Hox Genes

Hox Genes

http://www.researchgate.net/post/Why_do_researchers_continue_to_mislead_with_the_notion_that_Hox_genes_determine_the_body_plan

Genes code for proteins and RNAs. They don't code for brains, limbs or body plans. Yet many scientists insist that Hox genes, and other transcription factors, are responsible for "laying out the flooor plan" of the organism when all they are observed to do is activate genes in already established segments of the developing embryo. We have known this for 20 years. So why are the 39 Hox genes still portrayed as determining the geometry of anatomy when all they do is bind to DNA and RNA polymerase to affect gene expression in ontogeny?

Yes, mutations in hox genes do produce aberrant body plans..like legs where there should be antennae in fruit flies. But it is a mistake to assume that this is evidence that hox genes causally lay out the body plan, just like it would be a mistake to assume that a fault in a TV, causing a disruption in the reception of the signal, shows that the TV box produces the signal itself. Linear DNA cannot produce 3D form.

I am questioning th role of Hox genes in particular, as they are the most widely touted, but I am more generallty questioning the role of transcription factors and signalling proteins as a whole since their function is only to affect the production of other proteins, not to instruct cells how to form specific 3D structures like hearts and lungs. Yes, proteins are three dimensional entities, but there is no proof that their encoded amino acid sequence alone determines their final conformation - but that is not really an issue for developmental biology. My main argument is that the body plan of the organism is not encoded in DNA, or represented in the membrane/cytoskeletal patterns of the egg. Think about it: the human brain has 10^15 synaptic connections, which is 300,000 times more than the number of base pairs in the entire genome! There is a clear difference between genomic complexity and the complexity of the organism.


Darwins doubt, pg.239

WHAT ABOUT HOX GENES?

Hox (or homeotic) genes regulate the expression of other protein-coding genes during the process of animal development. Some biologists have likened them to the conductor of an orchestra who plays the role of coordinating the contributions of the players. And because Hox genes affect so many other genes, many evo-devo advocates think that mutations in these genes can generate large- scale changes in form.

But can mutations in Hox genes transform one form of animal life—one body plan—into another? There are several reasons to doubt that they can.
First, precisely because Hox genes coordinate the expression of so many other different genes, experimentally generated mutations in Hox genes have proven harmful.  in fruit flies "most mutations in homeotic [Hox] genes cause fatal birth defects." In other cases, the resulting Hox mutant phenotype, while viable in the short term, is nonetheless markedly less fit than the wild type. For example, by mutating a Hox gene in a fruit fly, biologists have produced the dramatic Antennapedia mutant, a hapless fly with legs growing out of its head  where the antennae should be



Other Hox mutations have produced fruit flies in which the balancers (tiny structures behind wings that stabilize the insect in flight, called "halteres") are transformed into an extra pair of wings. Such mutations alter the structure of the animal, but not in a beneficial or permanently heritable way. The Antennapedia mutant cannot survive in the wild; it has difficulty reproducing, and its offspring die easily. Similarly, fruit-fly mutants sporting an extra set of wings lack the musculature to make use of them and, absent their balancers, cannot fly. As Hungarian evolutionary biologist Eörs Szathmáry notes with cautious understatement in the journal Nature, "macromutations of this sort [i.e., in Hox genes] are probably frequently maladaptive."

Second, Hox genes in all animal forms are expressed after the beginning of animal development, and well after the body plan has begun to be established. In fruit flies, by the time that Hox genes are expressed, roughly 6,000 cells have already formed, and the basic geometry of the fly—its anterior, posterior, dorsal, and ventral axes—is already well established. So Hox genes don't determine body-plan formation. Eric Davidson and Douglas Erwin have pointed out that Hox gene expression, although necessary for correct regional or local differentiation within a body plan, occurs much later during embryogenesis than global body-plan specification itself, which is regulated by entirely different genes. Thus, the primary origin of animal body plans in the Cambrian explosion is not merely a question of Hox gene action, but of the appearance of much deeper control elements—
Davidson's "developmental gene regulatory networks" (dGRNs).Davidson argues that it is extremely difficult to alter dGRNs without damaging their ability to regulate animal development. Third, Hox genes only provide information for building proteins that function as switches that turn other genes on and off. The genes that they regulate contain information for building proteins that form the parts of other structures and organs. The Hox genes themselves, however, do not contain information for building these structural parts. In other words, mutations in Hox genes do not have all the genetic information necessary to generate new tissues, organs, or body plans.

Nevertheless, Schwartz argues that biologists can explain complex structures such as the eye just by invoking Hox mutations alone. He asserts that "[t]here are homeobox genes for eye formation and that when one of them, the Rx gene in particular, is activated in the right place and at the right time, an individual has an eye." He also thinks that mutations in Hox genes help arrange organs to form body plans. In a review of Schwartz's book, Eörs Szathmáry finds Schwartz's reasoning deficient. He too notes that Hox genes don't code for the proteins out of which body parts are made. It follows, he insists, that mutations in Hox genes cannot by themselves build new body parts or body plans. As he explains, "Schwartz ignores the fact that homeobox genes are selector genes. They can do nothing if the genes regulated by them are not there." Though Schwartz says he has "marveled" at "the importance of homeobox genes in helping us to understand the basics of evolutionary change," kind of (nonhomologous) leg. Another homologue of the Distal-less gene in echinoderms regulates the development of tube feet and spines—anatomical features classically thought not to be homologous to arthropod limbs, nor to limbs of tetrapods.34 In each case, the Distal-less homologues play different roles determined by the higher-level organismal context. And since mutations in Hox genes do not alter higher-level epigenetic contexts,35 they cannot explain the origin of the novel epigenetic information and structure that establishes the context and that is necessary to building a new animal body plan.

Szathmáry doubts that mutations in these genes have much creative power. After asking whether Schwartz succeeds in explaining the origin of new forms of life by appealing to mutations in Hox genes, Szathmáry concludes, "I'm afraid that, in general, he does not."Nor, of course, do Hox genes possess the epigenetic information necessary for body-plan formation. Indeed, even in the best of cases mutations in Hox genes still only alter genes. Mutations in Hox genes can only generate new genetic information in DNA. They do not, and cannot, generate epigenetic information. Instead, epigenetic information and structures actually determine the function of many Hox genes, and not the reverse. This can be seen when the same Hox gene (as determined by nucleotide sequence homology) regulates the development of different anatomical features found in different phyla. For instance, in arthropods the Hox gene Distal-less is required for the normal development of jointed arthropod legs. But in vertebrates a homologous gene (e.g., the Dlx gene in mice) builds a different

What sets the proteins made by Hox genes apart is the biochemical motif known as a homeobox, a stylized string of 60 amino acids that enables Hox proteins to stick to DNA like strips of molecular Velcro and, in the process, activate still other genes. Hundreds of genes belong to the extended homeobox family, but those that are also homoeotic- associated with changes in body parts-are the most important. Though they are few in number (38 out of an estimated 50,000 to 100,000 genes in modern vertebrates, the Hox genes control much of what happens during embryonic development.

https://groups.yahoo.com/neo/groups/CreationEvolutionDesign/conversations/topics/8839

Evolution and the Problem of Non-Functional Intermediates

Non-functionality and Irreducible Complexity: 
In the Origin of the Species, Charles Darwin said,"If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down."¹In evolution, natural selection only preserves those structures which confer some advantage for the organism. If a structure isn't functional, then it confers no advantage, is a waste of the organism's resources, and will be selected out. Darwin says that there may exist structures for which functional intermediate stages would be impossible, i.e. the intermediates would not function. This is essentially the same challenge of irreducibly complex structures, where intermediate structures wouldn't be functional. Biologist Michael Behe explains:

"A system which meets Darwin's criterion [listed in the above quote] is one which exhibits irreducible complexity. By irreducible complexity I mean a single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced gradually by slight, successive modifications of a precursor system, since any precursor to an irreducibly complex system is by definition nonfunctional. Since natural selection requires a function to select, an irreducibly complex biological system, if there is such a thing, would have to arise as an integrated unit for natural selection to have anything to act on. It is almost universally conceded that such a sudden event would be irreconcilable with the gradualism Darwin envisioned."⁴In the quote above, Behe notes that there is a fundamental quality of any irreducibly complex system in that, "any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.”⁴ Behe elaborates upon this definition saying"An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway."¹¹More than Just Behe?
Behe, who also compares the problem of functional intermediates to a "groundhog trying to cross a thousand lane highway,"⁹ is not alone in his sentiments. Many biologists see  the problem of non-functional intermediates to be a formidable challenge to Darwin's theory. 

Soren Lovtrup, professional biologist in Sweden, said


 "...the reasons for rejecting Darwin's proposal were many, but first of all that many innovations cannot possibly come into existence through accumulation of many small steps, and even if they can, natural selection cannot accomplish it, because incipient and intermediate stages are not advantageous."²


 Well known evolutionist vertebrate paleontologist Robert Carroll asked if the gradual processes of microevolution can evolve complex structures:"Can changes in individual characters, such as the relative frequency of genes for light and dark wing color in moths adapting to industrial pollution, simply be multiplied over time to account for the origin of moths and butterflies within insects, the origin of insects from primitive arthropods, or the origin of arthropods from among primitive multicellular organisms? How can we explain the gradual evolution of entirely new structures, like the wings of bats, birds, and butterflies, when the function of a partially evolved wing is almost impossible to conceive?"¹⁰To overcome the problems of non-functional intermediates, some biologists have proposed "macromutations" or "saltations" which would produce radically different organisms. Though Stephen Jay Gould is not a proponent of this theory, he noted that, "the absence of fossil evidence for intermediary stages between major transitions in organic design, indeed our inability, even in our imagination, to construct functional intermediates in many cases, has been a persistent and nagging problem for gradualistic accounts of evolution."⁸ Those who proposed that rare macromutations would produce "hopeful monsters", some of which might actually have some great advantage, have not been received well by biologists. Paleobiologists Douglas Erwin and James Valentine explain why:"Viable mutations with major morphological or physiological effects are exceedingly rare and usually infertile; the chance of two identical rare mutant individuals arising in sufficient propinquity to produce offspring seems too small to consider as a significant evolutionary event. These problems of viable "hopeful monsters" ... render these explanations untenable."³Erwin and Valentine said this in regards to the origin of the major body plans of life--the phyla--and some marine classes, however, others have found other unevolvable structures. Turkish evolutionist Engin Korur says, "The common trait of the eyes and the wings is that they can only function if they are fully developed. In other words, a halfway-developed eye cannot see; a bird with half-formed wings cannot fly. How these organs came into being has remained one of the mysteries of nature that needs to be enlightened."⁵ 

Hox-Mutations or Miracle Mutations? 
Some biologists have also envisioned special mutations in regulatory homeobox or "Hox" genes, where simple mutations might be able to make large developmental changes in an organism which might case a radically different phenotype. However, manipulating "Hox" genes does little to solve the problem of generating novel functional biostructures, for making large changes in phenotype are rarely beneficial. Hox gene mutations may be a more simple mechanism for generating large change, but they also do not escape the problem of the "hopeful monster":"The drawback for scientists is that nature's shrewd economy conceals enormous complexity. Researchers are finding evidence that the Hox genes and the non-Hox homeobox genes are not independent agents but members of vast genetic networks that connect hundreds, perhaps thousands, of other genes. Change one component, and myriad others will change as well--and not necessarily for the better. Thus dreams of tinkering with nature's toolbox to bring to life what scientists call a "hopeful monster"- such as a fish with feet--are likely to remain elusive." ⁶The figure below explains:





Furthermore, many biologists forget when invoking Hox gene mutations that Hox genes can only re-arrange parts which are already there--they cannot create truly novel structures. An oversimplified discussion is that genes can be thought of in two categories: "master control genes" (Hox genes) and "body part genes." "Body part genes" code for actual body parts while "master control genes" tell those "body part genes" when and where to be expressed and create their respective part. However, Hox mutations will never create new "body part genes", and thus cannot add truly new phenotypic functions into the genome, and at best we are left with the quandaries associated with "pre-adaptation". The majority of evolutionary change must take place through evolving new "body part genes", which Hox mutations cannot do. One reviewer in Nature recognizes this fact:"Schwartz ignores the fact that homeobox genes are selector genes. They can do nothing if the genes regulated by them are not there. It is these genes that specify in detail the adaptive structure of the organs. To be sure, turning on a homeobox gene at the wrong place can result in the appearance of an ectopic organ, but only if the genes for that organ are present in the same individual. It is totally wrong to imply that an eye could be produced by a macromutation when no eye was ever present in the lineage before. Homeotic mutations that reshuffle parts do happen, and sometimes they may have led to fixation of real evolutionary novelties, but this does not mean that such changes are implied in the majority of speciations. In fact, macromutations of this sort are probably frequently maladaptive, in contrast to the vast number of past and present species-not to mention the fact that morphological differences between related species can be minute."⁷Biologist Jonathan Wells discusses the issue of Hox mutations in his book, Icons of Evolution, where he recognizes that while Hox genes can be manipulated to cause fruit flies to sprout legs from their head. Three specific mutations are necessary to create this mutant fruit fly, and the legs are not functional, and are unbeneficial to the organism. This is a great example of why meaningful Hox mutations are complex and less simple in generating large biological change than many have promised, and how the resulting phenotype would usually be useless and disadvantageous. 

Since this issue is fairly easy to understand, we'd like to just provide a couple of examples of both micro and macro-morphologies which we think are could not have functional intermediates. They defy any gradualistic Darwinian explanation, and seem to hold a level of complexity which at least very strongly implies an intelligent designer as their cause. 

Biological systems for which functional intermediates seem impossible: 


[*]Major pathways of metabolism

[*]Defense Mechanisms in Hawkmoths

[*]The vertebrate heart

[*]The DNA-Enzyme system

[*]The cognitive and physiological requirements for human speech

[*]Non-Functional Intermediates in Human Physiology 

References Cited:
1. Origin of the Species by Charles Darwin
2. Lovtrup, S. [professional biologist specialising in Systematics and Developmental Biology, Dept. Animal Physiology, University of Umee, Sweden (also headed the organization of Swedish Developmental Biologists from 1979-87] (1987), Darwinism: The Refutation of a Myth, Croom Helm Ltd., Beckingham, Kent, p. 275
3. Erwin, D..H., and Valentine, J.W. "'Hopeful monsters,' transposons, and the Metazoan radiation", Proc. Natl. Acad. Sci USA 81:5482-5483, Sept 1984
4. Michael Behe, from "Molecular Machines: Experimental Support for the Design Inference" available at "http://www.arn.org/docs/behe/mb_mm92496.htm".
5. Engin Korur, "Gozlerin ve Kanatlarin Sirri"(The Mystery of the Eyes and the Wings), Bilim ve Teknik, No 203, October 1984, p. 25.
6. Nash J.M., "Where Do Toes Come From?," Time, Vol. 146, No. 5, July 31, 1995. Also at "http://www.time.com/time/magazine/archive/1995/950731/950731.science.html"
7. Book review of Sudden Origins: Fossils, Genes, and the Emergence of Species by Jeffrey H. Schwartz (Wiley: 1999). by Eors Szathmary in Nature 399:24, June 1999 pg. 745. 
8. Stephen Jay Gould (1982), "Is a new and general theroy of evolution emerging?," In Maynard Smith, J. (ed.), Evolution now A century after Darwin. 129-145. Macmillan Press, London. 239 pp. First published (1980) Paleobiology, 6: 119-130.
9. Darwin's Black Box by Michael Behe, pg. 141-142. 
10. Robert Carroll, Patterns and Processes of Vertebrate Evolution, Cambridge: Cambridge University Press, 1997, pp. 8-10
11. A Response to Critics of Darwin's Black Box, by Michael Behe, PCID Vol 1.1, Jan/Feb/March 2002; ISCID.org. 
12. Lynch, M., Conery, J. S., "The Evolutionary Fate and Consequence of Duplicate Genes" Science 290:1151-1155 (Nov 10, 2000). 
13. Huges, Austin L., "Adaptive Evolution of Genes and Genomes". (see chapter 7, "Evolution of New Protein Function" pp 143-180. (Oxford University Press, New York, 1999). 

http://www.ideacenter.org/contentmgr/showdetails.php/id/841
14. Science and Creationism: A View from the National Academy of Sciences (2nd Ed, 1999; NAP).

Hox Genes Permanently Pattern the A-P Axis

As animal development proceeds, the body becomes more and more complex. But again and again, in every species and at every level of organization, we find that complex structures are made by repeating a few basic themes, with variations. Thus, a limited number of basic differentiated cell types, such as muscle cells or fibroblast, recur with subtle individual variations in different sites. These cell types are organized into a limited variety of tissue types, such as muscle or tendon, which again are repeated with subtle variations in different regions of the body. From the various tissues, organs such as teeth or digits are built— molars and incisors, fingers and thumbs and toes—a few basic kinds of structure, repeated with variations. Wherever we find this phenomenon of modulated repetition, we can break down the developmental biologist’s problem into two kinds of questions: what is the basic construction mechanism common to all the objects of the given class, and how is this mechanism modified to give the observed variations in different animals? The segments of the insect body provide a good example. We have thus far sketched the way in which the rudiment of a single body segment is constructed and how cells within each segment become different from one another. We now consider how one segment becomes determined, or specified, to be different from another. The first glimpse of the answer to this problem came over 80 years ago, with the discovery of a set of mutations in Drosophila that cause bizarre disturbances in the organization of the adult fly. In the Antennapedia mutant, for example, legs sprout from the head in place of antennae, whereas in the Bithorax mutant, portions of an extra pair of wings appear where normally there should be the much smaller appendages called halteres

Homeotic Genes A set of 8 to 11 homeotic genes directs the formation of particular structures at specific locations in the body plan. These genes are now more commonly referred to as Hox genes, the term derived from “homeobox,” the conserved gene sequence that encodes the homeodomain and is present in all of these genes. Despite the name, these are not the only development-related proteins to include a homeodomain (for example, the bicoid gene product  has a homeodomain), and “Hox” is more a functional than a structural classification. The Hox genes are organized in genomic clusters. Drosophila has one such cluster and mammals have four (Fig. below).



The genes in these clusters are remarkably similar from nematodes to humans. In Drosophila, each of the Hox genes is expressed in a particular segment of the embryo and controls the development of the corresponding part of the mature fly. The terminology used to describe Hox genes can be confusing. They have historical names in the fruit fly (for example, ultrabithorax), whereas in mammals they are designated by two competing systems based on lettered (A, B, C, D) or numbered (1, 2, 3, 4) clusters. Loss of Hox genes in fruit flies by mutation or deletion causes the appearance of a normal appendage or body structure at an inappropriate body position. An important example is the ultrabithorax (ubx) gene. When Ubx function is lost, the first abdominal segment develops incorrectly, having the structure of the third thoracic segment. Other known homeotic mutations cause the formation of an extra set of wings, or two legs at the position in the head where the antennae are normally found (Fig. below).



The Hox genes often span long regions of DNA. The ubx gene, for example, is 77,000 bp long. More than 73,000 bp of this gene are in introns, one of which is more than 50,000 bp long. Transcription of the ubx gene takes nearly an hour. The delay this imposes on ubx gene expression is believed to be a timing mechanism involved in the temporal regulation of subsequent steps in development. Many Hox genes are further regulated by miRNAs encoded by intergenic regions of the Hox gene clusters. All of the Hox gene products are themselves transcription factors that regulate the expression of an array of downstream genes. Identification of these downstream targets is ongoing. Many of the principles of development outlined above apply to other eukaryotes, from nematodes to humans. Some of the regulatory proteins are conserved. For example, the products of the homeoboxcontaining genes HOXA7 in mouse and antennapedia in fruit fly differ in only one amino acid residue. Of course, although the molecular regulatory mechanisms may be similar, many of the ultimate developmental events are not conserved (humans do not have wings or antennae). The different outcomes are brought about by differences in the downstream target genes controlled by the Hox genes. The discovery of structural determinants with identifiable molecular functions is the first step in understanding the molecular events underlying development. As more genes and their protein products are discovered, the biochemical side of this vast puzzle will be elucidated in increasingly rich detail.

If evolution is to generate the kind of changes in an organism that we associate with a different species, it is the developmental program that must be affected. Developmental and evolutionary processes are closely
allied, each informing the other . The continuing study of biochemistry has everything to do with enriching the future of humanity and understanding our origins.

South America has several species of seed-eating finches, commonly called grassquits. About 3 million years ago, a small group of grassquits, of a single species, took flight from the continent’s Pacific coast. Perhaps driven by a storm, they lost sight of land and traveled nearly 1,000 km. Small birds such as these might easily have perished on such a journey, but the smallest of chances brought this group to a newly formed volcanic island in an archipelago later to be known as the Galapagos. It was a virgin landscape with untapped plant and insect food sources, and the newly arrived finches survived. Over the years, new islands formed and were colonized by new plants and insects—and by the finches. The birds exploited the new resources on the islands, and groups of birds gradually specialized and diverged into new species. By the time Charles Darwin stepped onto the islands in 1835, there were many different finch species to be found on the various islands of the archipelago, feeding on seeds, fruits, insects, pollen, or even blood. The diversity of living creatures was a source of wonder for humans long before scientists sought to understand its origins. The extraordinary insight handed down to us by Darwin, inspired in part by his encounter with the Galapagos finches, provided a broad explanation for the existence of organisms with a vast array of appearances and characteristics. It also gave rise to many questions about the mechanisms underlying evolution. Answers to those questions have started to appear, first through the study of genomes and nucleic acid metabolism in the last half of the twentieth century, and more recently through an emerging field nicknamed evo-devo—a blend of evolutionary and developmental biology. In its modern synthesis, the theory of evolution has two main elements: mutations in a population generate genetic diversity; natural selection then acts on this diversity to favor individuals with more useful genomic tools, and to disfavor others. Mutations occur at significant rates in every individual’s genome, in every cell. Advantageous mutations in singlecelled organisms or in the germ line of multicellular organisms can be inherited, and they are more likely to be inherited (that is, are passed on to greater numbers of offspring) if they confer an advantage. It is a straightforward scheme. But many have wondered whether it is enough to explain, say, the many different beak shapes in the Galapagos finches, or the diversity of size and shape among mammals. Until recent decades, there were several widely held assumptions about the evolutionary process: that many mutations and new genes would be needed to bring about a new physical structure; that more-complex organisms would have larger genomes, and that very different species would have few genes in common. All of these assumptions were wrong. Modern genomics has revealed that the human genome contains fewer genes than expected—not many more than the fruit fly genome, and fewer than some amphibian genomes. The genomes of every mammal, from mouse to human, are surprisingly similar in the number, types, and chromosomal arrangement of genes. Meanwhile, evo-devo is telling us how complex and very different creatures can evolve within these genomic realities. The kinds of mutant organisms shown in the figure above of the fruit fly were studied by the English biologist William Bateson in the late nineteenth century. Bateson used his observations to challenge the Darwinian notion that
evolutionary change would have to be gradual. Recent studies of the genes that control organismal development have put an exclamation point on Bateson’s ideas. Subtle changes in regulatory patterns during development, reflecting just one or a few mutations, can result in startling physical changes and fuel surprisingly rapid evolution. What it does, is creating monstrosities..... The Galapagos finches provide a wonderful example of the link between evolution and development. There are at least 14 (some specialists list 15) species of Galapagos finches, distinguished in large measure by their beak structure. The ground finches, for example, have broad, heavy beaks adapted to crushing large, hard seeds. The cactus finches have longer, slender beaks ideal for probing cactus fruits and flowers . Clifford Tabin and colleagues carefully surveyed a set of
genes expressed during avian craniofacial development.

In each organism, these genes are part of the much larger regulatory cascade that ultimately creates the correct structures in the correct locations in each organism.

Hox (homeobox) Genes—Evolution’s Saviour? 1

Some evolutionists hailed homeobox or hox genes as the saviour of evolution soon after they were discovered. They seemed to fit into the Gouldian mode of evolution (punctuated equilibrium) because a small mutation in a hox gene could have profound effects on an organism. However, further research has not born out the evolutionists’ hopes. Dr Christian Schwabe, the non-creationist sceptic of Darwinian evolution from the Medical University of South Carolina (Dept. of Biochemistry and Molecular Biology), wrote:

‘Control genes like homeotic genes may be the target of mutations that would conceivably change phenotypes, but one must remember that, the more central one makes changes in a complex system, the more severe the peripheral consequences become. … Homeotic changes induced in Drosophila genes have led only to monstrosities, and most experimenters do not expect to see a bee arise from their Drosophila constructs.’ (Mini Review: Schwabe, C., 1994. Theoretical limitations of molecular phylogenetics and the evolution of relaxins. Comp. Biochem. Physiol.107B:167–177).
Research in the six years since Schwabe wrote this has only born out his statement. Changes to homeotic genes cause monstrosities (two heads, a leg where an eye should be, etc.); they do not change an amphibian into a reptile, for example. And the mutations do not add any information, they just cause existing information to be mis-directed to produce a fruit-fly leg on the fruit-fly head instead of on the correct body segment, for example.

Evolutionists, of course, use the ubiquity of hox genes in their argument for common ancestry (‘Look, all these creatures share these genes, so all creatures must have had a common ancestor’). However, commonality of such features is to be expected with their origin from the same (supremely) intelligent Creator. All such homology arguments are only arguments for evolution when one excludes, a priori, origins by design. Indeed many of the patterns we see do not fit common ancestry. For example, the discontinuity of distribution of hemoglobin-like proteins, which are found in a few bacteria, molluscs, insects, and vertebrates. One could also note features such as vivipary, thermoregulation (some fish and mammals), eye designs, etc. For more detail, see The Biotic Message.




1) http://creation.com/hox-homeobox-genes-evolutions-saviour

The HOX code - a nightmare for proponents of Evolution

In order to know what mechanisms eventually provoke change and if unguided evolution of an organism is a viable explanation, it must be known what mechanisms do form phenotype,  body architecture, organs, various cell types, cell migration etc. Development biology ( Evo-devo ) is a rather new branch of biology, but, yesterday, I gave a look at the book   Development biology, Gilbert / Barresi. 11th ed 2018. Despite studying biology for years, I had the impression to know almost nothing of what is described there. Development biology might be the most complex branch of biology, and many open questions remain.

Homeoboxes have been found in fungi, plants and animals. In each "kingdom" homeobox genes occupy a key position in the genetic control of either cell differentiation, morphogenesis and or body plan specification.

All Hox genes and many other developmental transcription factors contain the homeobox,  known for their colinearity: conserved arrangement on chromosomes that is the same as their order of activation along the body axis. The regulation is very precise.  The degree of sequence conservation of the homeodomain is extremely high indicating strong functional constraints leading to a high pressure to retain the homeobox sequences constant.

What the Hox code represents is a somewhat digital mechanism for regulating axial patterning. By mixing and matching combinations of the expression of a small number of Hox genes, organisms generate a greater range of morphological possibilities.

It is obvious that not any arrangement of Homeobox genes will give rise to functional body architecture. The precise arrangement is key to have functional body plans.  Mutations in hox genes do produce aberrant body plans..like legs where there should be antennae in fruit flies. But it is a mistake to assume that this is evidence that hox genes causally lay out the body plan, just like it would be a mistake to assume that a fault in a TV, causing a disruption in the reception of the signal, shows that the TV box produces the signal itself. Linear DNA cannot produce 3D form. There is a higher orchestration, which directs the correct linear arrangement of Homeobox genes in the genome.

Hox Genes in Development: The Hox Code
https://www.nature.com/scitable/topicpage/hox-genes-in-development-the-hox-code-41402

This colinearity, arrangement, order of activation and precise regulation of Hox gene clusters indicates there is a HOX Code, which sets the right pattern of Hox gene cluster arrangement for correct sequential expression of segments and rhombomeres in the embryo.  

There is uncertainty in our understanding of homeobox gene cluster evolution at present. This relates to our still rudimentary understanding of the dynamics of genome rearrangements and evolution over the evolutionary timescales being considered when we compare lineages from across the animal kingdom.

The mechanisms responsible for the synchronous regulation of Hox genes and the molecular function of their colinearity remain unknown. Despite 35 years of active research, the mechanisms of Hox gene regulation have remained elusive. It has been argued that chromatin structure and histone demethylation play important roles in activation of Hox genes, but the mechanism precisely directing chromatin modifications to specific loci at the right time remains mysterious.

What does this elucidate? Life is not only composed of organic carbon-based matter but essentially, instructional information. Not any kind of information, but complex, specifying information, blueprints, which precisely orchestrates and directs how to develop, build, adopt animals, plants, fungi, bacterias, and perpetuate life in all its various forms.

1. Cells store codified information in DNA, and at least 18 epigenetic codes, which are complex instructional informational blueprints, essential for cells to make copies of themselves, animal development, adaptation, and body architecture
2. All Codes, and blueprints we know the origin of come from an intelligent mind. Evolution is a non-directed, non-intelligent process and does not suffice to explain the origin of biodiversity and body architecture.
3. Therefore we have 100% inference that DNA comes from an intelligent mind and 0% inference that it is not.


The Hox Code, Code biology, Barbieri, page 107
In 1979, David Elder proposed a model that was capable of accounting for the regularities that exist in the bodies of many segmented worms (annelids). The segments of these animals are often subdivided into annuli whose number varies according to a simple rule: if a segment contains n annuli, the following segment contains either the same number n (repetition) or n plus or minus 1 (digital modification). Elder noticed that this type of rules is known to the designers of electronic circuits as a Gray code, a code that is binary (because it employs circuits that have only one of two states), combinatorial (because its outcomes are obtained by combinations of circuits) and progressive (because consecutive outcomes must be coded by combinations that differ in the state of one circuit only). The results obtained with these rules describe with great accuracy what is observed in segmented worms, and Elder proposed therefore that the body plan of these animals is based on a combinatorial code that is a biological equivalent of the Gray code. He underlined in particular that the coding principle cannot be the classical “one geneone pattern”, but “one combination of genes-one pattern” and for this reason he called it epigenetic code (Elder 1979). After the discovery of the Hox genes, it became increasingly clear that they are used in many different permutations, according to a combinatorial set of rules that became known as Hox code. The term Hox code was introduced independently by Paul Hunt and colleagues (1991) and by Kessel and Gruss (1991) to account for the finding that the individual characteristics of the vertebrae are determined by different combinations of Hox genes. Later on, it was found that this is true in most other organs and it became standard practice to refer to any combination of Hox genes as a Hox code. The epigenetic code proposed by Elder, in particular, is a Hox code because it is Hox genes that are responsible for the body plan of the segmented worms. It must be underlined that the Hox genes can be used in different combinations not only in various parts of a body, but also in different stages of embryonic development. At the phylotypic stage, for example, the Hox genes specify characteristics of the phylum, whereas in later stages they determine characteristics at lower levels of organization. There is, in short, a hierarchy of Hox gene expressions, and therefore a hierarchy of Hox codes. At this point, however, we have to face a key definition problem: is it legitimate to say that the Hox codes are true organic codes? More precisely, that they have the basic features that we find, for example, in the genetic code? An organic code is a mapping between two independent worlds and cannot exist without a set of adaptors that physically realize the mapping. The Hox codes have been defined instead as patterns of combinatorial gene expression and do not require adaptors because a molecular pattern in one world is not a mapping between two independent worlds. We have therefore two different definitions of code, one based on mapping and the other on patterns, or sequences, and it is important to keep them separate because they have different biological implications.

The various codes in the cell
https://reasonandscience.catsboard.com/t2213-the-various-codes-in-the-cell

The Genetic Code
The Splicing Codes
The Metabolic Code
The Signal Transduction Codes
The Signal Integration Codes
The Histone Code
The Tubulin Code
The Sugar Code
The Glycomic Code
The non-ribosomal code
The Calcium Code
The RNA code
A domain substrate specificity code of Nonribosomal peptide synthetases (NRPS)
The DNA methylation Code
The coactivator/corepressor/epigenetic code
The transcription factor code
The post-translational modification code for transcription factors
The HOX Code

Homeobox and Hox Genes

Homeotic genes
It is a fascinating thought that the single cell zygote contains all the information required for the development of the adult organism. Understanding how this information is encoded and deciphered is a major uncompleted scientific challenge. 10

Homeotic genes act within cells to select their developmental fate. Homeotic genes, and other genes with analogous functions in controlling cell fate are therefore known as selector genes. They determine segmental identity. Systematic screening for homeotic genes led to the identification of eight linked genes, collectively referred to as Hox genes, that affect the specification of particular segment identities. The complete loss of any Hox gene function causes transformations of segmental identity and is lethal in early development.

One of the most intriguing features of these Hox genes is that they are linked in two gene complexes in Drosophila, the Bithorax and Antennapedia Complexes; each complex contains several distinct homeotic genes. Furthermore, the order of the genes on the chromosome and within the two complexes corresponds to the rostral (head) to caudal (rear) order of the segments that they influence, a relationship described as colinearity



The Hox genes of Drosophila
Eight Hox genes regulate the identity of regions within the adult and embryo. The color coding represents the segments and structures that are affected by mutations in the various Hox genes.

The ability to visualize Hox and other gene expression patterns during development was crucial to understanding the correlation between gene function and phenotypes. All Hox genes are expressed in spatially restricted, sometimes overlapping domains within the embryo. These genes are also expressed in subsets of the developing larval imaginal discs, which proliferate during larval development and differentiate during the pupal stages to give rise to the adult fly. Homeotic gene products exert their effects by controlling gene expression during development and that the homeodomain binds to DNA in a sequence-specific manner. The homeobox gene family is large and diverse. In fact, the homeodomain motif is found in approximately 20 other distinct families of homeobox-containing genes, all of which encode DNA-binding proteins.

Sections of genes codify Transcription factors, which are used by the cell to turn other genes on or off. There is a class of proteins, containing a region of about sixty amino acids called “homeobox.” This class of proteins is called Hox proteins. In subsequent years homeotic proteins and other classes of control proteins have proven to be master regulators of developmental programs in animals. In animals, a master switch sets in train a whole cascade of lesser switches, where the initial regulatory protein turns on the genes for other regulatory proteins, which turn on other regulatory proteins, and so on. Eventually, after a pyramid of control switches, a regulatory protein activates a gene that actually does some of the construction work to build an animal’s body. But there’s another complication. A gene in an animal cell might be regulated not by just one or a few proteins, but by more than ten. What’s more, there may be dozens of sites near the gene at which the regulatory proteins might bind, with multiple separate sites for some regulatory proteins. 1

Animal bodies contain many different kinds of cells that have to be positioned in definite relationships to other cells, in order to be formed into organs and to connect to other parts of the body.

Cal Tech biologist Eric Davidson emphasizes what the task of building an animal demands:
The most cursory consideration of the developmental process produces the realization that the program must have remarkable capacities, for development imposes extreme regulatory demands…Metaphors often have undesirable lives of their own, but a useful one here is to consider the regulatory demands of building a large and complex edifice, the way this is done by modern construction firms. All of the structural characters of the edifice, from its overall form to minute aspects that determine its local functionalities such as placement of wiring and windows, must be specified in the architect’s blueprints. The blueprints determine the activities of the construction crews from beginning to end.

Homeobox Genes and the Vertebrate Body Plan
This family of related genes determines the shape of the body. It subdivides the embryo along the head-to-tail axis into fields of cells that eventually become limbs and other structures.  Starting as a fertilized egg with a homogeneous appearance, an embryo made of skin, muscles, nerves and other tissues gradually arises through the division of cells. Long before most cells in the emerging body begin to specialize, however, a plan that designates major regions of the body-the head, the trunk, the tail and so on is established. This plan helps seemingly identical combinations of tissues arrange themselves into distinctly different anatomical structures, such as arms and legs. Individual genes mediate some of the developmental decisions involved in establishing the embryonic body plan.

The make of plans and blueprints prior something is made, and making decisions, is ALWAYS the result of intelligence. 

Key is a family of genes, known as homeobox genes, that subdivides the early embryo into fields of cells with the potential to become specific tissues and organs. 

Hox genes encode a group of transcription factors, responsible for developmental processes and the establishment of the body plan. All Hox genes and many other developmental transcription factors contain the homeobox, a DNA sequence encoding the functional DNA-binding domain. Hox genes are known for their colinearity: conserved arrangement on chromosomes that is the same as their order of activation along the body axis. The regulation is very precise, for example, the regions of activity of Hox genes are tightly confined to specific rhombomeres ( see picture below ) or to segments of the vertebrate anteroposterior body axis



The vertebrate Hox genes are synchronized: the expression domains of paralogs ( either of a pair of genes that derive from the same ancestral gene )  from the A, B, C and D clusters are virtually identical

The mechanisms responsible for the synchronous regulation of Hox genes and the molecular function of their colinearity remain unknown. Despite 35 years of active research, the mechanisms of Hox gene regulation have remained elusive. It has been argued that chromatin structure and histone demethylation play important roles in activation of Hox genes, but the mechanism precisely directing chromatin modifications to specific loci at the right time remains mysterious. Ultraconserved regions and regulatory elements have been found within the coding sequences of Hox genes, but the key questions remain unanswered. It is unknown what mechanism could be responsible for the exceptional synchronous colinearity of Hox gene clusters and the conserved synteny of other pairs of groups of homeobox-containing genes, however, the topology of chromatin has been proposed to play a role in the regulation of these genes. 2

The Homeotic Selector Genes




1. Behe, Edge of evolution, page 116
2. https://www.nature.com/articles/srep35415#ref32
10. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891803/

Hox genes
One of the most exciting and unexpected discoveries that occurred soon after the cloning of the Hox genes was the detection of genes with related sequences in all sorts of animals. Using the homeobox to search for similar sequences in other genomes by hybridization, researchers isolated Hox-related genes from a broad sample of other animals. The similarity between the sequences of the homeodomains of genes isolated from frogs, mice, and humans and the
original Drosophila Hox sequences was surprisingly extensive given the vast evolutionary distances between these animals. As many as 59 of the 60 amino acid residues were shared between the most similar homeodomains 


The similarities of Drosophila and vertebrate Hox protein sequences
The sequence of the Drosophila Dfd homeodomain and C-terminal flanking region and the sequences of several members of the vertebrate Hox 4 genes are shown. Note the great sequence similarity between the Drosophila and vertebrate proteins, and among the vertebrate Hox proteins.

An even greater surprise emerged with the physical mapping of vertebrate Hox genes. The map revealed that these Hox genes occurred in four large, linked complexes and that the order of the Hox genes within these complexes paralleled the order of their most related counterparts in the insect Hox complexes 


Hox gene complexes and expression in vertebrates
(a) In the mouse, four complexes of Hox genes, comprising 39 genes in all, occur on four different chromosomes. Not every gene is represented in each complex, however. 
(b) The Hox genes are expressed in distinct rostrocaudal domains of the mouse embryo.

The vertebrate complexes define groups of Hox genes, compared with the eight genes in Drosophila, although not every Hox gene is represented in each vertebrate complex. Furthermore, the relative order of expression of vertebrate Hox genes along the anteroposterior (rostrocaudal) axis of vertebrate embryos correlates with gene position in each complex. With the invention of techniques for knocking out gene function in mice, it became possible to analyze the functions of the 39 Hox genes in the four mouse Hox complexes. This analysis has been complicated by genetic redundancy that is, the expression and function of two or more similar Hox genes in overlapping domains. In some cases, loss of function of a specific Hox gene causes the homeotic transformation of the identity of particular repeated structures, such as vertebrae, and, in other cases, the loss of particular organs. 


The morphologies of different regions of the vertebral column are regulated by Hox genes. 
(a) In the mouse, normally six lumbar vertebrae arise just anterior to the sacral vertebrae. 
(b) In mice lacking the function of the posteriorly acting Hoxd11 gene, and possessing one functional copy of the Hoxd11 gene, seven lumbar vertebrae form and one sacral vertebra is lost. 
(c) In mice lacking both Hoxa11 and Hoxd11 function, eight lumbar vertebrae form and two sacral vertebrae are lost. The anterior limit of Hoxd11 expression is at the first sacral vertebrae. Loss of these Hox gene functions transforms the sacral vertebrae into lumbar vertebrae.

Conversely, the expression of Hox genes in more anterior sites often causes the reciprocal transformations. Similar results have been obtained in birds, amphibians, and fish, which indicates that in vertebrates, as well as Drosophila, Hox genes act as region-specific selector genes. Hox genes also affect the development of unsegmented animals. In the nematode Caenorhabditis elegans, for example, Hox genes regulate the differentiation of cell types and certain structures along the main body axis. As Hox genes have been found on all branches of the metazoan tree and play such important roles in body patterning, we will devote considerable attention to their evolution and function in later chapters.