The Evolution of Birds (Or: What missing link?)

Discussion in 'Biology & Genetics' started by Trippy, Sep 28, 2014.

  1. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

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    Why would adding two small air-storage sacks have 'negative utility'? It appears it would add a small positive benefit and be selected for. This is true for both the posterior and anterior sacs. So yes, initially they'd be small, but selective pressure would cause for them to become enlarged as in modern birds. alligators appear to be a 'dead-end' that happened across a strong environmental niche, surviving into the present time little changed from anciently, when they ate dinosaurs and primitive mammals that stumbled their way. far more sluggish, and far less environmental pressure to cause them to change over time.
     
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  3. exchemist Valued Senior Member

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    But clearly, since these features HAVE evolved, there was not the downside that you for some reason assume (without evidence), during their evolution.

    Or are you suggesting that they could not have evolved. If not, by what agency do you think they appeared?
     
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  5. Trippy ALEA IACTA EST Staff Member

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    It's not about rapid exhalation, it's about the pattern of circulation through the pulmonary system.

    My point here was straight forward - that in addition to the observation that lungs optimised for unidirectional flow are functional under bidirectional flow, unidirectional flow has also been observed in diaphramatic breathers.

    Maybe you should try doing some of your own research, or better yet, reading the damn article I linked to in the first place.

    That's your opinion, well, yours and creationists anyway. Did you realize that? You've taken an argument from personal incredulity, and turned it into an argument of irreducable complexity.

    On the one hand I disagree that it would have negative utility, and I also disagree that it would be selected against - lungs are already air storage sacks. And can you really think of no circumstances under which the ability to store some extra air might be advantageous?

    On the other hand, I never claimed alligators had evolved air-sacs, what I have said in that context is that they're unidirectional diaphramatic breathers. They, in a sense, represent one of the intermediate steps between bi-directional diaphramtic breathers and the avian pulmonary system. The very thing you claimed was impossible.

    Again with the irreducible complexity argument. Creationists tried that with the eye, didn't work there, won't work here.

    Look.
    Here's a schematic representation of how a bird breathes:

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    Here's an image of a alligator respiratory system:

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    The solid coloured portions are (as I understand it) airways - the yellow part is the trachea and primary bronchi (or the equivalent) the green and teal are secondary bronchi (or the equivalent to it). Don't ask me about the red bit because i'm not sure.

    Gas flow through the lung is from the teal portion to the lime green portion and is driven by the bernouli effect. The layout of an alligators lung isn't hugely different from our own. Compared to this:

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    I don't think it's as significant a modification as you seem to think it is.
     
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  7. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    TrippyYour post, showing all the extras that one way breathing requires makes my point better than I can. I suspect you don't understand what I am referring to with my term "binary change" (as contrasted with analog change) so I will clarify with the giraffe, where both are well illustrated.

    No one is certain but it seems likely that the distant ancestor of the giraffe was a four legged creature with probably shorter than average neck (or possibly none) as one of the nerves that told "cheek information" (i.e that bee stung there or he bit his cheek, happen to pass below a bone before going to the brain for processing. Getting it on top of that bone can not be done via a set of many very tiny "analog changes" accumulating over thousands of generations. The relocation of that nerve to the top side of the bone, which later became the "collar bone" is a "binary change" I.e. there are only two "states" ("under" or "on top" of the bone.) So the long necked giraffe of today learns he bit his cheek with considerable neural delay as the bite induced neural signals leave the cheek area, travel all the way down that long neck, go under the bone still and then travel all the way up that long neck and finally reach the brain. - EVOLUTION CAN NOT MAKE BINARY CHANGES.

    In contrast the length of the neck can increase via tiny incremental changes accumulating over thousands of generations. For example the average length of the giraffes in generation n+1 can be 0.1mm longer than the average neck length in generation n. Evolution can (and did) change the length of the neck of giraffes as that is an ANALOGUE CHANGE. I don't know why it happened but perhaps the short necked ancessor of the giraffe liked the taste of the leaves at the top of the short bush it feed on more than the slightly more dusty ones closer to the ground - Why the change occured is not important as it did occur as each tiny stage of that analogue change gave a slight benefit.

    Problem with a two way breather converting to a one way breather is that (1) only one of the many new items (in tiny version, most likely) has no benefit and is a biological cost to make it. Having only one new sack with no air flow tube leading to it, even if full size needed, would be as useful as one fax machine only in the entire world.
    (2) Adding in one air sack (or even a pair) inside a rigid rib cage, reduces the remaining volume for the two-way functional lungs. Thus not only is the new sack(s) totally useless and biologically expensive to make, but also they make the two-way respiratory system have less capacity. So when a herd of these creatures are running for their life trying to escape the carnivore chasing them - the one lagging behind with less capacity lungs is the one that gets eaten.

    Humans will never evolve the better eye design that the octopus has (retina in front of the nerve impulse collection network and the "blind spot" where they all join to form the optic nerve carrying the information to the brain. etc. for the network of blood vessels than make black random shaped shadows cutting the 2D image into many dozens if not thousands of separated odd shaped pieces that later processing in the brain must "fill in" * with best guesses as to what was blocked by the blood vessel shadows). Moving the retina to the other side of all this support structure (like moving the giraffe's nerve to the other side of a bone) is a "binary change."

    EVOLUTION CAN NOT MAKE BINARY CHANGES as there is negative utility and added biological cost to the small incremental changes evolution can make.

    * This automatic "filling in with best guess" is easy to demonstrate: Close one eye and fixate the other on small x located so part of a vertical line crosses the "blind spot" That line is red, except for the small green section that falls on the blind spot. I'll tell you that your perceive a continuous vertical line as the part of image falling on the blind spot is "filled in." I'll let you guess by what color.
     
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  8. exchemist Valued Senior Member

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    But it is only your assertion that the change to one-way breathing involved what you call a "binary change". Whereas the evidence I presented, in the item about alligators, casts doubt on this, since one-way breathing is possible in these creatures, without any air sacs. So the air sacs, at any rate, are not essential to the operation. There are other ways to do it, clearly.

    Secondly, why not consider for a moment the diagram Trippy posted of the bird breathing system? As I see it this involves 2 points at which the lungs can exchange air with the outside world. It seems to me perfectly possible that first there was only one (as we mammals have). Next, perhaps, there were two but neither unidirectional. This would work fine, just as our system with one does. Then, later, mechanisms started to appear (air sacs, valves etc) that made the flow predominantly, but not exclusively, one way. It would be a system in which most of the inspired air went into the lungs through one of the two openings and most of the expired air went out through the other. This too would work perfectly well.

    So all of these intermediate steps would work. It is thus not a "binary change", analogous to moving the nerve in the giraffe's neck from one side of the collarbone to the other, at all.

    Lastly, I repeat my question from earlier today: given that the one-way breathing structure is present in birds, if that you are contending evolution could not possibly have given rise to it, what would be your alternative explanation?
     
  9. wellwisher Banned Banned

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    This observation has implications for evolution. Bacteria are composed of 98% coding genes and about 2% junk genes, while humans are 98% junk genes and 2% coding genes. This shows that evolution has evolved in the direction of an increasing ratio of junk genes to coding genes. The current theory of evolution is more consistent with bacteria than with humans, relying much too heavily on coding genes and not enough on the impact of the evolving majority of junk genes.

    For example, humans have not evolved very many new coding genes over the past million years, yet the entire species has totally advanced behavior in thousand of ways. One or two changes in coding DNA cannot explain this. Losing wisdom teeth or not needing tonsils, does not explain the invention of the writing behavior. This strongly indicates that changes in the junk genes is the key to evolution of higher life forms. The coding genes is more of a bacterial bias.

    The junk genes are not junk. The junk genes are there to provide context for the coding genes. As an analogy picture a box of building blocks; coding genes. We will get ten children to use this same box of blocks to build something of their choice. We can get ten different sculptures with the same blocks. Twins with the same coding genes can have different contexts and therefore have differences.

    If we come back to the birds, changes in context can play a role in their evolution. One will not see a major change in coding genes cresting the illusion of a smooth transition. But contact can change from one to the other using the same building blocks. I have arguing context for years but was not yet aware that bacteria and humans differ by that much, in terms of the ratio of coding to junk.
     
  10. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    Trippy concluded by asking:
    "given that the one-way breathing structure is present in birds, if that you are contending evolution could not possibly have given rise to it, what would be your alternative explanation?"

    A different ancestor - The same answer as to how the octopus has better eye design - one with retina infront of the support structure, no blind spot, 2D images not cut in to dozens (or thousands for large image) separated pieces for later processing in the brain to "fill in." I.e. The ancestor of the bird may have had a more "shark like" system for extracting O2 from its environment. I. e. a one way flow system. The fish that land animals evolved form at least when they left the water, had an inhale then exhale breathing system. Fish, most eels, still do. I.e. their gill flaps close when the inhale more water. Then their mouth closes as the exhale it thru the gills- one way intermittent flow just like the humans that evolved from them.

    The real puzzle is how do we know that dinosaurs had two way flow? Perhaps like fish etc. they had one way flow so no problem for them to evolve into birds. If they had soft tissue gill like exit path for their breath it may have left no fossil record - I am just speculating - don't claim this to be the case.

    I raised guppies for a half year and as I recall they gulp air then expel it. (I wanted to get faster development of colored tails by selection of the females, which don't display their latent color - mate them with average color males then with more expensive highly colored males. Each female was keep in separate 1 gallon jar - I had an infinite free supply of them. I drop my project when I learned the female can store sperm for one mating and have even three later broods of live births form it.

    Collecting information by a radiation sensing system is so valuable it is one of the first things animals developed. The amoeba and the earth worm both avoid light shining on them if they can. The earth worm has an opaque skin. Thus the radiation detectors are closer to the light source than the blood supply system - just like the octopus's radiation detector are. In contrast the amoeba is quite transparent - the radiation detectors are probably behind the skin - I don't know, but that seems to be a reasonable guess.

    I am not asserting that birds did not evolve from some subgroup of dinosaur like creatures - just that it is quite a difficult problem to show how they could have evolved from creatures that were "two way flow" breathers. So many analogue transition steps required, most of which would have negative benefit in addition to extra biological cost.

    I can see how there could be benefit for the alligator's ancestor to evolve an addition to its two-way breathing system, a more rapid exhale path for spending less exposed time on the surface when it needed a "gulp of fresh air" but the alligator still has two way flow thru the lungs, not one way thru the lungs flow like the birds do. That 2-way to 1-way change is a binary change.
     
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  11. exchemist Valued Senior Member

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    1) It was me and not Trippy that wrote the sentence you are quoting.

    2) You do not seem to have addressed my reasoning as to why the change from two-way to one way breathing need not have been a "binary change". I would be grateful if you could address this.

    3) But, at the same time, I notice you are introducing another objection, which is that the costs associated with the incremental changes from two way to one way would not have been outweighed by the benefits. I find this a questionable assertion (how would you know?), but more importantly, if the process was incremental, it was not "binary". So what is it you are now saying?
     
  12. billvon Valued Senior Member

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    Sure it can. It only takes the removal of one gene to remove the eyes from a fish - and many cave-dwelling fish lose their eyes very quickly. A binary change. Or monkeys can gain a mutation in a single protein (TRIM-5) that confers immunity to retroviruses. One day they don't have it and one day they do - a binary change. Or the HOX gene complex - a single mutation there and a fly has an extra set of legs.

    OK, And then one day that bulbous eye underwent a single mutation and inverted. Instead of a lump of light sensing cells near the surface, there was now a cup of light sensing cells with an opening. This worked as a very crude pinhole camera - and the modern eye was born. Again a binary change.

    There's nothing that either prevents or requires step changes in evolution. You get a lot of gradual changes, and you sometimes get a radical, significant (i.e. "binary") change that is conserved. This is good for us; it is why (for example) we have bananas.
     
  13. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    sorry about (1) - I still have problems getting post I am posting about to appear at top of my posts. I have a touch screen computer and what worked in this case was to right click on the reply next to the post number, then click on the back arrow at top left, then with my finger hit the reply next to the post number.

    On (2) it only seems that way. When I speak of 1-way or 2-way I am speaking ONLY about the way air flows thru the surface that is mainly removing O2 form it an putting it into the circulating blood. I.e. that is what I call the lung. All the other air containers, passage ways etc. are unimportant - they may have (and some do in birds) have reversing or "2-way flow. I am focused on the lungs only. There it is a binary change to convert reversing flow into one way flow. - There is no intermediate state, unless you want to consider no flow (thru the lungs) but that is lethal.

    On (3) No I think all evolution supporters, me included, think it proceeds by small incremental stage changes, each of which must be beneficial. The alternative - one step change is called a "hopeful monster" in the literature - but no one thinks that happens - larger one step changes are normally not only useless but lethal "birth defects."
     
  14. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    Ok, I'll admit deletion of a structure is possible in one step - probably often happens that way, leaving a lot of "junk DNA." I even admit that normal structure (often normally occurring in pairs) can have a miss count like 6 fingers or three functional eyes (one Chinese war lord had three functioning eyes).

    I should have been more careful and said: Entirely new beneficial structures can not happen in one step.
     
  15. Trippy ALEA IACTA EST Staff Member

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    No it doesn't. It contradicts your point entirely. The only thing that is required if you compare a human lung to an alligator lung is the splitting of an air-way. Something that I'm reasonably confident could be achieved with a single mutation. As to why it hasn't happened?
    1. H. Sapiens is a young species.
    2. We live in a relatively oxygen rich atmosphere.
    3. There is no pressure selecting for it.

    Don't forget that the human lung is already divided into lobes. It's not that significant of a re-arrangement.

    No, I understood what you meant. You obviously haven't understood my points.

    Actually, as Billvon has also pointed out, it can, and there are a number of examples of this.

    Giraffe neck length is A) Irrelevant, B) A red herring, and C) Not the only adaptation that Giraffe's had to make.

    You're still focused on air-sacs. As I have proven, one way breathing is not dependent on air-sacs and exists in tidal breathers (alligators being one example, monitor lizards being another).

    On the one hand, you're ignoring the fact that one-way breathing arose before airsacs, not after it. On the other hand you're ignoring the EVIDENCE that we have that some dinosaurs - notably feathered theropods, including predators had air sacs - something that you would know had you read the article in the OP.

    Actually, it can, and it does.

    That was exchemist, not me.

    You have got to be kidding me.

    If you had read the damn article in the OP you would have seen that it explains that the evolutionary sequence that it posits is One way breathing -> Air sacs and that this was in place by the time birds evolved from the feathered theropods. We have physical evidence that (for example) Tyranosaurs (or some of them did anyway) had airsacs. Again, this is something you would know had you bothered to read the article I linked to in the OP.

    Clearly that makes you an expert in both paleonotology and evolutionary biology.

    The feathered theropods that birds evolved from were one way breathers, not two way breathers, some of them even had air-sacs. Billy. Do you even know what an Archosaur is? I'll bet you think that Archosaurs are a specific kind of dinosaur. They're not. Archosaur is the name of the clade that includes birds, dinosaurs, crocodillians, and pterosaurs, of which Archosaurus and Protorosaurus may have been the earliest members of (they were both late permian reptiles, sometimes classed as archosauroforms rather than archosaurs). The current hypothesis, as accepted by the mainstream, is that one way breathing evolved as long ago as 270 million years ago (late permian) in response to declining or low atmospheric oxygen levels. By the time of the Permian-Triassic boundary oxygen levels had dropped from arount 30% to around 10% and this is thought to have been the evolutionary pressure that gave rise to one way breathing in Archosaurs. This is supported or confirmed by the observation that Alligators and crocodiles have one way breathing because that suggests that it arose early in the archosaur timeline - before this split occured. The discovery of one way breathing among Therapsids is icing on the cake because either it evolved before the therapsid-archosaur split, or it evolved independently in therapsids.

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    No, it is not a binary change. The reason I say it is not a binary change is because one way plumbing works for two way breathing as well as one way breathing, and so it is possible to make small changes to the two way plumbing that are neither beneficial nor detrimental until one way breathing spontaneously arises - for example, see the alligator.
     
    Last edited: Sep 30, 2014
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  16. Trippy ALEA IACTA EST Staff Member

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    Actually, no, changes can and do occur that have no benefit but persist because they're not detrimental.
     
  17. exchemist Valued Senior Member

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    OK thanks for the reply. Re (1) it seems we are all having various sorts of trouble with the new system.

    Re (2), I think you still miss my point. I see no reason why, once you have two openings in a lung (using your definition), as birds have (cf.Trippy's diagram in yellow), you cannot have a two way flow that becomes biased towards mainly flowing one way. I rowed for many years on the tidal Thames, on which the direction of the water reverses with each tide, but it backs up less far on the flood than it flows down on the ebb. In a similar way, you can perfectly well conceive of a lung which starts off with 2 way flow through both openings and then progressively the flow becomes more and more asymmetrical, with most of the inspired air coming in through one channel and most of the expired air going out via the other, so that eventually it is almost all one way. That is not a "binary change", it is progressive and incremental. Do you understand what I'm saying?

    Re (3) once we have established this is not a "binary" change, the hopeful monster objection disappears.
     
  18. Trippy ALEA IACTA EST Staff Member

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    As an addendum:
    There are already congenital abnormalities that are of the nature that might eventually give way to one way breathing in humans.
    Congenital pulmonary airway malformation
    Pulmonary sequestration
    And ectopic bronchus - the point here being not so much a comment on whether humans will ever be one way breathers, but more that these kinds of abnormalities, which if left untreated can have relatively normal prognoses (but not always) are the kinds of abnormalities that have some of the features required by one-way breathers.
     
  19. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

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    Correct. Genetic drift. They can become fixed in a population.
     
  20. iceaura Valued Senior Member

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    What is the evidence that two way breathing was the original, in any lineage? If we are assuming one evolved from the other, it seems as likely to me that the two way evolved from the one way - and the incremental sequences involved may be more likely, or readily available, if that's a concern.
     
  21. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

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    Could be. But it was shown that one-way has superior oxygen absorption/CO2 release, and is thus presumed to have come after. But there might be advantages to the 2-way we've not considered to make up for that.
     
  22. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    Yes, but don't think the math works out. Consider part way in the transformation you out line has been achieved: Path A gives to lungs 2V of fresh air during time interval 0 to 2 and removes V of stale air during time interval x to x+1. (I allow x to be 2 or greater - you chose.) Path B needs to remove the one V that did not go back via path A, Unless you are postulation also a storage sack, that Magically appeared too but we don't do that magic do we. Please tell when path B gets in 1 V of fresh air intake and send its 2 V back out. (its 1 V intake and half of the 2 V intake that path A took in but only sent 1 V back out.)

    I.e. fill in a "time/ action table" like:
    Time / Actions
    0 to 1 A is taking in V
    0 to 1 B is....
    1 to 2 A is taking in V
    1 to 2 B is...
    etc. until we are back to step one above.

    YOUR rules of this game are: Can't add second nose, or temporary storage volume(s), etc. as that would be more than just modulation of the air flow fractions from equal volumes in equal intervals of only two-way or reversing flow to flow cycle with one path (A) doing 2/3 of the intake and 1/3 of the exhale. I.e. would be postulating a "hopeful monster" with all it needed came in one birth, I think, but not if you can fill in the full breath cycle of table above.
     
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  23. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    I agree. I don't think two-way was the original: Every land creature evolved from sea creatures. Fish have a one-way flow for getting O2 from the water - water comes in the mouth as it opens. Then mouth closes and internal volume contracts -forcing gill flaps to open and some "mouth water" to flow by the fine blood vessel containing gills so the water leaving the gills only flows one way and has slightly less O2 than the water that came in the mouth. This works well as water is incompressible - can force the gill to open.

    Air however can be compressed as the mouth volume contracts - may not break the attachment of the gill flap to body wall. That is why, I guess, that some fish slowly added lungs over many generations, but each could survive a little longer on the land before needing to go back to the water.* The compressed air could flow first into their lungs, (even it they were tiny and only small part of how they got O2), and then soon flow out of and slowly these adventuresome fish became adapted to every greater periods out of water.

    Some of the fish that adapted and lived on land invented two way reversing flow breathing I think and no longer used / activated / the "make gills" information in their DNA. - Became two-way land breathing animals. Perhaps some of the old one-way DNA genes got re-activated to help birds get their more efficient and needed for flight one-way breathing. Long unexpressed genes do sometimes get "awaken" - a socially very damaging case happens - typically at any time there are a few humans living with bodies completely covered with fur, except for bottoms of feet and palms of the hands.

    * Humans still develop those "gill like" structures in the first few months of life in the womb. The "ontogeny recapitulates phylogeny" ** theory of Haeckel is not taken very seriously now, but was based on this and many other facts. Read more here: http://en.wikipedia.org/wiki/Recapitulation_theory

    ** I have always liked that 3 word phrase - so much, so many concepts and ideas packed in those three words. It is a pleasure to roll it off your tongue. I once, while a little drunk said it to a "dumb blond" at a party - she pretended to know I was not just speaking gibberish.
     
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