Appendix II, UCLA (1981-2007), Birds & Avian Evolution

In 2003 I sought to publish my findings on relict reproductive behaviors in birds, and their implications for early avian evolution in a prominent journal. My primary purpose was to bring the new hands-on source of evolutionary data to the attention of evolutionists. Many spectacular recent paleontological discoveries were another reason to update my earlier treatments. The previous efforts in my book and journal papers in 1987-1990 were still scarcely or very little known or appreciated. But I felt it was not enough just to recall the existence of the new data sources. Compelling theoretical and factual background findings also were available. Accordingly, from the beginning of the project, I included much pertinent peripheral material, including three Appendices (Paleoclimatology and Paleobotany; Paleoentomology; and Reptilian Oviposition, Nesting, and Egg Care). The great length of the submitted new manuscript almost proved to be the projects Achilles heel. I hoped that my following letter of submittal to the editor would be passed on to reviewers and help smooth the way for the very lengthy MS.

Letter of submittal: Dear Editor. I would like to submit a paper titled, Relict reproductive for consideration for the Journal. Because of its length (over 26,000 words) and its review content, I am seeking your prior approval, concerning its suitability for the Journal.

    New findings of avian relict breeding behaviors, which provide the main rationale for the paper, are independent of data drawn upon by previous writers on avian evolution. They cast new light on several highly contentious issues. Prominent among these are the origin of flight (trees down or ground up); the origin of feathers (dependent on, or independent of flight); and primitive parental care in the avian lineage (biparental, male-only, or female-only). Only the first mentioned alternatives appear to be tenable when considered in the light of the newly elicited behaviors.

    The paper presents a synthesis of avian evolution, guided primarily by the implications of these relict behaviors. It also reviews topics relating to the persistence of, and ability to elicit, such behaviors, as well as the pertinent, spectacular avian and feathered theropodan fossil findings of the last 10 years or so. These being very numerous and of great relevance and interest, receive considerable space. Data from other biological disciplines pertinent to avian evolution also are drawn upon extensively.

    The portion devoted to the synthesis comprises the heart of the paper. It provides a much needed outline of the proposed course of avian evolution, consisting of six stages, demarcated largely on the basis of the new findings. The first stage consists of small bipedal shallow-nesting theropodan dinosaurs (or other archosaurs). Each proposed stage is described in terms of lifestyle and reproductive behavior, and rationalized in terms of the selective forces that led to it from the preceding stage. For example, answers are proposed to such questions as: how, why, and when did an ancestral practice of shallow-nesting evolve from deep-nesting, and how did the subsequent practice of surface-nesting evolve from the shallow-nesting, and why could not the surface-nesting have evolved directly from the deep-nesting, etc? Analytical treatments such as these are not to be found presently in the literature on avian evolution.

    An objective, up-to-date, comprehensive scheme of avian evolution of this nature, drawing upon data from all pertinent biological and paleo disciplines (paralleling those that exist in certain other fields) is much needed. It would provide a framework relative to which workers could propose concrete modifications or corrections based upon further considerations and more recent findings. At the present time new proposals by specialists in avian evolution usually stand alone, without reference to their position in any recognized hypothetical phylogenetic scheme of progression. In my view, the continuing absence of such a reference framework retards progress.

    The background for my paper traces to the 1980s when I began breeding small parrots to extend my studies of behavior and learning from mammals to birds. I discovered quite fortuitously that, in appropriate circumstances, the birds responded with relict behaviors. These relics were previously unknown, both because no one had sought to elicit them and because conventional studies of captive breeding parrots employed only dark nestboxes

    To facilitate observations in my initial exploratory studies I used large nestboxes with transparent sidepanes, and also adapted the birds to breed in open nests on cage floors. Though I planned eventually to study normal behavior, I soon learned that the breeding conditions I provided were approximating those of the birds remote theropodan ancestors for ground nesting. These conditions included exposure to light during breeding, as opposed to breeding in a dark nestbox or tree-hole, and the ability of both parents (both sexes of Cockatiels, for example, incubate) to have simultaneous access to the nest, eggs and young. It was the combination of these two conditions that elicited the relict responses, and diverted me to their study, instead of concentrating on normal behavior and learning.

    These responses changed more or less progressively during breeding and were repeated during each cycle. In essence, they appeared to retrace the birds ancestors adaptations during early stages of avian evolution. The findings are surprising only for their abundance (parrots may be exceptional in their degree of retention of the potential for relict behaviors to be elicited). The persistence of relict behaviors accords with our knowledge of the highly conservative nature of neural evolution (reviewed in my paper Conservative behavioural evolution, the neural substrate. American Naturalist 1990; 39: 758-767).

    Because the topics treated, and putatively partially resolved, involve central controversies that are under continuous animated discussion in the literature, because they provide a useful reference frame for such studies, and because relict behaviors have the potential to reveal practices of the remote past, I believe the paper will be of more than usual interest to your readers. I hope you will be agreeable to my submitting the manuscript.

Though I felt that reviewers would recognize that the key contribution of the manuscript was the unprecedented new source of data for studying avian evolution, this apparently was not the case. Most reviewer comments emphasized factual details rather than the significance of the new approach and findings. Many comments sought more to convey the reviewers own views on the subject than to objectively critique the authors views. Complaints about excessive length were most common. Of course, the manuscript did benefit greatly from factual corrections and new references called to my attention. In the following, I shall not go into details on these matters but touch more on the highlights.

For my first submission, I chose The American Naturalist, having published there several times before, including a paper 44 pages long that was divided between two issues. The submitted paper was titled, Relict reproductive. It was submitted on Dec. 6, 2003 and returned on January 5, 2004. The Assoc. Editor alone reviewed the paper. He found my general approach to be of great interest, and only offered general comments. Eventually, these proved to be more favorable than others received later, as follows:

    This long MS is potentially interesting, even important, because it synthesizes a wealth of disparate information with regard to important questions in vertebrate evolutionary biology (especially the origins of flight and of parental care mechanisms in birds). On the good side, it is innovative and provocative, synthetic across a wide range of topics that most biologists can handle effectively, and in fact the publication of this paper somewhere undoubtedly would inspire a wide variety of biologists to rethink their views on the topics covered.

After pointing out serious gaps in which the MS needed to be brought up to date, he concluded:

    .....the bottom line then is that this MS is WAY too long...would have to be MUCH shorter, different MS, not just shortened a bit, alternatively he should seek to publish....in one of the lengthy review venues.

Both he and the editor suggested Quart. Rev. Biol. as an appropriate venue. Unfortunately, the QRB, for which I had reviewed books 40 or more years earlier (see Chap. 9), required that copies of pages for all quotations employed be submitted with the MS. This would have entailed delays of at least weeks, because many of my references were from books obtained as interlibrary loans. Accordingly, after appropriate revisions and reformatting I submitted the MS, under the same name, to the British journal, Biol. Rev. on Jan. 20, 2004.

After considerable unavoidable delays, the MS was declined on June 18, 2004. Referee 2, who was most favorable, commented:

    There are certainly some useful and interesting ideas in this MS but I feel that significant changes are necessary before this work might be publishable:

There followed 3-1/2 single-spaced pages of comments plus annotated pages of almost the entire MS. This must have required many hours of work, even a day or two. In conclusion, he commented:

    I recommend that this MS needs a full rewrite followed by additional external reviews. I feel that there are some interesting ideas presented but they are lost to the reader due to poor organization and use of references, and unclear taxonomy.....Then researchers could work to revise either the phylogenies or the evolutionary theory and look for pertinent fossils in the right geologic context. I think the authors ideas would then contribute to both ecology and paleontology.

Neither Editor J. B. Losos of Amer. Nat. nor Editor W. Foster of Biol. Rev. had indicated that a revision would be considered. Meanwhile, new paleontological findings continued to accumulate and I had assembled the needed copies of quotations required by QRB. Many revisions of the MS also were needed in the light of reviewer comments. Additionally, I sought further comments from colleagues and my former student, Dr. Donald Perry, engaged himself in a revolutionary work on human evolution. It was not until mid-August, 2005, over a year later, that I submitted a revised MS to Editor A.D. Carlson of QRB. Its title was the same, but I had shortened the Appendices.

I received the declined MS from QRB on Oct. 18 of the same year with both specific and general, sometimes contentious, comments from only one reviewer. He or she clearly was a student of the origins and evolution of parental care. Numerous deficiencies in my MS in that area, including 20 overlooked references, were pointed out (although a second reviewer was referred to in the Editors letter, his or her comments must have been omitted in error).

Taking these new QRB comments on parental care into account contributed greatly to, and strengthened, my treatment of the topic. The most revealing comment, however, was, too reliant on Paul to support ideas. To me, this was like saying, too reliant on Darwin, or too reliant on Ernst Mayr. At least at the level of structure and its implications, Paul is the most gifted and incisive student of avian paleontology and evolution whom I have encountered.. Although my approach is quite different from his, our conclusions point in the  same directions.

Another year transpired before I was ready to submit a revised MS retitled, Roots of avian evolution: Implications of relict reproductive behaviors, including abbreviated Appendices. I submitted the paper in early October, 2006, to the Zoological Journal of the Linnean Society. Although The Journal was in the throes of changes in its Editor, the editorial office, and the manner of MS submission, this was accomplished after only several months delay.

In early January, 2007, I received word that the MS could not be accepted, together with rather detailed comments from two Reviewers. Length again was a principal problem, but Reviewer A called for much greater specificity in matters that hardly can be expected from a proposed theoretical evolutionary outline. If I had the answers to even of a fraction of Reviewer As questions I would be writing a textbook, not proposing an outline of early avian evolution and its roots. Nevertheless, the questions led me to include some helpful specific comments at appropriate places in the MS.

Reviewer B was more amenable to the approach taken. Thus, he commented:

    I find this MS very interesting but also challenging, and while I admire the attempt to create a comprehensive hypothesis of the origin of birds, including the evolution of flight, endothermy, and reproductive behaviour, I have serious reservations about it.

The reservations followed, including a need for drastic shortening. Paradoxically the meaning of ever funneled (as into the trees) was not clear, nor was the meaning of terrestrial-arboreality. At any rate, the stated reservations, as with those of Reviewer A, guided me toward making certain helpful additions and clarifications.

At this point in time (Feb., 2007), circumstances apparently came to my rescue. I received material from PLoS One, headlined, pen-access journal will publish first, judge later. Therein was contained the information:

    The Public Library of Science (PLoS), the most prominent publisher in the open-access movement, is setting out to challenge academias obsession with journal status and impact factors. The online-only PLoS ONE, which launched on 20 Dec., will publish any paper that is methodologically sound. The journal will initially publish 10 to 15 papers a week, but this could reach a few hundred each month, says Chris Surridge, Managing Editor based in Cambridge, UK. Were trying to make a journal where the papers are not the end point, they are the start of a discussion.

I lost no time in revising and organizing my MS for submission to PLoS ONE. After over 60 successful years of experience in writing books and papers, I surely could produce a methodologically-sound MS for them. The organization of MSs for PLoS ONE was required to adhere to one of several basic formats, without exception, all of which included a Discussion. I was able to adjust the organization of the paper to meet one of the possible forms but there was no alternative but to provide an otherwise absent, new section and Discussion, which was as follows:

Discussion. Regarding the present findings, it is noteworthy, that the underlying studies were entirely fortuitous, not the result of careful planning. Whether the use of small parrots was a lucky choice, or whether similar results would have been obtained with many other species will not be known until other similar investigations have been carried out with others. The findings also were fortuitous in having depended on my practice of always being present when the ambient lights were turned off for the night, and of remaining for a time afterward, else I might never have discovered how the early brooding hen in the nestbox responds at that time. This, in turn resulted from the need to spend almost every waking hour living with the birds. The discovery of elaborate suites of relict behaviors, upon which the present analyses of early avian evolution is largely based, should perhaps be regarded only as a first step into a little explored but highly promising domain for illuminating past events in vertebrate evolution.

The findings give clear evidence of preservation in the brains of endothermic vertebrates, perhaps even more so for cold-blooded ones, of much ancient circuitry that, when appropriately stimulated or disinhibited, can support the reenactment of behaviors that trace back to very ancient times. Stimulation of these behaviors generally results when the conditions the birds encounter duplicate those of the past or, alternatively, when otherwise sustained inhibitory influences are overcome by certain brain injuries, in hybrids, or adventitiously.

Normal relict behaviors often are inconspicuous, and detected only on close observation of birds thoroughly adapted to an observers presence. Behaviors elicited by unobtrusive experimental manipulations, though also often inconspicuous, sometimes are strikingly different from the expected. Conventional procedures for behavioral studies often must be radically altered. Instead of interfering minimally with the courses of actions of the birds, so as to introduce no bias, one takes advantage of favorable opportunities to unobtrusively ask them questions, frequently obtaining clear-cut answers. For example, when the questions have to do with the care of eggs or chicks in the nest, all manipulations by the experimentalist are carried out with the nest entrance temporarily blocked, usually just after a sitting bird exits for any reason.

As a general rule, the best time to make any change in the status quo is when the birds are deeply occupied with some interaction. When a birds view cannot be obscured readily during a desired alteration of circumstances, long, thin forceps sometimes can be employed without being detected. On the other hand, certain manipulations sometimes can be carried out in clear sight of birds, without alarming them, for example when returning a chick to a bird brooding in a floor nest. Carrying out observations automatically, relying on recorded closed-circuit television would be restrictive. Thus, one often must observe the birds actions, or listen, very closely, and take advantage in real time of every favorable opportunity to alter circumstances toward some end (say, asking some question).

Events occurring during functional cycles in Budgerigar ovaries, already part of the literature, suggest that reproductive cells normally develop in hierarchical sequences. These appear to recapitulate, and have the potential to reveal, detailed aspects of past ovipositional practices, such as clutch size and relative sizes of eggs in different evolutionary stages. Since such hierarchical development of reproductive cells is even more pronounced in reptilian ovaries, it is likely that ovarian development in other birds also could give valuable clues.

The results obtained in the present study are sufficiently promising, and in some instances give such unambiguous results, as to encourage comparable programs of study of a variety of other avian species. Although these results give every indication of being representative of early evolutionary stages in the origin of birds, only the extension of similar studies to other species can establish this with relative certainty. At any rate, new hands on observational and experimental approaches to studying avian evolution from remnant signs preserved in living birds appear to be on the horizon.

Preferred submissions for PLoS ONE were electronic, so I logged in on March 13, uploaded the paper and letter of submittal, and began fulfilling other requirements. As I neared the end of submission, two questions were: (1) give the names and email addresses of 5 researchers qualified to review your MS; and (2) give the names of 5 researchers you wish to exclude from reviewing your MS. The latter question, in particular, hardly was consistent with PLoS ONEs avowed claim to publish any methodologically sound MS.

Questions of naming possible reviewers had come up before in connection with this MS. I always responded that the topics of the MS were very highly contentious, and that my suggesting reviewers would very much bias the review process. Moreover, I felt that my treatments were very even handed so I would rather that the editors made such selections. This, also, was essentially the answer I gave PLoS ONE.

Three weeks later I had my answer. Dr. Sean Rands, Academic Editor. concluded after careful consideration that the MS was not suitable for publication. The two referees found many of the arguments in the paper to be extremely controversial, and to require a much greater degree of justification than given. But the main problem was that the MS didn't fit the criteria for publication in PloS ONE, since novel experimental results weren't being presented,

....assuming that all the experimental observations you describe are already explained in detail in your 1987 book or the other works of yours that you have referenced.....Therefore, your paper really doesn't present any novel results, and since PLoS ONE doesn't publish review papers, Im afraid your paper doesn't fulfill the criteria necessary for this journal.

There was no disputing the main problem, as the MS was largely of a review nature. Dr. Rands email was accompanied by the comments of two Reviewers. These were the most contentious of any already received. Reviewer A went so far as to reproduce my Abstract with 14 bracketed expressions introduced at points of disagreement, 9 of which were of the nature of no evidence. However, none of my proposals with which Reviewer A disagreed was arbitrary. All were backed by carefully reasoned ecological, behavioral, neurological, hormonal, and/or climatic rationales, all of them worthy of serious consideration. I, as a reviewer in the same position, would have concluded that thanks was owed to the author for constructing such an in-depth, hypothetical, outline of main-line avian evolution, against which other researchers could compare their data and conclusions.

The comments of Reviewer B were even more specific and contentious. Citing my conclusions, It is reasonable to assume that there was only one safe, generally available method for small theropodan ancestors of birds to maintain close nighttime watch over ground nests in mild, equable, late Triassic-early Jurassic climates. This would have been by occupying nearby resting sites at relatively low heights in vegetation, and quickly accessing and protecting nests threatened by small egg-predators by jumping to the ground. To these conclusions, he countered:

It is not at all clear that this is a reasonable assumption, for many reasons.

1. We don't know that these animals laid their nests on the ground. We assume that they did based on outgroup assumptions, but the simple fact is that we don't know. Fossil nests have been found for some derived theropods and some ornithopods, but the nesting behaviors of early theropods are unknown.

2. We don't know where the parents slept. Maybe they slept on the nests. Maybe they abandoned the nests and only came back at hatching times, as do extant crocodiles. Maybe they hid in burrows, as we now know some small ornithischian dinosaurs did. Maybe they wedged themselves into narrow clefts in rocks or stumps, as do many small birds today. Nothing about the anatomy or taphonomy of early theropods suggests that they spent any time climbing.

3. The clich of generally equable Mesozoic climates is insufficient to infer local seasonable and climatic patterns and doubly insufficient to infer the microclimate of the nesting area.

All these no evidence and we don't know comments of both reviewers suggest that neither had read the paper carefully, possibly not even the last half of the title, Clues from relict reproductive behaviors. Nor had they apparently even taken note of the crucial, previously unappreciated, circumstance that, in the evolution from the practice of deep nesting to that of ground nesting, relatively lengthy shallow nesting phases would have been unavoidable (because of the high water-conducting pores of deeply buried theropod eggs).

There is evidence and we do know. The birds, themselves, have told us so! Because of the highly, even unprecedentedly, conservative nature of vertebrate brain evolution, bird brains still possess much of the same breeding circuitry they possessed 50 and more millions of years ago. When confronted by the same conditions met way back then, at the same stage in the breeding cycle, they still respond in the same way they responded then. From their responses we can directly infer what the conditions were. That is the main message of the paper, unfortunately seemingly totally overlooked by both reviewers.

At any rate, my patience was wearing thin. I had exhausted possible journals for lengthy papers. At age 85, it was time to bring my new effort to fruition, even if compromises were in order. The main reason to publish in an established journal in the field was to reach a wide readership therein. Much the same end could be reached by publishing in a new journal with only a small readership, followed by sending out reprints to leading researchers in the fields covered. For such a long paper as mine (32 pages), it was unrealistic to expect people in the field to download copies and devote the considerable time necessary to read them. But with a reprint in hand, and their name in the list of references, few researchers would resist to temptation to investigate further. That is the direction in which a lesser but swift success lay.

On Nov. 17, 2006, I had received an invitation to submit a paper to Scientific Research and Essays (SRE), founded only the previous month. It purported to publish high-quality solicited and unsolicited articles, in English, in all areas of science, medicine, agriculture and engineering. All papers published by SRE are peer reviewed. SRE is a very rapid response journal with two issues published every month.

 [Incidentally, for those who might have an interest, the handling fee to publish my paper in SRE was $500. In PLoS ONE it would have been $1,250. Also, it is noteworthy that the next day after the paper came online in SRE, the phrase roots of avian evolution already was referenced by Google, Yahoo, Metacrawler, etc., carrying one back to SRE and the entire paper, itself.]

After examining several issues of SRE (sre@academicjournals.org), and finding that paper lengths ran to a maximum of about 5-7 printed pages, I contacted SRE concerning papers of much greater length. Upon receiving a favorable reply, I promptly prepared a MS titled, Roots of avian evolution: clues from relict reproductive behaviors, for SRE. Both a Table of Contents and the three Appendices were omitted in the interests of brevity.

This time, however, I recommended as reviewers two acquaintances who were familiar with my studies and the MS (and so informed the Editor), and had made valuable suggestions, themselves. These are Prof. William Hamner of UCLA, and my former student, Dr. Donald Perry. As reviewers, both highly lauded the MS, which was accepted . At Dr. Perrys suggestion to the Editor, the Table of Contents was restored, much to the papers benefit. The paper appears in Appendix III.