note that before Copernicus and Kepler and Galileo, the scientific consensus was absolute in favour of a Ptolomaic view of the universe, before Pasteur there was a consensus that flies formed out of dirt; until about 150 years ago there was a consensus that there was an aether filling the universe as a medium for propagation of electromagnetic radiation. Appeal to consensus is anti-scientific. Someone in this thread asked if I thought that all the scientists who believe in evolution could be wrong. My answer is “Yes”; emphatically yes. It has happened many times in the past. It can happen today. When people turn from science to polemics for their answers, I assume their theory is flawed. It may only be that they do not know how to defend it, but I stand in doubt until someone defends it with science, not polemics and sneers.

  66. #66 DeafScientist
    December 21, 2008

    I think you are contradicting yourself, as well as totally misunderstanding me. If you want to clarify your position you are welcome to, of course, but I am not contradicting myself. That you think that is the case actually makes it even clearer to me that you don’t understand. I am not playing games when I write that: if you don’t understand why it is not contradictory, then you don’t understand it at all. I went to some trouble to point out what you were missing, but it would seem that you either are not unable to understand that, or want to avoid or ignore it. I don’t know which, but I am not pointing out that you really need to do to make an effort to learn what these methods actually do before telling people “how things are” for no reason or for some petty attack. I’m pointing these out because you are getting it wrong. It should be no hair off your back to look for the texts I pointed you towards and at very least try verify your position. You will need to use the more formal texts, as “popular science” deals in metaphor and can sometimes be misleading.

    However, you do not hesitate to call those who disagree with your view creationists. Because that’s what creationists voluntarily choose to call themselves. Scientists who agree with evolution don’t call themselves “evolutionists”; that is a term made up by one “side” to use in framing the other. My point stands and your framing of me as a hypocrite, is hypocritical :-)

    (And, please don’t tell me you don’t have a sense of humour!)

    You asked for a definition of my view. You haven’t given any detail. I pointed out that without precision it’s not useful.

    not polemics and sneers If you think that you will either get a rise out of me or can smear me by misrepresenting what I write as polemics and smeers, you are mistaken. I may write to the point, but I am no polemic, nor do I “sneer”. In particular, I do not attack people. I do “attack” what they write if the argument is poor ;-)

  67. #67 Bob O'H
    December 21, 2008

    Don @63 – no, I’m not interesting in ultimate causes: they’re not amenable to empirical investigation, so I can’t see how to resolve any arguments. There are theologies that are compatible with evolution – Ken Miller is a strong advocate for them, for example.

    If your question is not directed at the ultimate cause, then most creationist scientists I have read or had contact with would be right there beside you trying to determine why, what factors led to this presumed development. Certainly none that I have read would have any problems with differences evolving within a bird family.

    You can’t have read widely – a lot of creationists will happily try to attack evidence for evolution within a species. Look at what they write about industrial melanism. If they were satisfied with it, why would they attack it? I’m thinking of people like Jonathan Wells, and a lot of the people at Uncommon Dissent.

  68. #68 DeafScientist
    December 21, 2008

    Don,

    Excuse me if my posts show a little of my frustration at having tried to politely and clearly explain things, only to have my efforts dismissed as “self-contradictory” by a “student” (yourself) who would on the face of it appear to be trying hard not to “get it”! With that in mind, I’m going to leave (I have to go anyway) but let me leave you with a few things to think about:

    but I stand in doubt until someone defends it with science

    While you can certainly remain in doubt, I’ve seen plenty of creationists play this card dishonestly so this statement immediately comes under suspicion, as it should (see below). When these people are presented with evidence, etc., they simply deny that the evidence is “good enough for them” so that they might carry on asserting that there is no evidence, etc. It makes their “demand” for evidence a sham and is, of course, not constructive.

    A way to show that you are not doing this, and to be constructive, would be to read the relevant theory from those proposing it (or at least a respected account by those supporting it) so that you understand it in sufficient detail to comment on it; then present a positively-worded objection, that is, present some line of reasoning that details your objections and back your line of reasoning with evidence, etc.

    If you have some genuine reason for doubting it, you should be able to detail it. If you can’t then people (including yourself) have every reason to point out that you don’t seem to have a “thing” that you’re objecting to.

    By arguing only “in the negative”, i.e. in the absence of presenting a position, let alone an understanding of what you criticise, you are not being constructive and you will likely fall foul of being accused of trying to make your alternative position credible by default. (Which is a fallacy: failing to “prove” evolution would not make creationism any stronger. Only positive evidence for creationism could do that.)

    While you can ask for others to help fill in the blanks for you, in the end it’s really for you to do yourself. Realistically, people can only offer pointers, especially given their limited time and limits blogs, etc., impose. I have done this despite being very busy with work and Xmas preparations, but have been met with you brushing what I have written aside for whatever reason. Naturally, I’m not terribly impressed. Science has many textbooks on every area you can imagine for the very reason of presenting the arguments to those want to learn the area covered in the particular book. There really is nothing stopping you from getting them and learning…

    I would add that to those working on evolution, it is no “evolution vs. creationism” debate, but simply the question “how do new species arise?” The “debate” is something created by creationists in order to create a “concern” over evolution that they can point at and claim, in circular fashion, that there is a debate! There isn’t a debate of this kind within scientific circles, and for good reasons, which you might learn if you took the trouble of reading the subject properly (not that I hold any real hope).

    I am very turned off by the fact that all parties tend to answer challenges that their theory does not seem to account for either by pointing to similar flaws in their opponent’s theory or by claiming that scientific “consensus” supports them or by denying the legitimacy of their opponent as a scientist.

    Leaving aside that this is a sweeping stereotype, etc., several people here did none of these things you object to in this sentence, yet here you are writing this.

    I suspect that many or most of the people you are interacting with may not be scientists or may not have a full understanding of the issues. This wouldn’t surprise me at all, as most scientists don’t give this “debate” much head-space, let alone actual time. (Partly as there isn’t a debate really, as I mentioned earlier.) Having said that, given you don’t seem to have much of an understanding yourself, so isn’t it a bit rich to ask that other non-biologists should?

  69. #69 Don Codling
    December 21, 2008

    Bob O’H wrote “You can’t have read widely – a lot of creationists will happily try to attack evidence for evolution within a species. Look at what they write about industrial melanism. If they were satisfied with it, why would they attack it? I’m thinking of people like Jonathan Wells, and a lot of the people at Uncommon Dissent.”

    You have me blushing. I do the same thing I have been objecting to others doing. I confess. :( I tend to write off a lot of creationists because they grab at straws, at best. I remember years back being given a pamphlet, “99 reasons why evolution isn’t so”. After reading it I wanted to write “99 reasons why this pamphlet isn’t so”. As I recall, all 99 arguments were specious, though one or two may have had some reasonable ground that I don’t remember. So my comment which you picked out really focused on those I consider serious opponents of evolutionary theory.

    Let me re-phrase it to say that there are lots of creationists who would very happily work beside you in trying to figure out how Honey Eaters and other groups were formed.

  70. #70 Jordan
    December 24, 2008

    It is sad that the science of biology gets tied down in the unproductive mire of this so called controversy.

    As a layman, some observations:

    - pastuer was raised earlier on. This is a conflation of evolutionary theory (well established science) with abiogenesis (which is essentially lacking any current scientific explanation, and is only subject to speculation.) The two are related bit definitely distinct. Think cosmology’s take on the seconds after the big bang vs our complete ignorance of the earliest moments, and most of all any possible cause of the big bang itself. Note decent from a common ancestor with natural selection is utterly compatible with a god-created original organism. (or alien created, or came on a meteor, or whatever….)

    - don expresses skepticism about the current models. This is healthy and scientific – the best model, darwinian evolution, is imperfect; it has contradictions, and gaps. It just happens to be the best current understanding (no alternative comes close. Any specific creationist model is easily refuted by evidence). The gaps and contradictions will shrink with time as more evidence and better theories come to light. This is science.
    Can any physicist claim general relativity and quantum mechanics,as currently understood, are remotely compatible? No. Because of this huge gap in physics, do we throw put either or both of the theories? Of course not. The theories are both resounding successes. We are confident science will give us the full picture in due course. But we certainly don’t resort to theories of gravity from the Greek philosophers or the Koran or Confucius or whatever in the meantime. We use the imperfect, flawed, current best model (remaining skeptical about it’s less testable predictions.) Again, science. Only in biology – and really, I hate to say, nearly entirely in the US and the 3rd world – does this seem to cause any consternation or brook any ‘debate’.

    - to be slightly on topic: a reason the original article supports a Darwinian evolution model? Because such a model predicts, correctly, that geographical factors of migration (north American birds access to Hawaii) can be a much better marker of shared ancestry (evidenced by DNA) than a strong phenotypic resemblance, due to the nature of speciation and selction pressure in ecological niches. Before modern biological theory, would zoologists have taken seriously the notion that these bird families were such distant relatives? This point has already been made by other people but I thought it needed summarizing.

    Apologies for the quality of this post – it was composed on a phone. But I hope I got the gist of the things I wanted to express across accurately.