Research on Intelligent Design

To put together scientific advances from the perspective of Intelligent Design.

Wednesday, November 30, 2005

Limits of Nanotechnology: The Molecular Motors!

On November 28, 2005 Dr. William A. Dembski wrote:

"Ask yourself, Why do biological systems exhibit molecular machines at the smallest level permissible by the properties of matter? “Evolution” provides less and less a convincing answer."

Dr. Dembski linked then to Molecular Motors (9 Nov. 2005)

That reminded me of my previous posting to Dr. D.:

"Discover how researchers interpret aspects that can be seen as products of a common pattern and design!"

At the end, the practical applying of how an organ works or the function of a pathway, will help us to mimic such primeval designs and their plasticity; like the next one, for which we have a recent update and still is on the making.

We design based on their inherent designs:

You can find a lot of earlier and related articles by posting in Google words like the next ones: gecko lizard attach, i.e.:

Robo-Gecko - Gecko Robots

You can also check another "reverse engineering" article at:

Douglas L. Smith, “TMI, Meet IST,” Engineering and Science (LXVIII:1/2), [summer] 2005, pp. 6-15.

However, I can emphasize here my own expertise in the molecular field with a kick of genetic compatibility at the reproductive level.

To be able to see the link between "reverse engineering" and "intelligent design" we can also review the article by Jonathan Wells entitled:

Using Intelligent Design Theory to Guide Scientific Research, by Jonathan Wells, Ph.D. Senior Fellow, Discovery Institute. PCID 3.1.2, November 2004

In my work, I can see the fruitfulness of the perspective of "common design" in opposition to the Darwinian perspective of "common descent" as my search is for the differences between organisms at the molecular level and similarities between them at the biological level (read, its "genetic compatibility").

My own molecular "reverse engineering" looks for a species-specific target within a tissue-specific molecule in my molecular fight against obesity. Evolutionists tend to dismiss the existence of "species-specific" molecules or pathways, thus missing the view of such fruitful avenues of research.

The current Darwinian paradigm, by using a flawed logic does the opposite to that, as it strives to see similarities at the molecular level because of a presupposed "common descent". Surprisingly, at the same time Darwinism exaggerates the supposed differences between "genetically compatible" organisms because of this other preconceived idea that evolutionists 'must' find 'evidences' of new and incompatible 'species', which, they assume, are emerging all the time. On doing that, they ignore the thousands of already existent examples of the opposite.

"I find it telling that "evolution" (meaning the Darwinian mechanism of RM&NS) is often used in biology textbooks in a context where it could be replaced with "God" with no significant lessening of the scientific value"
(Aelfric at ARN)

A similar remark has been done recently brightly on the scientific press (in The Scientist):

"In the peer-reviewed literature, the word "evolution" often occurs as a sort of coda to academic papers in experimental biology. Is the term integral or superfluous to the substance of these papers? To find out, I substituted for "evolution" some other word - "Buddhism," "Aztec cosmology," or even "creationism." I found that the substitution never touched the paper's core. This did not surprise me. From my conversations with leading researchers it had became clear that modern experimental biology gains its strength from the availability of new instruments and methodologies, not from an immersion in historical biology." (Dr. P. Skell)

As a graduate in Biotechnology and Molecular Biology, in my research I need Genetics and Biochemistry, however I don’t need Darwinism, if you take Evolution as its synonym.

Just a practical example: Working in molecular biology of bacteria, the symbiotic bacteria with leguminous plants, I have analyzed plasmids which are like genetic modules containing programs for specific functions, i.e., nodulation of plants, antibiotic resistance, formation of surface structures, etc.

I have done selection of those bacteria to salinity to produce legumes in saline soils.

Darwinian people can say that by inserting a new plasmid in non symbiotic bacteria, then this bacteria “evolves” into a symbiotic one. Or that it “evolves” onto an antibiotic or saline resistant one. When you remove the plasmid, the bacteria turns back again to non symbiotic. When you remove the antibiotic or the salinity, many bacteria that were adapted to live only over such specific and altered environment, dies; few colonies survive and readapt to live back under normal conditions.

It seems that those colonies have an “agreement” to leave 5 % of them as the ‘backup guys, if you know what I mean.

Events in nature like these ones can 'a posteriori' and using bad logic, be rationalized as 'examples' of “Darwinism”.

A similar example of misuse of examples and of words is when Eric Lander declared that yeast was “evolving” because it duplicated its full genome. Here, another natural event, polyploidy, common in the botanical kingdom, was again 'a posteriori' rationalized as an example of “Darwinism”, when it is not.

Bback to our bacteria, when we turn them back to nature out of the lab, those artificially mutated or more deeply altered molecules (plasmids) or individuals (microbial colonies) tend to dilute and soon disappear. In our engineered Rhizobia we need to reload them every season, as they disappear under the dominance of the native ones.

Here again, mental commitment is not the same as reproducible facts to be found in nature, not in vitro.

Darwinism tried to tie to itself the field of genetics 'a posteriori' as well, after many of the facts were already discovered. I most add that Darwinism prevented the initial progress of genetics, as the next link can prove it:

Breeders active in promoting Mendel’s work were biologists generally affiliated with the USDA or state agricultural colleges and experiment stations and they aimed to combine practical public interests with theoretical science. “In sharp contrast with naturalists…” (read, Darwinists). The first mention of Mendel in a naturalist’s Darwinian journal was a dismissive comment by the editor of the Botanical Gazette, John Merle Coulter, in a review of the third edition of Liberty Hyde Bailey's Plant Breeding (Botanical Gazette, 1904, 37: 471-472). The American Naturalist was also unimpressed. Other than a passing reference in a Botanical Note of 1902, there is no mention of Mendelism until 1904, and then only in Charles Davenport's book reviews. Editorial notes and articles first appear in 1907.” (Mendel in America: Theory and Practice, 1900-1919, by D. B. Paul and B. A. Kimmelman, 1988, U. of Pennsylvania Press).

Likewise, because of a constant Darwinian insistence in ‘the origin of species’, meaning that new species can be originated from the older ones, the Darwinian concept of ‘speciation’ has prevented the progress of the study of variation or of varieties within genetically compatible groups of organisms. Examples of this are extremely abundant.

Evolution is deliberately blurring, until this day, the evident differences between varieties and species because it is 'convenient' for the Darwinian (Materialistic, Agnostic, Atheistic...) worldview.

So, people just studying variation and varieties within compatible groups of animals, because of how ‘oversold’ has been the Darwinian term of ‘speciation’ [which means precisely ‘the origin of new species’], those people concludes thinking that Darwinism is 'vital' for their studies [well, let me cry and smile at the same time here. As you are well aware, peer-reviewers of today reject any sort of non Darwinian research, no matter its quality].

I insist here and everywhere that such term of ‘speciation’ is in bad shape and is a ‘misleading’ one. When you read carefully the related literature on ‘speciation’ you end up concluding that what the authors are meaning is variation or the study of different varieties within genetically compatible organisms (or different "breeds", if you are talking about dogs).

Classic examples of the deliberate misuse of the term ‘speciation’ can be seen in the studies of birds, in which each case can be seen as evidence of variation only within their groups, like in finches, gulls, cranes, etc. The same can be said within fishes like the Gasterosteus, Cichlids, Xiphophorus, Lepomis, etc. In Mammals: Canis, Dolphins, Camels, etc. In insects: Laupala, Carabus, etc…

So, all genetic compatible related studies can be done with a better and practical use without any reference to Darwinism, as the statement of Bateson, excluded of any Darwinian context, can confirm it:
Soon every science that deals with animals and plants will be teeming with discovery, made possible by Mendel's work.”

The real and practical progress was and is done thanks to Mendel’s work, not Darwin’s.

Neo-Darwinism was the Darwinists attempt to merge both, blurring until now the practical progress of genetic compatibility and variation within similar groups of organisms.

Other work that doesn't need Darwinism includes the microarray analysis of knock out mice. Using 'common design' to produce antiobesity targets which are tissue-specific (read adipocytes) and species-specific (read humans) with an Intelligent Design perspective!

Saturday, November 26, 2005

Design principles of a bacterial signalling network

Nature 438, 504-507 (24 Nov. 2005)
Markus Kollmann, Linda Løvdok, Kilian Bartholomé, Jens Timmer and Victor Sourjik

From the Abstract:
"Cellular biochemical networks have to function in a noisy environment using imperfect components. In particular, networks involved in gene regulation or signal transduction allow only for small output tolerances, and the underlying network structures can be expected to have undergone evolution for inherent robustness against perturbations. Here we combine theoretical and experimental analyses to investigate an optimal design for the signalling network of bacterial chemotaxis, one of the most thoroughly studied signalling networks in biology".

"Moreover, the underlying topological design principles compensating for intercellular variations seem to be universal among all known or predicted bacterial chemosensory systems."

[bipod wrote: "The “evolution of robustness against perturbations” is a worthy research project, don’t ya think".]

In that same link [bipod's] we can read the next comments:

"... a “gene net” [is] a gathering, a grouping of a network of gene actions and their products into discrete units during the course of development. ... The gene nets must become isolated from one another and proceed independently. It is not total independence; they still must keep in touch with one another, for this is the way pattern formation is achieved. But the signals between them are likely to be few and quite specific. ... (An interesting aside: It has been pointed out to me [to Krauze] by my former colleague Jon Seger that a properly structured “modular” computer program is put together in a way that is analogous to the gene nets postulated here.)”

Krauze's Reference:
John Tyler Bonner, The Evolution of Complexity by Means of Natural Selection (Princeton University Press, 1988), pp. 174-5.

AdR commented:

"That sounds much like ‘design-by-contract’.

"So studying the underlying design, one can deduct the gene organization."

"...gene nets show a striking similarity to the design patterns that software architects would use. The best (and scientific) approach would then be that you start modelling the gene nets on software methodologies... That’s more than neodarwinism ever dreamed of."

"The question in this stage is whether it is a coincidence that the gene nets show similarities with design patterns. I’d say it is not, because the design patterns just define ‘best practices’ for the architecture of complex systems."

Friday, November 25, 2005

Non-Linear Biology, Independent Convergence and Independent Solutions.

Convergent Evolution.
(RealPlayer, 56 min)

A seminar by Dr. Fazale Rana on "the surprising ability of nature to repeatedly arrive at nearly identical DESIGNS (e.g. the eye of the octopus and the vertebrate eye) without descent from a common ancestor."

Thursday, November 24, 2005

Lyrics and Song, "Accidentally", by Good Seed

Good Seed
PFAL (Power For Abundant Living, according to John 10:10)
mp3 [647kb; 3:41 min, 24kbps]

To watch the rolling clouds move with the night time to the day
And watch the burning sun fall to the sea.
Something deep inside tells me that what I've been seen
Just could not happen accidentally.

Hear the sea gull cry, spread their wings and watch their fly
And hear the mighty tide rolling
To think that is affected by the moon so far away
I know that it’s not coincident.

Some say that it all happened one billion years ago
Some say, Lord we will never know
But God said, "In the Beginning"
And that's good enough for me.

He created the Heavens and Earth for you and me.

To know that we are just wonderful sons of God
And all is ours as far as we can see.
To think that we are more perfect than the finest machine
To know that we are God's Masterpiece.

Some say that we all came from just one single cell
Some say, Lord, it's just too hard to tell
But I'll say, let's give the credit where the credit is due
God made, formed then created me and you.

Just could not happen accidentally.

[On USA's Thanksgiving Day!]

Note: If you want to own the full Albums of "Good Seed", performers of "Accidentally" in RealPlayer, go to:

And look for the group "Good Seed", which also offer their songs "Born Again" and "Resurrected"; Other songs: Dean Ellenwood - Pentecost Song (Gentle Songs); Lisa Tracy - Happy To Be Here (Emmaus); Patty (P.K.) Krywos - All I'm Meant to Be; Jack Folz (w. Kathy Mabry) - Good Plan; Dennis R. Foster - Take Care of You (Sheri's Song) (No Darkness... At All); David Trussa - The Windows of Heaven (title cut, fragment), Craig Peterson (with Greg Anderson) - Autumn Leaves (The Craig Peterson Project, Jazz Standards); and for your Windows Media Player: A Land of Milk and Honey (The Singing Ladies, 2005), (We Are) Valiant for the Truth (The Present Truth, 2004), and Lift Up Your Eyes (The Singing Ladies featuring Claudettee Royal, 2004.)

Wednesday, November 23, 2005

Bionanomachines in Japan and Intelligent Design classes in Australia

If in the U.S.A. Intelligent Design in Science is not allowed, both in classrooms and in laboratories, other countries more open to detecting the precious designs in nature and to copy them are going to take over the next step for the freedom and progress in science!

The irony is that the U.S.A. was the initial cradle for Intelligent Design in Science!

The next amazing movie demonstrates the discovery, in Japan, of the gears and coordinated functions of the Bacterial Flagella (Windows Media Video, 36.12 MB):

A written interview entitled “Revealing the mystery of the bacterial flagellum — A self-assembling nanomachine with fine switching capability” featuring Keiichi Namba, Professor from Japan (Graduate School of Frontier Biosciences, Osaka University) can be seen at:

The Advance of Intelligent Design in the Colleges of Australia can be seen at:

Where we read that “More than 100 schools are already teaching intelligent design as science, alongside the mandatory curriculum requirement to study evolution.” And 3,000 Schools have been showing to their students the great documentary that is “Unlocking the Mystery of Life : Intelligent Design” (in RealPlayer):

This video has been opening the minds and eyes for a new generation of students and researchers.

New students will emerge without the pernicious Evolutionary Darwinian thinking thanks to the faithful efforts of the U.S.A. and of its love for progress and freedom!


Dr. William Dembski's Update (USA's Day of Thanksgiving to God! Nov. 24, 2005, 8:17 am)
Unveiling of New ID Website in Australia
Intelligent Design Network Australia
The unveiling of this website coincides with the distribution of Unlocking the Mystery of Life to 3000 High Schools.

Tuesday, November 22, 2005

John A Davison and the discrete nature and stability of species

Yesterday, Dr. John A. Davison posted a comment presenting his view that:

"Intelligent design is not a matter for debate. It is a mandatory assumption without which nothing in either ontogeny or phylogeny can ever make sense."
As I have declared elsewhere, on reading the writings of John A. Davison I have learned that the role of sexual reproduction is to prevent evolution. I have learned also that the origin of reproduction among living organisms was, in Dr. Davison's words "an independent occurrence..."

Recently, Dr. John A. Davison wrote a brief Essay for ISCID:

Julian Huxley’s Confession (30 Oct. 2005, PDF)

Abstract: The history of any science often reveals aspects of that science that have escaped attention in the intervening years. As someone so wisely put it - ”The one thing we learn from history is that we don’t learn from history.” I present, in this brief essay, one particularly revealing demonstration of that phenomenon, one that is especially significant to the current status of the Darwinian hypothesis.

From the Full Text:

"Where did he [Julian Huxley] get the notion that evolution was finished? This I feel I was able to do [to discover] from a paper by the anti-Darwinian paleontologist Robert Broom. Huxley and Broom had corresponded on the subject as revealed by Broom:

"It is important to remember that Darwin wholeheartedly subscribed to Lyell’s Uniformitarian Doctrine; namely, that the forces we now see shaping the world are the same forces that have operated in the past. While that is what most geologists still accept there is no a priori justification for extending that concept to the living world.... And a few zoologists are beginning to recognize that evolution is slowing down, if not quite stopped. In a letter I had from Professor Julian Huxley only a few months ago he says, ‘I have often thought about your idea of the fading out of evolutionary potency, and though I cannot pretend to agree with some of the philosophical corollaries which you draw from it, I more and more believe that it is of great importance as a fact.’” [Broom, R. (1933) Evolution - Is there intelligence behind it? South African Journal of Science, 30: 1-19]."

I [Dr. Davison] was disappointed to discover that the only reference Huxley made to Broom was in a footnote on page 568: “A small minority of biologists, such as Broom (1933), still feel impelled to invoke ‘spiritual agencies’ to account for progressive evolution, but their number is decreasing as the implications of modern selection theories are grasped.” [Huxley, J. (1942) “Evolution: The Modern Synthesis.” Harper, New York and London.]

[Dr. Davison notes:] The reference to “spiritual agenciesby Broom was his suggestion that there had been a Plan, a word he capitalized.

The reason I [Dr. Davison] have presented this brief essay is to demonstrate that, even from within the Darwinian establishment, grave doubts have surfaced concerning its basic tenets from one of their most prominent spokespersons. I am not surprised Huxley is rarely referenced these days.

Davison's recent comments:

Referring to ontogeny and phylogeny:

"Neither in the one nor in the other is there room for chance." Leo Berg, Nomogenesis, page 134.

When Schindewolf published his "Basic Questions in Paleontology" in 1950, it was perfectly acceptable to say as he did such things as, when comparing the skulls of marsupial and placental saber-toothed cats:

"The similarities of form are present even in such details as the structure of the flange on the lower jaw, DESIGNED TO GUIDE AND PROTECT THE UPPER CANINES." [page 261 in the 1993 English translation. (my [Dr. Davison's] emphasis)].

Dr. Davison affirms:

"I really don't know what else to say except that I enjoy immensely being a part of an intellectual revolution in progress.

It is quite exhilarating."
Let's see other of the vital statements by Dr. Davison:

"Sexual reproduction tends to prevent rather than promote chromosome restructuring."
This provides a reasonable explanation for the stability of fossil species as Julian Huxley realized at the end of his Synthesis.

"Huxley’s conviction that evolution is no longer going on has been completely ignored by the neoDarwinians."
As seen above, Dr. Davison discovered that Broom and Huxley had corresponded on this matter as early as 1933.

"Leo Berg insisted that chance played no role in either ontogeny or phylogeny" [Berg, L. (1969) Nomogenesis; Evolution Determined by Law. M.I.T. Press, Cambridge. (Original Russian edition 1922.)]
We also read in

"A sufficient factual body now exists to warrant serious consideration to the proposal that there has been, as Robert Broom had suggested, a teleological origin (plan) for biological information" [and, I must add, its expression].
John A. Davison also declares that there is a

"discrete nature and stability of the vast majority of all species, both recent and fossil," "they were produced by instantaneous all-or-none devices (chromosome restructurings) which, by definition, can have no intermediate states."

"I accept the physiological definition of species. Two forms that can produce a viable hybrid will be considered separate species if that hybrid proves to be sterile."

"... in nature, sexual reproduction seems incapable of proceeding beyond the subspecies. I am unaware of a single instance of the production of a new species through the known agency of sexual reproduction.";f=6;t=000481

"Sexual reproduction [is] a highly conservative device... a virtual standstill... a function which serves to prevent rather than promote progressive change."

"The capacity of the sexual reproductive mode [is] to fine-tune the genetic makeup."

"Sexual reproduction has one great advantage in its capacity to produce virtually unlimited variation within a narrow range. The sexual mode then could be very useful in adapting the organism to minor environmental changes."

"Sexual reproduction is incapable of producing progressive evolutionary change."

"Needless to say, the realization of this prospectus will have a profound effect on the way in which man regards his position in the universe."

"The Darwinians might simply say that the sexual model could also produce chromosome and gene homozygosity through the inbreeding associated with small or insular populations. It is precisely here that their hypothesis fails. For example, the biota of the Galapagos Islands closely resembles that of neighboring Ecuador. Darwin's celebrated finches have all been placed in the genus (or subgenus) Geospiza. Since they are all extremely similar, it is not surprising to learn that they produce spontaneous fertile and genetically fit hybrids" [Grant PR, Grant BR. Genetics and the origin of bird species. Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):7768-75.].

"[Then, Dr. Davison compares dogs, declaring that] in addition to size, great variations in [canine] coat quality, color and temperament have been produced. All of these differences are due to the action of Mendelian genes segregating and recombining in sexual reproduction, with the result that dogs are still able to hybridize freely with wolves. The hybrids are of course fertile which is to say that they are not really [different] species-hybrids at all."

"Thus, by a physiological criterion they [finches] are one species and, as with dogs and goldfish, no significant evolution has really taken place. They too reproduce sexually."

"The standard Darwinian response is that evolution takes too long to be observable, an assumption which renders that proposal untestable."

"The [evolutionarily conceived] horse series shows an increase in size coupled with a decrease in digits. However, this series is not linear so the intermediate organisms cannot be arranged in any certain fashion. Furthermore, they differ from one another in so many independent factors that they must be relegated to separate genera. What we actually observe is the appearance of discrete phenotypes with no evidence of what might be described as missing links. This is exactly what one sees when one observes extant related organisms."

"There are limits to the developments possible, and these limits follow a law (the Law of the Reversion to the Average)."

"I know from my experience that I can develop a plum half an inch long or one two and a half inches long, with every possible length in between, but I am willing to admit that it is hopeless to try to get a plum the size of a pea, or one as big as a grapefruit" [Taken from: Burbank, L. (1939) Partner of Nature. D. Appleton-Century Co., New York; Burbank, L., 1931 The Harvest Of The Years. Houghton Mifflin Co., Boston, New York.]

"The ratio of five to one in the lengths of his plums corresponds to a mass ratio of 125 to 1 (five cubed), which agrees favorably with what man has been able to achieve with dogs (Great Danes versus some of the miniature breeds) or, for example, with the size of the fruits of tomato varieties. Burbank admits the futility of exceeding the limits he indicates and the prospect of speciation apparently never crosses his mind."

"Mendelism is of course the genetics associated with sexual reproduction... Luther Burbank and William Bateson each independently questioned the capacity of sexual reproduction to support evolutionary change... These were not mere coincidences but reasoned conclusions reached after a careful consideration of all the facts which were then available.

None of this can be accommodated within the Darwinian model. We owe these men [Burbank, Bateson, etc...] a great debt... i.e. sexual forms are incapable of progressive change. The obvious inference is that sexual reproduction is the "Blind Alley" of evolution."

"Note Bateson's use of the expression blind alley." "Bateson had the insight to recognize and the courage to admit." "Just as William Bateson indicated even before 1900, I too find it amazing how long the Darwinian view has prevailed in the face of an enormous and continually growing body of information with which it cannot possibly be reconciled."

"Subspecies are actually, therefore, neither incipient species nor models for the origin of species. They are more or less diversified blind alleys within the species"

"The male-determining (Y) chromosomes lack, both quantitatively and qualitatively, the semblance one would expect had the four genera [man, chimpanzee, gorilla and orangutan] evolved through sexual reproduction. Other differences include alterations in chromosome ends or telomeres as well as variations in the position of nucleolar organizers..." [Davison on a critical review of: Yunis JJ, Prakash O. The origin of man: a chromosomal pictorial legacy. Science. 1982 Mar 19;215(4539):1525-30.]

"It has yet to be demonstrated that any creature reproducing by obligatory sexual means is capable of evolution beyond the generic level. Since 1984 no response to that challenge has been forthcoming and so I repeat the proposition. I hope the present paper will serve to stimulate a lively response from the community of evolutionists."

"It has yet to be demonstrated that any diploid organism, reproducing by obligatory sexual means, is capable of exceeding the subspecies level..." "I place the burden of proof on the Darwinians by challenging them to present karyotypic, genetic, taxonomic, fossil, or any other kind of evidence indicating that true species, genera, families, or any of the higher taxonomic categories have ever been produced or can now be produced through the agency of sexual reproduction. I, in general agreement with [Michael J.D.] White, can find nothing in support of that proposition." [Davison on commenting, White, M.J.D. (1973) Animal Cytology and Evolution. Comstock Publ. Co., Ithaca, New York; and Davison, JA (1984) J. Theor.Biol. 111: 725-735.]

"I agree with Michael J.D. White... there is no compelling evidence that point (base pair) mutations have ever played a role in evolution beyond the production of varieties or subspecies. Quite the contrary, all expermental attempts with selection for such mutations has met with not only failure but with a decrease in general fitness... The time is long past due to consider some alternatives to the Darwinian model" [Posted by nosivad (Member # 767) on 14. April 2004, 07:34]

"Like differentiation, ecological succession and growth, phylogeny has been, in my opinion, a self-limiting process in which sexual reproduction has served to terminate and stabilize the creative sequence. This view demands only the original actions of an incomprehensibly intelligent creator" [Posted by nosivad (Member # 767) on 20. April 2004, 08:01]

"Why might some insist that evolution is still in progress? I propose it is in large part due to the acceptance of authority. For centuries, Aristotelian physics was accepted because it made intuitive sense that the heavier an object was, the faster it would fall... Darwin and Wallace unhesitatingly accepted the authority of Lyell and his doctrine of Uniformitarianism."
"Is sexual reproduction incapable of supporting evolutionary change?" [a question raised by Dr. Davison, who then proceeds to answer it by his studies on the evidence.]

The Russian cytologist N.N. Vorontsov was one of the first to call attention to the independence in sex determination: i.e., "an independent occurrence of the XX-XY system in Melandrium as well as in many Insects and Mammals, whereas the ZW-ZZ system evolved independently in Trichoptera, Lepidoptera, Serpentes and in Aves [Birds]. Against the background of these facts it is unclear whether the male species of different groups are homologous to each other or not; they appear to be nonhomologous." [Vorontsov, N. N., 1973 The Evolution Of The Sex Chromosomes. In: Cytotaxonomy and Vertebrate Evolution, edit. A. B. Chiarelli and E. Capanna. p. 646. Academic Press, New York. See page 646]

"Notice specially Vorontsov's indication:

"Males seem to be nonhomologous, a conclusion that would, by definition, demand that they were independently produced and accordingly could not be involved in a macroevolutionary continuum."

"Vorontsov says:

"Just as the transition from isogamy to anisogamy and to oogamy took place independently of each other in the various phyla of plants so the formation of mechanisms of the cytogenetical sex determination with differentiated heterochromosomes follows the same pattern in various kingdoms and phyla and results in an independent occurrence of the XX-XY system [Mammals]" and "the ZW-ZZ system [Birds]."

"In addition to the devices mentioned by Vorontsov, other independent mechanisms include, "In the social insects, the female is diploid, the male haploid, a situation that also occurs in certain rotifers. In addition to these chromosomal mechanisms, the temperature during sensitive embryonic stages can serve to determine the sex as in some turtles and crocodilians. Sex reversal is common in certain animals as well as other forms of sex determination such as the age of the eggs when fertilized. This huge and varied literature has been reviewed by Bull [Bull, J.J. (1983) Evolution of Sex Determining Mechanisms. Benjamin Cummings, Menlo Park.] This is hardly the sort of situation one would anticipate if sexual reproduction were a requirement for evolutionary change."

"Any theory of evolution must recognize and incorporate nonhomology when that becomes evident. It is to the credit of Vorontsov that he did so when describing the various sex determining systems which have evolved. They have indeed evolved independently and accordingly are by definition nonhomologous. Another example of nonhomology which correlates beautifully with the various sex determining devices which have evolved is demonstrated by the origins of the germ cells in contemporary vertebrates."

"Not only are the cytological mechanisms of sex determination often nonhomologous but the expression of the sexual phenotype may also be nonhomologous. For example, both Drosophila and all mammals have a heteromorphic (different form) XY male - XX female system. However, sexual differentiation is mediated at the local cellular level in Drosophila but by means of hormones in all mammals. It is obvious that the two systems are in no sense related but independent."

"One of the hitherto most baffling features of vertebrate ontogeny is offered by the origin of those cells (oogonia and spermatogonia) destined to become the eggs and sperm."

"I regard this conclusion as inescapable."

"All known mammals have male heterogamety with the familiar XY male and XX female. By contrast, all birds are the opposite with ZW females and ZZ males." And a similar dichotomy "within the amphibia with most urodeles (newts and salamanders) like birds and all anurans (frogs and toads) except Xenopus like mammals. In reptiles examples of both kinds occur as well as temperature determination of sex in certain turtles and crocodilians."

"Among the arthropods similar differences prevail. Diptera generally have heterogametic males while Lepidoptera are like birds and urodeles with heterogametic females. In the social insects a haplo-diplo (male-female) system operates. In certain parasitic forms even the size of the host can determine the sex of the parasite. The literature is well reviewed in Bull's (Bull 1983, ref. given above) book significantly titled "Evolution of Sex Determining Mechanisms".

"The vertebrate gonad develops from portions of the urogenital ridge, a bipartite structure consisting of an outer cortex and inner medulla. The gonadal cortex develops into the ovary, the medulla into the testis. Oddly the vertebrate gonad is a sterile organ completely incapable of functioning as a germinal epithelium. During embryonic development the gonad receives, by a process of invasion, presumptive germ cells from extra-gonadal sources. Gonads failing to receive these cells remain sterile, while those receiving presumptive germ cells differentiate with the sex of the host organ not that of the donor cells. Thus the gonad proper is clearly a part of what Weismann called the somatoplasm."

"The important point to make here is that the sources as well as the means of induction and modes of reaching the gonad vary in nonhomologous fashion from vertebrate group to group in a manner which remarkably parallels the equally nonhomologous modes of sex determination."

"In mammals, including man, the presumptive germ cells are first seen in the region of the allantois corresponding roughly to the position of the urinary bladder in the adult. From here they migrate anteriorly and laterally to enter the embryonic gonad. In birds the future germ cells originate outside the embryonic axis in the extra-embryonic endoderm consisting of the so-called germinal crescent anterior and lateral to the head. From here they enter the vitelline circulation and after a period in the circulatory system invade the gonad after first passing through the walls of the venous circulation."

It is in the amphibia that the most dramatic differences are manifest in the origin of the germ cells. From their monograph Nieuwkoop and Sutasurya write (see below):

"When comparing PGC formation in the urodeles with that in the anurans, one is unavoidably led to the conclusion that not only do the PGCs originate from two different sites in the two groups, but that there are moreover two fundamentally different mechanisms at work... In the anurans all the PGCs originate from the endodermal moiety of the egg in the vicinity of the vegetal pole, whereas in the urodeles they arise from the animal 'ectodermal' moiety, more particularly the presumptive lateral plate mesoderm in the ventral to ventro-lateral equatorial region. In the anurans all the descriptive and experimental evidence pleads in favor of the predetermined nature of the PGCs, based on the presence of a germ-cell-specific sytoplasmic component, the germinal plasm, which is present in the embryo from the very beginning of development. In constrast, in the urodeles the PGCs develop strictly epigenetically from common, totipotent cells of the animal moiety under the inductive influence of the ventral yolk endoderm" [Nieuwkoop, P.D. & Sutasurya, L.A. (1979) Primordial Germ Cells in the Chordates. Cambridge Univ. Press, Cambridge.]

"Note the clear correlations between nonhomologous modes of sex determination and equally nonhomologous methods and sources for germ cell formation. As I have indicated elsewhere any theory of evolution must include in its postulates these fundamental differences (Davison 1984, see above). As well as I can determine the neo-Lamarckians, the neo-Darwinians, and the Creationists all fail even to acknowledge the existence of this experimental and descriptive literature, not to mention its significance for their particular views. In that respect the Creationists are missing an opportunity for their case since nonhomology means separate origin, which prima facie might be interpreted to mean special creation."

"First, since the definitive sex cells of the various vertebrate groups cannot be homologized, they cannot be considered as ancestral cell lineages. Rather they are secondary or derived lineages correlated in their origins with the equally independent and nonhomologous invention of sexual reproduction."

"The actual facts are as follows. In birds the cells destined to become the germ cells first appear in the extra-embryonic endoderm (germinal crescent) anterior to the head of the developing embryo. Incidentally, this region has no homologue in the hatched bird as the extra-embryonic endoderm is, by definition, resorbed as nutrient for the developing chick. From there the presumptive germ cells enter the circulatory system and, after a period of time in the bloodstream, penetrate the walls of the venous circulation and invade the gonad where they differentiate into the definitive gametes. In mammals the presumptive germ cells first appear in the endoderm of the allantois, a structure destined to become the urinary bladder of the adult. From here they migrate in amoeboid fashion anteriorly and laterally to reach the gonad where they complete their differentiation. Thus, there is no way that the reproductive cells of mammals can be homologized with those of birds as they originate from opposite ends of the embryonic axis and reach the gonads by completely different means."

"Similarly, the eggs and sperm of the Anura (frogs and toads) arise in an entirely different way than do those of the Urodela (salamanders and newts). Staining methods reveal that in frogs, the cells destined to become the germ cells result from the presence of preformed granules near the vegetal pole of the unfertilized egg, a region destined to become part of the endoderm. From there they move first dorsally and then laterally to enter the embryonic gonads which are mesodermal structures. In salamanders the presumptive germ cells first appear in the mesoderm as a result of the inductive action of the underlying endoderm on the lateral plate mesoderm. From there they migrate medially to invade the embryonic gonads."

"Thus the germ cells of the Anura and the Urodela do not even arise from the same germ layer! In short, there is not a scintilla of evidence to support the notion of germ cell continuity. The details of these differences have been discussed elsewhere (Davison 1984). Also, the vertebrate gonad is a sterile organ unable to produce germ cells from its own epithelium (Nieuwkoop and Sutasurya 1979). Instead, the testis or ovary receives its complement of eggs or sperm by a process of invasion from extragonadal sources early in development. Since the sources and modes of invasion are not homologous from group to group, the continuity of the germ plasm is a myth."

"Note that these nonhomologies correlate favorably with the nonhomologous devices that serve to determine the sex differences…"

"Repeating the simple facts again: "There is no way that the reproductive cells of mammals can be homologized with those of birds. Similarly, the eggs and sperm of frogs arise in an entirely different way than do those of salamanders and accordingly cannot be assumed to exhibit homology. In short, there is not a scintilla of evidence to support the notion of the continuity of the germ plasm" [between the different real species.]

"These nonhomologies correlate beautifully with the equally nonhomologous devices that determine the sexes."

"This remarkable conclusion is of course totally incompatible with the neo-Darwinian concept of the evolutionary process."

"Understanding the nature of sexual reproduction and the manner in which eggs and sperm are produced:

"In all diploid animals and plants the chromosomes occur in pairs. One member of each pair comes from one parent, the other from the other parent. Thus, each egg or sperm must have only one of each kind of chromosome, a condition known as haploidy. The process by which this reduction takes place is known as meiosis or chromosome reduction... If one were to imagine the simplest way that chromosome reduction could take place it might be as follows. The chromosomes would align in pairs and a single division would take the chromosome number from diploid to haploid. Not a single living creature undergoes meiosis in this way. Instead, each chromosome is duplicated taking the chromosome number from diploid to tetraploid. Then while they are in alignment (synapsis) a very important step occurs. Breaks occur in some of the chromosomes and exchanges occur between the original pairs of chromosomes a phenomenon known as crossing over. Following this event, the chromosomes undergo the first meiotic division returning the chromosome number from tetraploid to diploid... The two originally identical chromosomes (known as sister strands) always remain together. Note that this first meiotic division is a perfectly valid form of diploid reproduction... meiosis involves two steps."

Some References:

Davison JA. A Prescribed Evolutionary Hypothesis. Riv Biol. 2005 Jan-Apr;98(1):155-65. Review.

Davison, John A. An Evolutionary Manifesto: A New Hypothesis For Organic Change (2003). PCID Journal.

Davison, John A. Evolution as a Self-limiting Process (1998). Rivista di Biologia (Biology Forum), 91:2 199-220.

Davison, John A. The Blind Alley: Its Significance for Evolutionary Theory (1993). Rivista di Biologia (Biology Forum), 86:101-110.

Davison, John A. The Case for Instant Evolution (2004). ISCID Brainstorms.

Davison, John A. Is Evolution Finished? (2004). ISCID Brainstorms. In PubMed.

Davison, JA (1984) Semi-meiosis as an Evolutionary Mechanism. J. Theor.Biol. 111: 725-735.

Davison JA (2004) ISCID Brainstorms and other boards: , , , ,

The Non-Darwinian Mechanism of Sexual Reproduction (Research guidelines provided by John A. Davison)


Other Species-Specific Sexual Issues.

Bookbinder LH, Cheng A, Bleil JD. Tissue- and species-specific expression of sp56, a mouse sperm fertilization protein. Science. 1995 Jul 7;269(5220):86-9.
[From the Scripps Research Institute, San Diego, California]

"Sperm-egg recognition and binding in mammals is largely species-specific"
"sp56 expression is restricted to mouse spermatids and the presence or absence of sp56 on sperm from different species accounts for species specificity of sperm-egg recognition in mice."
"Suggesting that molecular recognition between the sperm head plasma membrane and the Zona Pelludica (ZP) surface involves different molecules in different species… Mouse and hamster sperm, which bind to the ZP of mouse eggs, contained sp56. However, sp56 was not detected in guinea pig.sperm or human sperm, which do not bind to mouse egg ZP… If sp56 mediates sperm-egg recognition in mouse, its presence or absence accounts for the species specificity of that event."

It was performed immunological and biochemical identification of sp56 and also the identification of its transcript.

Some Appendix References:

1-) Schmell ED, Gulyas BJ. Mammalian sperm-egg recognition and binding in vitro. I. Specificity of sperm interactions with live and fixed eggs in homologous and heterologous inseminations of hamster, mouse, and guinea pig oocytes. Biol Reprod. 1980 Dec;23(5):1075-85.

2-) Moller CC, Bleil JD, Kinloch RA, Wassarman PM. Structural and functional relationships between mouse and hamster zona pellucida glycoproteins. Dev Biol. 1990 Feb;137(2):276-86.
" Like mouse ZP2, hZP2 undergoes limited proteolysis following artificial activation of hamster eggs in vitro. Results of in vitro assays employing intact eggs and isolated zonae pellucidae demonstrate that hamster eggs possess a ZP2-proteinase which has a substrate specificity similar to that of the mouse enzyme."

3-) Inoue M, Wolf DP. Sperm binding characteristics of the murine zona pellucida. Biol Reprod. 1975 Oct;13(3):340-6 [see also, Inoue M, Wolf DP. Fertilization-associated changes in the murine zona pellucida: a time sequence study. Biol Reprod. 1975 Dec;13(5):546-51.]

4-) Bedford JM, Cross NL. Normal penetration of rabbit spermatozoa through a trypsin- and acrosin-resistant zona pellucida. J Reprod Fertil. 1978 Nov;54(2):385-92 [see also, Moore HD, Bedford JM. An in vivo analysis of factors influencing the fertilization of hamster eggs. Biol Reprod. 1978 Nov;19(4):879-85; Moore HD, Bedford JM. Ultrastructure of the equatorial segment of hamster spermatozoa during penetration of oocytes. J Ultrastruct Res. 1978 Feb;62(2):110-7; Bedford JM, Anat. Rec. 188:477, 1978]

5) Lambert H. Role of sperm-surface glycoproteins in gamete recognition in two mouse species. J Reprod Fertil. 1984 Jan;70(1):281-4.

6) Cheng A, Le T, Palacios M, Bookbinder LH, Wassarman PM, Suzuki F, Bleil JD. Sperm-egg recognition in the mouse: characterization of sp56, a sperm protein having specific affinity for ZP3. J Cell Biol. 1994 May;125(4):867-78.
"Immunohistochemical and immunoblotting studies, using monoclonal antibodies, demonstrated that sp56 is a peripheral membrane protein located on the outer surface of the sperm head plasma membrane, precisely where sperm bind ZP3." "Collectively, these results suggest that sp56 may be the sperm protein responsible for sperm-egg recognition in the mouse."

7) Suzuki-Toyota F, Maekawa M, Cheng A, Bleil JD. Immuno-colloidal gold labeled surface replica, and its application to detect sp56, the egg recognition and binding protein, on the mouse spermatozoon. J Electron Microsc (Tokyo). 1995 Jun;44(3):135-9.

8) Bleil JD, Wassarman PM. Identification of a ZP3-binding protein on acrosome-intact mouse sperm by photoaffinity crosslinking. Proc Natl Acad Sci U S A. 1990 Jul;87(14):5563-7.
"These and other findings suggest that this protein may be a "ZP3-binding protein" that, together with the sperm receptor, supports species-specific binding of mouse sperm to unfertilized eggs."

9) Bleil JD, Wassarman PM. Mammalian sperm-egg interaction: identification of a glycoprotein in mouse egg zonae pellucidae possessing receptor activity for sperm. Cell. 1980 Jul;20(3):873-82.

10) Wassarman PM. Sperm receptors and fertilization in mammals. Mt Sinai J Med. 2002 May;69(3):148-55.
"During fertilization in mammals, sperm must first bind in a species-specific manner to the egg s thick extracellular coat, the zona pellucida."

11) Wassarman PM, Litscher ES. Towards the molecular basis of sperm and egg interaction during mammalian fertilization. Cells Tissues Organs. 2001;168(1-2):36-45.
"mammalian fertilization is a carbohydrate-mediated event. It is possible that changes in the structure of these oligosaccharides (e.g., composition, sequence, linkages, modifications, etc.) could account for species-specific binding of sperm to eggs."

12) Wassarman PM. Fertilization in animals. Dev Genet. 1999;25(2):83-6.
"species-specific binding of sperm to eggs"

13) Litscher ES, Wassarman PM. Recombinant hamster sperm receptors that exhibit species-specific binding to sperm. Zygote. 1996 Aug;4(3):229-36.
"Unlike hamster egg hZP3, which binds to both mouse and hamster sperm, EC-hZP3 and CHO-hZP3 exhibits species-specific binding to hamster sperm and induce hamster sperm, but not mouse sperm, to undergo the acrosome reaction in vitro... recombinant forms of mammalian sperm receptors may be useful in assessing the molecular basis of species-specific fertilisation in mammals."

14) Wassarman PM. Profile of a mammalian sperm receptor. Development. 1990 Jan;108(1):1-17.
"Complementary molecules on the surface of eggs and sperm are responsible for species-specific interactions between gametes during fertilization in both plants and animals... ZP3 gene expression is an example of oocyte-specific and, therefore, sex-specific gene expression during mammalian development... unique nature, highly restricted expression, and multiple roles of ZP3..."

15) Kinloch RA, Wassarman PM. Profile of a mammalian sperm receptor gene. New Biol. 1989 Dec;1(3):232-8.
"ZP3 regulates the initial species-specific interactions between male and female mouse gametes."

16) Wassarman PM. The biology and chemistry of fertilization. Science. 1987 Jan 30;235(4788):553-60.
"In both mammals and nonmammals, the pathway that leads to fusion of an egg with a single sperm consists of many steps that occur in a compulsory order. These steps include species-specific cellular recognition."

17) Wassarman PM, Bleil JD, Florman HM, Greve JM, Roller RJ, Salzmann GS. Nature of the mouse egg's receptor for sperm. Adv Exp Med Biol. 1986;207:55-77.
"sperm must bind to the outer margin of the zona pellucida. Such binding is mediated in a relatively species-specific manner by "sperm receptors" in the zona pellucida"

18) Keichline LD, Wassarman PM. Developmental study of the structure of sea urchin embryo and sperm chromatin using micrococcal nuclease. Biochim Biophys Acta. 1977 Mar 2;475(1):139-51.
"…the oligomers are nearly exact multiples of the respective monomers. These results are discussed in relation to those studies which have shown that the histone complement of the sea urchin embryo and sperm changes during development."

Friday, November 18, 2005

Problems with Characterizing the Protostome-Deuterostome Ancestor

Problems with Characterizing the Protostome-Deuterostome Ancestor by Paul Nelson and Marcus Ross.


"Since Darwin’s time, the origins and relationships of the bilaterian animals have remained unsolved problems in historical biology (Conway Morris 2000).

One of the central difficulties is characterizing the common ancestor of the protostomes and deuterostomes.

We argue that an unresolved conceptual puzzle has plagued the many attempts to describe this Urbilaterian, or, in Erwin and Davidson’s (2002) terminology, the protostome-deuterostome ancestor (PDA).

Any organism sophisticated enough to be a realistic candidate for the PDA, with such characters as an anterior-posterior axis, gut, and sensory organs, must itself have been constructed by a developmental process, or by what we term an ontogenetic network (Ross and Nelson 2002).

But the more biologically plausible the PDA becomes, as a functioning organism within a population of other such organisms, the more it will tend to “pull” (in its characters) towards one or another of the known bilaterian groups. As this happens, and the organism loses its descriptive generality, it will cease to be a good candidate Urbilaterian."

Comments by Dr. Nelson:

"... the poster focused on an unsolved conceptual problem arising from data familiar to any developmental biologist or evo-devo theorist. Only a handful of biologists (e.g., Eric Davidson; see below) currently are trying to solve the problem, which deserves to be much better known."

In the Drosophila system, the anterior-posterior (A-P, or head-to-tail) and dorsal-ventral (D-V, or back-to-front) axes of the egg (body plan) are specified in the mother’s ovary. For instance, Mom deposits bicoid mRNAs at the anterior pole of the egg. After fertilization, these mRNAs will be translated into DNA-binding proteins, which will then diffuse along a gradient towards the posterior pole of the egg.

The diffusion of bicoid begins the process (or is an important aspect, anyway) of specifying the body plan of the fly. The events occur in a single large cell, the syncitium. Cellularization –- the formation of cells within the syncitium –- is yet to come.

But not all insects establish their body plans this way. In some wasps, for instance, studied by Miodrag Grbic and Michael Strand, complete celluarization is the first noteworthy event. That is, the embryo divides into two (and then many more) distinct cells immediately, in what is known as holoblastic cleavage. "Initial cleavage events in these tiny eggs differ from the canonical type of insect syncytial cleavage. [The] wasps undergo total (holoblastic) cleavage in which nuclear division is immediately followed by cytoplasmic division, forming individual cells (blastomeres)" (Grbic 2003, p. 635).

Here's the problem. If we suppose that the syncitial developmental architecture is primitive for long germ-band insects, as is widely accepted, then how did complete cellularization evolve in some wasps? In particular, if the segmentation cascade requires the diffusion of maternal transcription factors throughout the syncitium, what would happen if a cell membrane suddenly arose in the path of those diffusing morphogens?

The celluarized environment of the C. floridanum [a wasp] embryo violates the most important paradigm of Drosophila patterning: Initiation of the segmentation cascade begins with the diffusion of transcription factors in a syncytial environment. Even though C. floridanum lacks a syncytial stage, it still undergoes long germ-band development. ...

Early cellularization of the C. floridanum egg, however, makes it unlikely that protein gradients could form by diffusion as occurs during syncytial cleavage in other long germ-band species....embryonic cells become dye uncoupled at the very beginning of embryogenesis and no syncytial stage ever exists during germ-band formation. (Strand and Grbic 1997, p. 140)

"Dye uncoupled" refers to experiments where Grbic and Strand injected early blastomeres with a dye smaller in molecular dimensions than the bicoid protein.

The dye stayed in the injected blastomere and not did not diffuse. If the dye couldn't get past the cell membrane, then it is likely that the bicoid protein couldn't either.

Reviewing these fundamental differences, Grbic muses, "It is hard to conceptualize the evolution of a novel stage that disrupts one of the crucial paradigms of Drosophila development, maternal specification of the embryonic axis" (Grbic 2003, p. 640).

These are differences of developmental architecture just within Insecta. As one moves to large groups -- e.g., the phyla, or the superphylum Ecdysozoa -- the differences becomes much more dramatic…

"Classical authors…and those of their successors who have attempted to deal with more than one embryonic form, have been struck by the amazing variety in the modes of embryonic development that exist in the various phylogenetic reaches of the Animal Kingdom… All embryos do indeed achieve the imposition of spatial patterns of differential gene expression, and yet some begin this process by intercellular interaction, and others even before there are any cells that could carry out such interactions; some rely on lineages that are autonomously committed to given functions from the moment they appear, others deal wholly in plastic, malleable cell fate assignments; some utilize eggs that before fertilization are cytoskeletally organized in both axes, some in one axis only, some apparently in neither; for some kinds of embryos every individual has a different cell lineage, while for others development depends on a set of rigidly reproducible canonical cell lineages; and some embryos display truly amazing regulative capacities….the differences among taxa in their modes of embryonic development are anything but trivial and superficial (certain hopeful reductionist delusions of recent years to the contrary)." [Davidson, 1990, pp. 365-66]

If one assumes that two (or more) taxa showing divergent early development share a common ancestor, then one has prima facie evidence that early development can vary dramatically.

In his plenary lecture at Calgary, for instance, Brian Hall said (I’ll paraphrase), ‘Once upon a time the neo-Darwinians thought that early development was functionally constrained, and thus unlikely to vary much. Now of course we know better: We’ve got hundreds of examples of divergent early development.’ What Hall didn’t show (because, to my knowledge, it doesn’t exist) was experimental evidence showing heritable changes in such characters as cleavage patterns or modes of gastrulation.

[Note: PZ Myers drew what he calls a “crude triploblastic worm.” It would be relatively easy, he argued, for this organism to vary so that it would qualify as a reasonable PDA (protostome-deuterostome ancestor)... problems arise as soon as one tries to put flesh on the bones of the [PZ Myers'} hypothesis. Suppose the crude worm were something like known flatworms. A flatworm egg wants to turn into a flatworm, with its gut, muscles, germ line, sensory organs, and epidermis in more or less the right place –- and not something else. (I would say the constraints we see in developing organisms are a generic feature of causally asymmetric systems, where entrenched upstream features govern downstream consequences...)]

It [this problem] existed for Darwin and it exists today. The problem will either be solved or it will persist. I predict it will persist, and will worsen, because of the conceptual and evidential difficulties outlined in the poster.

Dr. Nelson's References:

Britten, Roy J. and Davidson, Eric. 1971. Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Quarterly Review of Biology 46:111-131.

Davidson, Eric. 1990. How embryos work: a comparative view of diverse modes of cell fate specification. Development 108:365-389.

Grbic, Miodrag. 2003. Polyembryony in parasitic wasps: evolution of a novel mode of development. Int. J. Dev. Biol. 47:633-642.

Strand, Michael and Miodrag Grbic. 1997. The Development and Evolution of Polyembryonic Insects. Current Topics in Developmental Biology 35:121-159.

Thursday, November 17, 2005

Origins of introns based on the definition of exon modules and their conserved interfaces

de Roos AD. Origins of introns based on the definition of exon modules and their conserved interfaces. Bioinformatics. 2005. Jan 1;21(1):2-9 (PDF).

From the Abstract:
The design-by-contract methodology of software development offers a modular approach to design that seeks to increase flexibility by focusing on the design of constant interfaces between functional modules.

From the Introduction:

Modern software designs seek to increase flexibility by using a modular approach which allows for the addition, replacement and changing operations within individual modules.

Complex software architectures are based on a methodology in which a software system is viewed as a set of communicating modules whose interaction is based on precisely defined interfaces. The interfaces can be viewed as specifications of the mutual obligations or contracts

The effect of constant interfaces across modules is a reduction of the interdependences across modules or components and a reduction in the risk that changes within one module will create unanticipated changes in other modules. This methodology is also known as design-by-contract (Meyer,B. (1997) Object-Oriented Software Construction, 2nd ed. Prentice-Hall, NY.). is hypothesized here that genome architecture reflects the paradigms of design-by-contract: definition of functional modules that interact with each other by well-defined interfaces.

From the Full Text:

In our design-by-contract model, the recognition sequence represents the interface for the splicing of the exons and therefore, any mutation in this sequence would be deleterious since it would result in the inactivation of the splice site (Fig. 3B) and resulting loss of function of the encoded protein.

Fig. 3. mRNA intron phase shifts can change the amino acid sequence without changing the ancient splice recognition site.
(A) The sequence at the splice junctions codes for the amino acids glutamine and valine that would result from concatenation of the exons [at the top in this figure].
(B) Mutations in the splice site recognition sequence will disrupt splicing.
(C) Phase shifts can change the splice junction amino acid sequence without disruption of the recognition site. In phase 0, there is only one amino acid sequence possible, glutamine followed by valine. In phase 1 and 2, translation will read through the splice junction in a different way, making various combinations of amino acids possible. Note the conservation of the sequence at the splice junctions (in red).

The application of the design-by-contract methodology by viewing the exon as a module that interacts with its environment by its interface, led to a series of logical steps explaining the intron–exon structure of genes and intron phase differences.

Other works by the same author in PubMed and in Scholar Google , as well as some ARN postings:

Half saved from ARN's broken threads:
"The ribosome is, in fact, a nano-scale computer"

Biology as Technology (synthetic biology)

Double trouble: Cells with duplicate genomes can trigger tumors

The ARN's broken threads:
Topic: Does cell design sacrifice energetic efficiency for conceptual integrity?

Critique of Endosymbiosis

Berlinski vs. Scott (I know where I'm placing my money)

Designed Errors and Deliberately Bad Designs
does ID propose a mechanism?

Evolution of an Arbitrary Sequence

populations vs individuals

Wednesday, November 16, 2005

Estimating the prevalence of protein sequences adopting functional enzyme folds.

Axe DD. Estimating the prevalence of protein sequences adopting functional enzyme folds. J Mol Biol. 2004 Aug 27;341(5):1295-315.


"Proteins employ a wide variety of folds to perform their biological functions. How are these folds first acquired? An important step toward answering this is to obtain an estimate of the overall prevalence of sequences adopting functional folds. Since tertiary structure is needed for a typical enzyme active site to form, one way to obtain this estimate is to measure the prevalence of sequences supporting a working active site."

"Although the immense number of sequence combinations makes wholly random sampling unfeasible, two key simplifications may provide a solution. First, given the importance of hydrophobic interactions to protein folding, it seems likely that the sample space can be restricted to sequences carrying the hydropathic signature of a known fold. Second, because folds are stabilized by the cooperative action of many local interactions distributed throughout the structure, the overall problem of fold stabilization may be viewed reasonably as a collection of coupled local problems. This enables the difficulty of the whole problem to be assessed by assessing the difficulty of several smaller problems. Using these simplifications, the difficulty of specifying a working beta-lactamase domain is assessed here."

"An alignment of homologous domain sequences is used to deduce the pattern of hydropathic constraints along chains that form the domain fold."

"Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function."

"The prevalence of low-level function in four such experiments indicates that roughly one in 10(64) signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77), adding to the body of evidence that functional folds require highly extraordinary sequences."

Tuesday, November 15, 2005

Irreducible Complexity in Interacting Systems

Dr. Albert Voie declared in his recent comment:

I noticed that the lac repressor binds to a palindromic sequence. The DNA binding is performed by two identical dimers that is bound together strongly by multiple interaction.

There are four principle clusters of amino acids in the tetramer that comprise the interface between the two monomers of each dimer <> : residues 70-100, 221- 226, 250-260, and 275-285 <>. Point mutations in any of these clusters, excluding 250-260, will result in only the monomeric form of the repressor. The binding between the two dimers is extremely strong due to the number of interactions.

One could ask the question; what came first, the palindrome or the protein-protein interactions. Both seems to be required to form a complete tetrameric lac-repressor

If we use our main stream science hats, are palindromes thought to be some kind of mutations?
My answer is that we can think of such interacting systems as being Irreducibly Complex (IC) as each one needs the other in order to work.

See for example the next figure:
"This arrangement of two identical sequences of base pairs running in opposite directions is called an inverted repeat."
So, truncated palindromic fragments are called inverted repeats. Let's see the CAP binding region in context:
A close-up of the "inverted repeats" (highlighted in bold) is:


"The strategy illustrated by CAP and its binding site has turned out to be used widely. As more and more DNA-regulating proteins have been discovered, many turn out to share the traits we find in CAP"
Let's see the protein itself:
The recognition helices of each polypeptide of CAP are, of course, identical. But their orientation in the dimer is such that the sequence of bases they recognize must run in the opposite direction for each recognition helix to bind properly."
"...the traits we find in CAP:
1) They usually contain two subunits. Therefore, they are dimers.
2) They recognize and bind to DNA sequences with inverted repeats.
3) In prokaryotes, recognition and binding to a particular sequence of DNA is accomplished by a segment of alpha helix. Hence these proteins are often described as helix-turn-helix proteins."
"CAP consists of two identical polypeptides (hence it is a homodimer). Toward the C-terminal, each has two regions of alpha helix with a sharp bend between them. The longer of these is called the recognition helix because it is responsible for recognizing and binding to a particular sequence of bases in DNA.

The graphic shows a model of CAP. The two monomers are identical. Each monomer recognizes a sequence of nucleotides in DNA by means of the region of alpha helix labeled F. Note that the two recognition helices are spaced 34Å apart, which is the distance that it takes the DNA molecule (on the left) to make precisely one complete turn."


The status of the paper by Dr Voie has changed from In Press to:

Biological function and the genetic code are interdependent
Øyvind Albert Voie
Chaos, Solitons & Fractals
Volume 28, Issue 4 , May 2006, Pages 1000-1004.

2- More personal correspondence related to my Palindromati article can be seen next:
"It was my belief that Genbank filters submitted data to identify linker sequences and other 'clutter'.

Your abstract indicates that either this is not the case anymore or that Genbank does a rather sloppy job.

Because of their intrinsic nature (Being linkers containing at least one common restriction site and used in libraries), such sequences cannot have ORF stop codons, thus, are predetermined for ORF continuation in concatenated sequences.

In other words, heterotranscripts (normally) escape being spotted in laboratory settings (they should, however, trigger a flag if scientists would more often run sequence analysis software (such as BLAST), or would interpret multiple transcripts in Northern analysis more carefully).

By the way, my first clone isolated here at _____ was a chimeric cDNA!"
"Your manuscript on hetero trans-splicing between chromosomes is very interesting."

"Your new work on heterotranscripts of mRNA sounds VERY interesting."

"I think the topic of trans-splicing sounds fascinating.

Perhaps large scale analysis of deposited ESTs and other transcripts may shed more light into this phenomenon, as the current SAGE tags would seem to me too short to easily observe trans-splicing events, or to reliably indicate trans-splicing enhancer sequences. At any rate, I think this is certainly worth pursuing and I wish you the best of luck.

Although I do not have the resources to devote more time to this topic at the moment, I would be happy to keep in touch as you pursue your research."
My answer to the last researcher was the next one:

"With thousands of mRNA sequences, we can now identify their ways of assembly.

When using “Affymetrix oligo-arrays”, I find that almost all the mRNAs have a specific pattern in which five or so, of the sixteen fragments with 25 bases in length are the ones that make the “peak(s)” of intensity, and those patterns are conserved even in different tissues.

As you know, the first report of Trans-Splicing in humans showed a “naturally” occurring palindromic linker (CCGAATTCGG) which being originated from an unknown location in the genome, tied information from two chromosomes, 1 and 7.

It doesn’t need to be necessarily a palindromic sequence, but because of the novelty of the first report I decided to explore the natural presence of linkers in mRNA sequences.

Other significant sequences in the Trans-Splicing process are enhancers of that mechanism, i.e., GAAGAAG and GAGGAGGAGGG, to name a few.

In reviewing ___ supplementary material (Nature Genet. 23:387-8, 1999) the study of sequences reported (i.e. CCTGTAATCC and GTGAAACCCC) gives me reason to continue my research.

I think that the experiments are not going to be so expensive in the first stage, because basically is to selectively pick up the mRNAs that respond to that probe from different tissues, to sequence them and to report them.

P.S. Also from the most repetitive sequences ____ in ____ 1999 Nat. Genet. Letter until now in my search I can see that amazingly that sequences are only present in humans, it seems that some signaling of specificity are they giving..."

Friday, November 11, 2005

Habitable Zones in the Universe

Habitable Zones in the Universe. By Guillermo Gonzalez. Origins of Life and Evolution of Biospheres. September 1, 2005. (PDF)

Comments: 71 pages, 3 figures, 1 table.
Habitability varies dramatically with location and time in the universe. This was recognized centuries ago, but it was only in the last few decades that astronomers began to systematize the study of habitability. The introduction of the concept of the habitable zone was key to progress in this area. The habitable zone concept was first applied to the space around a star, now called the Circumstellar Habitable Zone. Recently, other, vastly broader, habitable zones have been proposed. We review the historical development of the concept of habitable zones and the present state of the research. We also suggest ways to make progress on each of the habitable zones and to unify them into a single concept encompassing the entire universe.

Other writings by Guillermo Gonzalez:

Gonzalez, Donald Brownlee and Peter D. Ward, Refugees for Life in a Hostile Universe, Scientific American, October, 2001.

Guillermo Gonzalez, Donald Brownlee, Peter Ward. "The Galactic Habitable Zone I. Galactic Chemical Evolution." Icarus, Vol. 152(1):185-200; July 1, 2001.

Guillermo Gonzalez and Jay W. Richards. Good reason to shoot for the moon. Seattle Post-Intelligencer. Jan 21, 2004.

Guillermo Gonzalez, Alien Intelligences, Think Again. ( February 29, 2000.

Guillermo Gonzalez. The controversy over ID at ISU.

Guillermo Gonzalez. Letter: Don’t Restrict the Direction of Research. Iowa State Daily. Aug 26, 2005.

Other comments related to the findings of Dr. Guillermo Gonzalez can be found at my:

Critical Analysis of Evolution

Thursday, November 10, 2005

The Intelligent Design Management of Wildlife

"Pet Kotoob" in Maya means "Rounded Walls", and was discovered by Arturo Gomez-Pompa in the Maya Ruins, where he found big circular (rounded) stone cages. Inside them he found exotic seeds from far and foreign regions. By analogy, we took such name like an emblem for our rational breeding of wildlife, which is the Mendelian Bioengineering within an Intelligent Design framework.

The references that we used then in our local publications where the next ones:

1.) The Holy Bible, Leviticus 11, which deals with every edible animal for humans, for example:
"Whatsoever parteth the hoof, and is cloven-footed, and cheweth the cud, among the beasts, that shall ye eat" (Lv. 11:3).
2.) Hopcraft, D. 1980. "La Tecnología de la Naturaleza" (The Natural Technology), Banco del Atlántico (Atlantic Bank), México.

"When I was adolescent I experienced the first great dust storm registered in our cattle and agriculture region... some families continued to live there, starving, bewildered and resisting to leave their birth places. There still was left a few starved cattle eating the barks of dead trees. After that I became aware that only 25 years before, in that very same land, in the past there were beautiful crop fields. I was terrified and decided to investigate what had happened..."
Hopcraft was the founder of a Swara ranch, 40 Km south-east of Nairobi, his "Wildlife Ranching and Research". He pointed out the advantages of the breeding of the wildlife: they maintain their ecological niche with minimal expenses, nutritional efficiency, high growth and reproduction rates, resistance, full benefits, adaptability and high yielding.

"To eliminate native animals by introducing cows is like cutting a vital organ of a living body, soon the remainder gets deteriorated and dies. If we learn again how to use the native animals we can revert that destructive process:

1- The ranches and reserves need to be in harmony with the original ecological equilibrium,
2- They need to promote the return to the several species that used to live there initially, and their interactions,
3- The energetic cycle needs to be stable in the ecosystem without the need of energetic imports."

3-) Granados Espitia, H. 1985. "La cría de mamíferos salvajes como fuente de alimentos" (The Breeding of Wild Mammals as a Source of Food), Ciencia y Desarrollo (Science and Development). 63. México.

"We need to divide in two the breeding of wild mammals:

1- The ones that still exist in numerous amounts (White-Tailed Deer, wild-hog, tepescuintle...), they can provide natural protein as a business,

2- The ones that are in danger of extinction (Bura Deer, "Borrego Cimarrón", tapir, temazate), need first to be breed in order to repopulate them"

"So, we need first to do the ecological selection of the land. Second, we need to plan and to establish the ranch or reserve (we need to determine the necessary personnel, the access roads, fencing, periodic stocks, to educate the surrounding population, the facilities (housing, offices, workstations, meat and coats processors...), as well as the first year's costs). Third, we need to do the commercialization of our product (meat in its different presentations, skins and coats, horns and hoofs...)"

"To apply this solution has been, since a long time ago, a very urgent need"

4.) Leopold, A. S. 1987. "Fauna silvestre de México" (The Mexican Wildlife). Instituto Mexicano de Recursos Renovables [Mexican Institute of Renewable Resources] (4ta. Reimpresión [Fourth Printing]). México.

"An excessive and inadequate agriculture is dangerous for the ecosystem, bringing dangers such as erosion, desertification and ecological instability."
5.) Villarreal, G. J. 1987. "Manejo del venado cola blanca (Odocoileus virginianus texanus) con fines de aprovechamiento cinegético en el norte de México" (Management of the White-tail Deer with Hunting Purposes in the North of Mexico). Memorias del V Simposium Sobre Fauna (Memories of the Fifth Wildlife Symposium), UNAM (Autonomous National University of Mexico). México.

These same references in Spanish:

I was then in the UAG, Universidad Autónoma de Guadalajara (Autonomous University of Guadalajara) taking my Specialty in Agroecosystems (the Rational Exploitation of all kinds of Plants) and Zootechny (the Rational Exploitation of all kinds of Animals). Some of the most interested colleagues in such field were Engineers Cota, Gonzalez and Acevedo. Cheers to all of them!

My Specialty’s ‘Alma Mater’ is going to be hosting Intelligent Design with Dr. Paul Nelson:

Click here to read Dr. Paul Nelson at the Discovery Institute.

Click here to hear Dr. Paul Nelson (in mp3) at Justice Talking (NPR) debating Atheist N. Shanks on April 19, 2005.

Thanks to Dr. William A. Dembski for informing us of such news.