Evidence for the Evolutionary Model

(p.26-30)              The pdf of the entire book, with Ray's 50 page introduction, can be found here.

      Many people have not objectively examined evolutionary theory to consider specifically how creatures may have developed. For example, consider the following.

      It is very hypocritical of Ray to say this, considering that he clearly hasn't done any research on the topic, himself. Despite that the following questions he asks have been the subject of research for many decades, he seems to remain oblivious to any of the publications that answer them.

      Zoologists have recorded an amazing 20,000 species of fish. Each of these species has a two-chambered heart that pumps cold blood throughout its cold body.

      There are 6,000 species of reptiles. They also have cold blood, but theirs is a three-chambered heart (except for the crocodile, which has four). The 1,000 or so different amphibians (frogs, toads, and newts) have cold blood and a three-chambered heart.

      There are over 9,000 species of birds. From the massive Andean condor with its wingspan of 12 feet to the tiny hummingbird (whose heart beats 1,400 times a minute), each of those 9,000 species has a four-chambered heart (left and right atrium, left and right ventricle)—just like humans.

      Of course, the 15,000 species of mammals also have a pumping, four-chambered heart, which faithfully pumps blood throughout a series of intricate blood vessels to the rest of the body.

      These are interesting thoughts to ponder: Which do you think came first—the blood or the heart—and why? Did the heart in all these different species of fish, reptiles, birds, and mammals evolve before there were blood vessels throughout their bodies? When did the blood evolve? Was it before or after the vessels evolved?

      If it was before, what was it that carried blood to the heart, if there were no vessels? Did the heart beat before the blood evolved? Why was it beating if there was no blood to pump? If it wasn’t beating, why did it start when it had no awareness of blood?

      If the blood vessels evolved before there was blood, why did they evolve if there was no such thing as blood? And if the blood evolved before the heart evolved, what was it that caused it to circulate around the body?

      As explained in the following paraphrase of a publication on research into cardiac evolution by Dr. Bishopric (2005), the first to evolve was the heart, followed by the 'blood vessels:'

      The cells surrounding the endoderm-lined coelom of early multicellular life specialized to form a mesoderm in the Bilateria phylum. Covering of the coelom by mesodermal cells then formed a gastrovascular structure responsible for digestion, gas-exchange, and nutrient/waste movement to and from cells. In accordance with the observation that the tubular heart(s) of insects begin as an invagination from the gut and that continuity persists into adulthood, increased efficiency of this system was achieved in the ancestor of Ecdysoa and Deuterostoma by modifying the structure, forming a tubular heart with a single layer of contracting mesoderm that moved interstitial fluid between cells. Although still using the same systems for digestion and gas-exchange, the development of Deuterostomes marked beginning of the separation of the gastric and vascular systems. As Chordates developed and as the vascular system increased in complexity (Ex. branching of vessels), continuity between the two systems ceased, and they became independent of one another. The result was a vascular system consisting of a heart or hearts pumping fluid through vessels.

As explained by Dr. Jordan (1933), the blood was the last to evolve:

      The primary purpose of blood is tissue respiration. This necessitates the transportation of oxygen. Accordingly, efficient blood must have oxygen-carrying capacity. Under the simple conditions in certain worms the celomic fluid subserves this function in slight degree. Where a simple vascular system has appeared the blood plasma assists or takes predominance in this function. The oxygen-carrying property of these fluids is enhanced by the presence of a respiratory pigment, like hemoglobin. A still more efficient respiratory mechanism is developed with the segregation of the respiratory pigment in certain cells, first of the celomic fluid, secondarily of the blood vessels. The cells available for this purpose are the primitive lymphoid hemoblasts. In annelids these are free peritoneal elements, circulating originally in the celomic fluid. In the vertebrates they are lymphocyte-like cells derived from the reticular stroma enveloping venous sinusoids, whether in spleen or bone marrow. The shift from exclusive splenic erythrocytogenesis to predominant bone-marrow erythrocytogenesis at the level of the Anura may mean largely a gain in bulk of hemopoietic tissue necessitated by an increasing degree of metabolic activity in the transition from cold to warm blooded animals. The shift was made readily possible by reason of the favorable vascular conditions of the marrow, in essential respects closely similar to those of the spleen. The initial purpose of blood vessels was apparently to permit a more intimate circulation of plasma. Cells were only secondarily added, by process of invasion. The vascular system furnishes a ready means for the wide and rapid distribution of granulocytes and phagocytes. At the level of the higher worms, the ancestral leukocytes (lymphoid hemoblasts) became utilized for the elaboration of respiratory pigment in the service of tissue respiration, in the form of erythrocytes.

Taking note of the date on Dr. Jordan's publication demonstrates just how long research on these subjects has been going on, and what an utter lack of research Ray has done. 

      The marvelous human body (and the bodies of all the other creatures) consists of so many amazingly interdependent parts: a heart, lungs (to oxygenate the blood), kidneys (to filter wastes from the blood), blood vessels, arteries, blood, skin (to protect it all), etc. The intricate codependence of just the respiratory system and the circulatory system—not to mention all the other bodily systems—is difficult to explain.

      Many aspects of the physical world are complicated, thus coming to an understanding of them is inherently difficult. Fortunately, many people devote themselves to applying the scientific method in studying these systems. they form models that best fit the most observations and build on the research conducted by those that came before them. These scientists continue to expand and refine our understanding of how the world operates. To simply state that this process is difficult is hardly an argument against the accuracy of any given model.

      Or, consider the human eye. Man has never developed a camera lens anywhere near the inconceivable intricacy of the human eye. The human eye is an amazing interrelated system of about forty individual subsystems, including the retina, pupil, iris, cornea, lens, and optic nerve. It has more to it than just the 137 million light-sensitive special cells that send messages to the unbelievably complex brain. About 130 million of these cells look like tiny rods, and they handle the black and white vision. The other 7 million are cone shaped and allow us to see in color. The retina cells receive light impressions, which are then translated into electric pulses and sent directly to the brain through the optic nerve.

      A special section of the brain called the visual cortex interprets the pulses as color, contrast, depth, etc., which then allows us to see “pictures” of our world. Incredibly, the eye, optic nerve, and visual cortex are totally separate and distinct subsystems. Yet together they capture, deliver, and interpret up to 1.5 million pulse messages per millisecond! Think about that for a moment. It would take dozens of computers programmed perfectly and operating together flawlessly to even get close to performing this task.

      The eye is an example of what is referred to as “irreducible complexity.” It would be statistically impossible for random processes, operating through gradual mechanisms of genetic mutations and natural selection, to be able to create forty separate subsystems when they provide no advantage to the whole until the very last state of development. Ask yourself how the lens, the retina, the optic nerve, and all the other parts in vertebrates that play a role in seeing not only appeared from nothing, but evolved into interrelated and working parts.

      ... Even Charles Darwin admitted the incredible complexity of the eye in On The Origin of Species:

      To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have formed by natural selection, seems, I freely confess, absurd in the highest degree.⁴⁶

      ... Admittedly, it’s difficult to imagine that the amazing, seeing eye could have evolved gradually purely by blind chance. Something as astonishingly complex as the eye gives every appearance of having been uniquely designed for each creature. 

      Firstly, as Ray has forced me to repeat ad nauseum, although mutation is random, natural selection is the nonrandom change in allele frequencies in a population, with time, as per environmental pressures on genetic configurations that make the organisms in that population either more or less able to survive and to compete for resources—evolutionary change is far from "blind chance."

      Secondly, he is dead wrong when he says that an eye's subsystems "provide no advantage to the whole until the very last state of development." The following publication summary (posted here) by a user named 'wattsr1' (Roland, 2009) explains just how wrong Ray is:

I thought it important to summarize one article from that online journal. It is tilted “The Evolution of Complex Organs” (1). I may later deal with other articles, depending on time and inclination.

I shall refer to the author as TRG. His paper is “a general overview of the various processes that play a role in the evolution of complex biological systems”, targeting the eye as his prime example. Toward the end, TRG notes several misconceptions held by opponents of evolution, and spends some time addressing these. The end of the article contains more than three pages of references.

WARNING

Errors in this essay are mine, not TRGs. Character limitations in posting forced all sections to be significantly cut and for some very important sections, I simply refer the reader to the link at reference (1).

THE ARTICLE

~~(first part of Roland's summery omitted—view the whole summary here)~~

Case Study: The Evolution of the Eye. (Putting the above into context)

TRG begins by mentioning Paley and his argument that the intricacies of the eye could only be explained by an intelligent designer. Darwin however, offered a different kind of explanation and here the author offers in full the oft quoted (and misquoted) passage from him:-

“To suppose that the eye, with all its inimitable contrivances … can hardly considered real”.

The considerable research done since Darwin’s time has revealed many of the details of eye evolution and the recent developments of molecular biology, phylogenetics and evo-devo has accelerated and deepened this understanding. This has been so much so, that TRG’s fairly long article is only cursory review of the available information. Accordingly he does provide a three and a half page set of references in support of his review.

Definition and diversity
Eyes are defined. There can be two definitions, one which essentially incorporates anything that detects light, even if it is not related to vision. The other concerns itself only with light detection and vision.

TRG explains the evidence for the importance of vision. It arose early in the fossil record of complex multicellular life and most of the world’s phyla that do not have light sensitive organs (a third of the phyla) tend to be groups showing low diversity..

The author then discusses the types of eyes, chambered eyes like ours or compound eyes like those of spiders – both types of eyes that use reflection, refraction and shadows to form images. Most questions regarding the evolution of the eye center on the evolution of the chambered eye. These outdo compound eyes when it comes to image forming and they form the basis of most of TRG’s discussion.

Direct Adaptive Evolution: “From Eyespot to Eyeball”
TRG describes an influential paper published in 1994 (2). In this paper the authors, Nilsson and Pelger were able to provide a rough estimate for a camera type eye to develop from a light sensitive tissue. The “evolution” involved the inward folding of the flat tissue to form a deep, curved light sensitive area, the formation of a lens, and the closure of the aperture. They used well understood optical principles in their analysis, allowing that each step along the way must improve functionality (as defined by application of these principles). Each step involved only a 0.005% change in some parameter.

Doing this, the researchers found that only some 365,000 generations were required to go from flat light sensitive patch to a camera type eye.

The intermediates as “defined” in Nilsson and Pelger’s paper were abstract, and the question was, did they really exist in nature? Again, other research showed that this was the case. Organisms (not representing a line of descent in any way) having these intermediate eyes, did exist, illustrating that the Nilsson/Pelger intermediates had functionality.

However, as TRG points out, the model was a serial one of direct adaptive evolution and while it illustrated the feasibility of a rapid evolution of the eye, the nature of the model omitted a great deal of very important evolution that was required for the whole thing to become feasible. For example, it did not touch on the evolution of the light receptors, the molecules causing the refraction in the lens, etc. It is at this point that the indirect evolution comes in to play. So while the Nilsson, Pelger paper showed the feasibility of eye evolution in a direct, sequential manner, it did nothing to address all the intricacies ‘under the bonnet’ so to speak. And it is these intricacies to which TRG turns to, showing how indirect evolution (gene duplication, expatation, tinkering, etc.) all come in to play.

Photopigments and Photoreceptors
TRG notes, “vision is not the only function for molecules capable of interacting with light”. Light interacting molecules can be found in plants, bacteria and various animal tissues, and have nothing to do with vision.

The author begins by describing the important molecules making up photopigments. These are retinal – a molecule which changes shape when it interacts with light, and opsin, a molecule which sits in the cell membrane and is involved in a cascade of chemical reactions which end up causing a small electrical signal. Thus, between them the two molecules cause a light signal to become an electrical signal.

Opsin itself comes in over 1000 different molecules, representing seven subfamilies and these seem to have originated in organisms alive before the split between the protostomes (most invertebrates) and the deuterostomes (chordates, and their relatives including the echinoderms) – well before the advent of vision as we understand it. And this diversity appears to have arisen via extensive gene duplication and divergence. Such duplication and divergence would later become useful in allowing opsins to react to different wavelengths of light – thus allowing color vision.

Photopigments are membrane bound (via the opsins) and as a result the membrane needs to be modified if the number of photoreceptor cells is to be increased. Two ways exist in nature to do this – either the cells grow projections (rhabdomeric photoreceptor cells) or they grow lots of folds (ciliary photoreceptor cells). These two cell types also have different opsins and the ways in which they change photon signals to electrical signals, differ as well. It used to be thought that the rhabdomeric cells belonged only to the protostomes while the ciliary cells belonged only to deuterostomes. Research is however, turning up ciliary cells in some invertebrates and rhabdomeric cells in some vertebrates (humans).

However, when these ‘out of place’ cells turn up, they are not involved in vision, but rather are used in circadian functions.

Further evidence reveals that these cell types were present in the common ancestor to all bilaterally symmetrical animals and that a duplication followed by divergence brought about their origin. That is, they are related ‘sister cells’.

So before the vision functioning eye developed, the important molecules and cells used in transforming light to electrical signals were present in organisms but were serving different functions (e.g. circadian rhythm) and much of their evolution involved not exactly a step by step route, but rather gene duplication followed by divergence.

Lenses
TRG treats lenses in a similar fashion.

In this case though, the origin of the lens appears to be different. The tissue for the lens may well have been important initially for triggering the invagination of the eye vesicle, only later finding another function as a vehicle for focusing light. And in support of a series of intermediates for this, the early development of vertebrate embryos shows this kind of transformation, although as TRG writes, care must be taken when making similarities between development and evolutionary history.

But what about the molecules (crystallins) forming the lens itself, rather than the containing tissue? They are not descended from a common ancestral protein (like the opsins), but rather they have been co-opted from “a wide range of preexisting proteins in different lineages”. Often they are very similar, even identical to other proteins that serve different functions in the eye or in other parts in the body. Thus they provide an example of both co-option and gene sharing. For example, within a proto lens, only minor changes in the amount or position of protein expressed by existing genes would have an effect on light refraction. Natural selection would then take over to refine all this (gene expression and containing tissues) to produce the remarkable lens we see today.

But what about that initial expression of the crystallins in the proto lens, such that there could then be selection on their arrangement, abundance and other properties to enhance their refractive function? Well, recent research shows that the sea squirt, (a representative of an organism that has its roots in the lineage leading up to the vertebrates), possesses a crystallin gene that is expressed in its larval stage, in light sensing structures that consist of one single pigmented photoreceptor cell. So although it is associated with vision, it cannot be important in lens refraction, because these light sensing structures in sea squirts have no lens. The regulatory genes producing this tissue specific expression are also very similar to those that direct crystallin expression in vertebrates. This similarity is underscored by the fact that the gene can produce functioning proteins for a lens. Transfer the gene to a frog and the frog will still produce a viable lens.

The idea is that the gene for the crystallin and the regulatory genes which specify where it is expressed, already existed in the ancestor to the vertebrates and was later co-opted into the new role of vertebrate vision, by subsequent evolution.

Further confirmation of this process is related as follows:-

Originally posted by TRG

An independent example of this process was recently highlighted in an elegant study of squid lenses by Sweeny et al. [ref omitted]. In cephalopods, the lenses include only one type of crystalline, S-crystallin, which was derived by gene duplication and divergence from the liver enzyme glutathione S-transferase. The major difference between the two copies is that the S-crystallin sequence includes an exon (protein-coding region) that the liver enzyme gene does not, with the result that the crystalline protein exhibits an extra loop in its three-dimensional structure. This loop turns out to be functionally significant in the lens, and there is evidence that it began small and was accentuated by gradual selection as the crystallin took on its new visual function [reference omitted]. Thus, the history of the squid lens includes gene duplication and divergence, small scale mutation and natural selection, regulatory mutations, and co-option [reference omitted], all of which left ell-tale traces that are now being uncovered by careful scientific study

Corneas
TRG continues with a shorter discussion on the evolution of the cornea. The origin of this structure, important in refracting light in terrestrial vertebrates, is more uncertain.

How many times have eyes evolved
This question turns out to be complex and TRG spends some space dealing with it, offering an excellent discussion on homology and homoplasy and how it all depends on context as to whether a structure is homologous (similar between species due to presence in a common ancestor) or a homoplasy (similar between species but not due to presence in a common ancestor).

He writes that “eyes exhibit deep homology with regard to their underlying photoreceptors, photopigments, and regulatory genes but are homoplasious in terms of their crystallins, and overall organization”, noting that other genes, such as the Pax6 gene potentially derails even this tidy description.

TRG concludes that the question of how many times eyes evolves in an open one and that definitions (what is an eye) and level of analysis have much to do with the answer.

Constraints and Historical Contingency
TRG discusses Darwin’s notion that eyes are an example of extreme perfection, observing that in many ways, they are actually examples of imperfection. They are imperfect due to constraints imposed by history. That is, while optimized, they are only so with respect to the evolutionary path they followed. As a result they are open to many aliments. And once adaptation followed a particular path, it was unlikely to be able to reverse and follow a new and better route. “Natural selection has no foresight or objectives – it is simply the greater reproductive success of certain individuals relative to others in the population based on heritable traits that they happen to posses.”

And so TRG goes on to discuss some of these limitations visual systems acquired because of the routes they took in evolutionary history.

Misconceptions about complex organ evolution
TRG spends a couple of pages dealing with common misconceptions regarding the evolution of complex organs, PRATTS if you like. I will not discuss them, due to space limitiations, but I will mention them:-

1) supposed intermediate stages cannot be functional,
2) ancestral intermediates are missing or still present,
3) biologists propose that complex organs arose by chance,
4) all features of complex organs are optimal,
5) indirect evolution implies that various preexisting structure are assembled instantaneously into a new organ,
6) hypotheses about complex organ evolution cannot be tested,
7) an inability to explain every detail of a complex organ’s history challenges the validity of ToE.


Concluding remarks
TRG concludes by noting that the evolution of complex features is itself a complex problem and for any particular organ, may never be known with absolute certainty. However, research over the last 150 years has provided a solid understanding of the processes involved.

The do not come into being fully formed. Nor do they necessarily originate in a step by step linear fashion.

Complicated histories appear to be the norm – involving not only direct adaptive evolution, but also indirect evolution as components, evolved for different functions are brought in to fulfill new roles, to fulfill similar roles, but in different contexts and so on. Not only that, natural selection is not the only process at work. Thus fortunate duplications may occur, allowing new divergences upon which selection can act.

That is, complex organs show the signs of having traveled “a circuitous evolutionary path.

TRG offers a two page summary of a model suggested by another researcher. The model incorporates many of the ideas reviewed by the author in his paper.

My conclusion

And so it is. My essay has been very brief summary of a general overview of complex organ evolution, centering on the origin of the chambered eye. TRG offered a two page summary of a model put forward by one prominent researcher, a model that incorporates much of what he reviewed.

His paper concludes with about three pages of references which expand on the topics he discussed.

Clearly, much has been learned about the evolution of the eye – its history and the processes involved.

To do the topic of eye evolution justice, the reader of this essay really should read the online link and consult many of the references cited by TRG.


REFERENCES

(1) T. Ryan Gregory, “The Evolution of Complex Organs”, Evolution: Education and Outreach 1:358-389

Link:-

http://www.springerlink.com/content/t125078h5p201442/?p=6d485ab707654559a7aa594c0490288c&pi=3

(Click on the PDF or the HTML to get the article up)

(2) Nilsson D.E., Pelger S. “A pessimistic estimate of the time required for an eye to evolve.” Proc R Soc Lond B Biol Sci. 256:53-8. 1994

      Evolutionist Robert Jastrow acknowledges that highly trained scientists could not have improved upon “blind chance”:

      The eye appears to have been designed; no designer of telescopes could have done better. How could this marvelous instrument have evolved by chance, through a succession of random events? Many people in Darwin’s day agreed with theologian William Pauley, who commented, “There cannot be a design without a designer.”⁴⁵

      Surely the complexity and diversity of life implies a mechanism by which it was designed, and that is wasn't the result of purely random events—no one denies that. The question is, "what mechanism was it?" In examining the physical world around us, it is quite evident that it was multiple natural mechanisms, such as decent with modification via mutation, natural, neutral, and sexual selection, gene flow, genetic drift, etc—some are random, some are nonrandom.

      A watch, for instance, also implies design, however, in examining the physical world around us, it is quite evident that that beings (in this case, humans) designed it. This is quite observable. In fact, if you doubt that humans make watches, you can observe the process done before your very eyes. You can even go out and chat with the designer about it over dinner.