Wednesday, September 15, 2010

Punctuated equillibria

Explanation of stasis:
1. Require very strong selection pressure , at normal (casual) condition species tends to remain unchanged because there is a high price to pay to break a already-well-adapted team of genes. But when the selection pressure is sufficiently high paying the price may be feasible.
2. animal respond to minor change in environment by migrating.
3. Different directionality of change in a population (I don't favor it).

Monday, August 23, 2010

chital deer and Lengura

In Mangrove forests an interesting relation is observed between chital deer and Lengura. Chital deer graze in the jungle floor where lengura are found on the branches of the trees above. When lengura spot any danger (especially tiger) they give alarm signal and this help chital to escape. But why lengura help chitals?

Actually the relation is not one-sided, both group are benefited by mutual co-operation. From the tree branches the langura can visually cover a significant portion of the surrounding, the chitals have good sense of smell which can detect the presence of hidden danger. So these two group complement each other.

Friday, August 13, 2010

Feline versus Canine muscle

Felines are very agile and athletic
Felines have predominantly fast twisting muscle

Canine muscles are slow twisting, they have greater stamina.

Tuesday, July 27, 2010

Ecosytem

What is eco-system?

Ecosystem is the inter-relationship among the living-things inhabiting a certain part of the world and between living and non-living thing at that part of the world.

All parts of the world is part of a system which is highly interconnected, disturbing one component can effect seemingly remote and superficially unrelated component.

why we need functioning ecosystem?

Practically we are dependent on certain product of the eco-system. we need some animals as food, some plants for drugs, wood, etc. We may like to protect them. But there are other plants and animals that are considered menace, we may try to get rid of them. But the point is we can't consider this or that organism separately. All animal and plant are part of a system called eco-system. If we try to exterminate all bad (in naive view) species of life and help the good ones to flourish, it will not work. Because all good or bad are connected in intricate way, destroying one will inevitably effect the other. Non-living part of the environment is also part of the eco-system so should also treat abiotic component of the environment with discretion.
We stumble into the world and we find that the world is ready there to provide us with certain facilities. There are certain systems that keep us alive. oxygen level, co2 level, ozone layer, fresh water etc. A lots of narrow parameters are maintained , the world is in a kind of dynamic equilibrium and we evolved to live in certain fixed condition. Living organism can tolerate mild fluctuation but extreme alternation of the environment they live- is lethal. The dynamic equilibrium observed in the natural world is maintained by a intricate connection among many components. The whole bio-sphere is a kind of machine. Loss of a part can destroy the whole system. All components are important because they are connected. Agitation at one end is capable of reaching the other end so disturbing any part of ecosystem can have very far-reaching effect.

Why we are so frightened about changing the eco-system, after-all if we consider the history of the life on earth it has changed all the way from the very beginning to now?

The truth is that the eco-system was never in a fixed condition. It has been changing all the time. The history of life on earth is mostly about extinction, ecosystem changed (for various reason) some species fall short, other species more suited the need of the changed situation and replaced the unfit ones or some species ramified and given birth to completely new specie. The fact is - about 99.9999% of all life on earth ever existed has gone extinct. So extinction is a natural process it is nothing new. But it's not good for existing species. The life on earth will still survive after all of our activities but we are the ones going to perish.

Friday, June 4, 2010

Evolution

Possibility of falsifying evolution:
Only a single fossil in the wrong place.


Evidence:


1. Fossil always comes out in right place
2. Vestigial organ, relic ( coccyx, appendix, wing of flightless bird, ear muscle in human etc)
3. vestigial gene (hen's tooth, our vitamin C gene)
4. Distribution of animals across the globe is consistent with evolution (why there so many marsupials in Australia)
4. Intermediate fossil (toothed bird archeopterix, lungfishtype fossil fish)
5. Imperfection in design (consistent with evolutionary mechanism e.g dummy eyes, Body parts are not arranged beautifully enough, aesthetic value is ignored only usefulness is considered)
6. Rube goldberg machine (evolution progress by tinkering existing machine, un-necessary complication)
7. Every single animal body plan is consistent with this view
8. New knowledge is acquired every day, up to now each one of them is consistent with this view
9. Animal behavior completely consistent with darwinism (e.g no genuine altruism can be found in nature which is against darwinism)
10. Laboratory demonstration (bacteriophage evolving, antibiotic resistance, evolution machine)
11. Existing example of speciation (ring species of lizard)

Evidence is so overwhelming and comes from every corner and every branch of science
that there is only two possibilities

i) origin of species through natural selection

ii) God created all of the organisms separately but he has also arranged the anatomy in such a way that we can construct a consistent family tree.
He has also placed each and every fossil in the rocks in such a way to support the
constructed tree.
He has also deliberately placed specific sequence in different organisms from which we would be able to deduce the same tree.


He hasn't done it in mistake. Because mistake can't be so well organized so he must had a motive when he did it. Likely motive can be to mislead those who wants to know the truth. It doesn't go with godly nature. So it may be that he didn't create any creatures separately.

Now the question arise do we need any outside intervention to produce diverge life forms as we have here on earth. The answer is no.
In appropriate condition (early earth) life can origin from inanimate matter in its most simplest form and subsequently evolve to more and more complex organisms.
How we know?
From experiment in laboratory ,
through examples in the nature
and through our understanding of life.



How can we distinguish i) from ii)?
If ii) is right then there is chance that oneday fossil will began to rise from wrong places.

Still theory of evolution will not be falsified because there is laboratory and real life demonstration that it can work though it was not the case for our planet. In other words evolution through natural selection can create complex life from simplicity but it didn't happened in our earth , god choose to do it in his own hand one by one- each species. Not only that to resist evolution from creating new species he must come down frequently to interrupt evolutionary process and fail it. He has to make constant effort in restraining evolution from creating new species and as a result break the laws of nature very frequently.
We are also confident that if god don't interfere, evolution of life can take the exact trajectory that we have worked out by studying fossils, DNA so on. That is our tree of life is a valid and consistent one in virtually every detail -we looked at.

Evolution through natural selection is not a local theory its a global theory.

Will God punish evolutionary biologist?


If there is a personal God, we expect him to be just. A just God can't punish peoples who searched for truth. If a God hasn't interfered in the creation process then the evolutionary biologist are correct it would be outrageous if they are punished. And if God really created all species one by one then he has also planted false evidences everywhere on the earth, in rocks,in body anatomies of organisms ,in their cellular anatomies ,in their DNA sequences , RNA sequences and structures, protein sequences and structures and so-on and so forth. Everywhere on our planet from rocks to DNA there is the signature of evolution. If this whole things are arranged then it seems as GOD is trying to convince truth-seekers in most convincing way that evolution has brought all the species on our planet. It will not only be unjust but also very deceitful to trap honest peoples and punish them in this way. This kind of act is not consistent will Godly nature.

Thursday, June 3, 2010

What is a species and what is not?

by Ernst Mayr

1. What is a species, and what is not? As someone who has published books and papers on the biological species for more than 50 years, and who has revised and studied in detail more than 500 species of birds and many species of other groups of organisms, the reading of some recent papers on species has been a rather troubling experience. There is only one term that fits some of these authors: armchair taxonomists. Since many authors have never personally analyzed any species populations or studied species in nature, they lack any feeling for what species actually are. Darwin already knew this when, in September 1845, he wrote to Joseph Hooker: "How painfully true is your remark that no one has hardly the right to examine the question of species who has not minutely described many." (Darwin 1987, 253). These authors make a number of mistakes that have been pointed out again and again in the recent literature. Admittedly, the relevant literature is quite scattered, and some of it is perhaps rather inaccessible to a non-taxonomist. Yet, because the species concept is an important concept in the philosophy of science, every effort should be made to clarify it. It occurred to me that instead of criticizing certain recently published papers individually, it would be more constructive and helpful if I would here attempt to present, from the perspective of a practicing systematist, a concise overview of the philosophically important aspects of the problem of the 'species'. There is nothing of the sort in the literature.

The species is the principal unit of evolution and it is impossible to write about evolution, and indeed about almost any aspect of the philosophy of biology, without having a sound understanding of the meaning of biological species. A study of the history of the species problem helps to dispel some of the misconceptions (Mayr 1957, Grant 1994).

2. Species of organisms are concrete phenomena of nature. Some recent authors have dealt with the concept of species as if it were merely an arbitrary, man-made concept, like the concepts of reduction, demarcation, cause, derivation, prediction, progress, each of which may have almost as many definitions as there are authors who have written about them. However, the concept biological species is not like such concepts. The term 'species' refers to a concrete phenomenon of nature and this fact severely constrains the number and kinds of possible definitions. The word 'species' is, like the words 'planet' or 'moon,' a technical term for a concrete phenomenon. One cannot propose a new definition of a planet as "a satellite of a sun that has its own satellite," because this would exclude Venus, and some other planets without moons. A definition of any class of objects must be applicable to any member of this class and exclude reference to attributes not characteristic of this class. This is why any definition of the term 'species' must be based on careful study of the phenomenon of nature to which this term is applied. Alas, this necessity is not appreciated by all too many of those who have recently discussed the species problem after a mere analysis of the literature.

The conclusion that there are concrete describable objects in nature which deserve to be called "species" is not unanimously accepted. There has been a widespread view that species are only arbitrary artifacts of the human mind, as some nominalists, in particular, have claimed. Their arguments were criticized by Mayr (1949a, 371).

3. Why are there species of organisms? Why is the total genetic variability of nature organized in the form of discrete packages, called species? Why are there species in nature? What is their significance? The Darwinian always asks why questions because he knows that everything in living nature is the product of evolution and must have had some selective significance in order to have evolved. (1) He therefore asks: What selection forces in nature favor the origin and maintenance of species? The answer to this question becomes evident when one makes a certain thought experiment.

"It is quite possible to think of a world in which species do not exist but are replaced by a single reproductive community of individuals, each one different from every other one, and each one capable of reproducing with those other individuals that are most similar to it. Each individual would then be the center of a concentric series of circles of genetically more and more unlike individuals. What would be the consequence of the continuous uninterrupted gene flow through such a large system? In each generation certain individuals would have a selective advantage because they have a gene complex that is specially adapted to a particular ecological situation. However, most of these favorable combinations would be broken up by pairing with individuals with a gene complex adapted to a slightly different environment. In such a system there is no defense against the destruction of superior gene combinations except the abandonment of sexual reproduction. It is obvious that any system that prevents such unrestricted outcrossing is superior'' (2) (Mayr 1949b, 282). The biological species is such a system.

The biological meaning of species is thus quite apparent: "The segregation of the total genetic variability of nature into discrete packages, so called species, which are separated from each other by reproductive barriers, prevents the production of too great a number of disharmonious incompatible gene combinations. This is the basic biological meaning of species and this is the reason why there are discontinuities between sympatric species. We do know that genotypes are extremely complex epigenetic systems. There are severe limits to the amount of genetic variability that can be accommodated in a single gene pool without producing too many incompatible gene combinations" (Mayr 1969, 316). The validity of this argument is substantiated by the fact that hybrids between species, particularly in animals, are almost always of inferior viability and more extreme hybrids are usually even sterile. "Almost always" means that there are species interpreted to be the result of hybridization, particularly among plants, but except for the special case of allopolyploidy, such cases are rare.

Among the attributes members of a species share, the only ones that are of crucial significance for the species definition are those which serve the biological purpose of the species, that is, the protection of a harmonious gene pool. These attributes were named by Dobzhansky (1935) isolating mechanisms. It is immaterial whether or not the term isolating mechanism was well chosen, nor is it important whether one places the stress on the prevention of interbreeding with non-conspecific individuals or the facilitation ("recognition") of breeding with conspecific individuals. The concept I have just developed is articulated in the so-called biological species definition: "Species are groups of interbreeding natural populations that are reproductively isolated from other such groups." The isolating mechanism by which reproductive isolation is effected are properties of individuals. Geographic isolation therefore does not qualify as an isolating mechanism.

Reproductive Isolation. The Biological Species definition includes the statement that the populations of one species are "reproductively isolated" from the populations of all other species. Typologically conceived, this would mean that no individual of species A would ever hybridize with any individual of species B. Botanists soon pointed out that this did not correctly describe many situations in nature. They discovered case alter case of occasional (sometimes even rather frequent) hybridization between seemingly "good" sympatric species. Anderson (1949) went so far as to claim that this was the normal situation with closely related sympatric species and that through such "introgressive hybridization," as he called it, either species would be enriched by genes from other species. Other authors minimized the frequency of such hybridization and considered parallel variation in sympatric species as the residues of ancestral polymorphisms. Recent molecular analysis has, however, confirmed the frequency of clandestine introgression. However, if the two species continue their essential integrity, they will be treated as species, in spite of the slight inefficiency of their isolating mechanisms.

There is at least one case among oaks (Quercus) and one among birches (Betula) where such introgression has apparently been going on for millions of years without leading to a fusion of the parental species. Similar cases apparently occur also in animals. After the destruction of much of the southern periphery of the habitat of the gray wolf, the area was invaded by coyotes and, owing to the fertility of the hybrids, the crossing of male wolves with female coyotes led to an introgression of alien genes into both wolf and coyote populations. The same was shown by Templeton and associates (1989, 12) for the sympatric Hawaiian species Drosophila silvestris and D. heteroneura. The fact that the mitochondria are inherited only through the females greatly facilitates the discovery of such cases of hybridization.

It is thus well established that a leakage of genes occurs among many good "reproductively isolated" species. This induced me to revise the definition of isolating mechanisms to "biological properties of individuals which prevent the interbreeding [fusion] of populations"(1970, 56). Thus, isolating mechanisms do not always prevent the occasional interbreeding of non-conspecific individuals, but they nevertheless prevent the complete fusion of such species populations. Clandestine hybridization is apparently far more common among plants than among higher animals.

Among the invalid objections to the biological species concept is the claim that it would work only if the acquisition of the isolating mechanisms was a teleological process (Paterson 1985). However, Darwin already knew that reproductive isolation between species is not acquired by teleological ad hoc selection but simply as a byproduct of the process of divergence. H. J. Muller and E. Mayr have further emphasized this point in their writings and Mayr in particular has demonstrated that indeed behavioral isolating mechanisms can be acquired through a change of function of factors favoring sexual selection. Paterson's arguments do not in the least weaken the validity of the BSC (Mayr 1988b, Coyne et al. 1987). The contingent nature of the acquisition of isolating mechanisms is documented by their great diversity. It would seem to be merely a matter of chance what kind of device is made use of by a given incipient species to protect itself against outcrossing. It includes not only purely genetic mechanisms such as sterility factors, but the use of ecological and life history factors and (in animals) a number of behavioral devices.

The evolutionist always stresses the genetic uniqueness of every individual of a sexually reproducing population. However, the members of any species also have in common many species-specific properties. This includes, in particular, the isolating mechanisms but also many adaptations, for instance, for niche utilization, as well as certain contingent, species specific properties. If one knew the genetic basis of all the species specific characters, one might be able to give a genetic characterization of a species taxon.

The BSC is based on the recognition of properties of populations. It depends on the fact of non-interbreeding with other populations. For this reason the concept is not applicable to organisms which do not form sexual populations. The supporters of the BSC therefore agree with their critics that the BSC does not apply to asexual (uniparental) organisms. Their genotype does not require any protection because it is not threatened by destruction through outcrossing. There are a number of suggestions of how species taxa in asexual organisms can be delimited and defined, but this is outside the present discussion. However, I find that any endeavor to propose a species definition that is equally applicable to both sexually reproducing and asexual populations misses the basic characteristics of the biological species definition (the protection of harmonious gene pools).

It is important to emphasize that in the study of biological species one deals with biological populations. Some non-biologists, including some philosophers, seem to have difficulties appreciating how different biological populations are from classes of inanimate objects (Kitcher 1989, 189 ~ 194). Only a small fraction of any biological population reproduces, because not every individual in a population survives up to the reproductive age and reproduces successfully. This is true on the average for only two of the total number of offspring of a prenatal pair in a sexually reproducing species. A mentally retarded individual may have no opportunity to reproduce but he is still a member of his population. In most marine organisms, with their high number of larvae, successful survival and reproduction is to a large extent a matter of chance, but most of the zygotes have, at the moment of their formation, an equal probability of success. Kitcher describes six situations which to him seem to cause difficulty for the concept of population as presented by me. I believe that his objections can be answered, although it would take me too far afield to do so here. The simplest solution in most cases is to say that whatever is the product of the same gene pool belongs to the same population, together with any new immigrants.

4. The two meanings of the term species. What the scientist actually encounters in nature are populations of organisms. There is a considerable range in the size of populations, ranging from the local deme to the species taxon. the local deme is the community of potentially interbreeding individuals at a locality (see also Mayr 1963. 136), and the species taxon has been referred to by Dobzhansky as the "largest Mendelian population." The task of the biologist is to assign these populations to species. This requires two operations: (1) to develop a concept of what a species is resulting in the definition of the species category in the Linnaean hierarchy, and (2) to apply this concept when combining populations into species taxa.

A number of recent writers on the species problem have failed to appreciate that the word 'species' is applied to these two quite different entities in nature, species taxa and the concept of the category species. As a result, their so-called species definition is nothing but a recipe for the demarcation of species taxa. This is, for instance, true for most of the recent so-called phylogenetic species definitions. It is also largely true for Templeton's (1989, 1994) cohesion species concept. A paper often quoted as a decisive refutation of the BSC (Sokal and Crovello 1970) is perhaps an extreme example of the confusion resulting from the failure to discriminate between the species as category (concept) and as taxon.

(1) The species taxon. The word taxon refers to a concrete zoological or botanical object consisting of a classifiable population (or group of populations) of organisms. The house sparrow (Passer domesticus) and the potato (Solanum tubersum) are species taxa. Species taxa are particulars, "individuals," biopopulations. Being particulars, they can be described and delimited against other species taxa.

(2) The species category. Here the word 'species' indicates the rank in the Linnaean hierarchy. The species category is the class that contains all taxa of species rank. It articulates the concept of the biological species and is defined by the species definition. The principal use of the species definition is to facilitate a decision on the ranking of species level populations, that is, to answer the question about an isolated population: "Is it a full species or a subspecies?" The answer to this question has to be based on inference (the criteria on the basis of which such a decision is made are listed in the technical taxonomical literature, e.g., in Mayr and Ashlock 1991, 100-105). A complication is produced by the fact that in the Linnaean hierarchy asexual "species" are also ranked in the species category, even though they do not represent the BSC.

The literature traditionally has referred to the "species problem." However, it is now quite clear that there are two different sets of species problems, one being the problem of how to define the species (what species concept to adopt), and the other being how to apply this concept in the demarcation of species taxa. It is necessary to discuss these two sets of problems separately.

Let me begin with a discussion of the meaning and history of the term 'biological species'.

5. Typological species versus biological species. The biological species concept developed in the second half of the 19th century. up to that time, from Plato and Aristotle until Linnaeus and early 19th century authors, one simply recognized "species," eide (Plato), or kinds (Mill). Since neither the taxonomists nor the philosophers made a strict distinction between inanimate things and biological species, the species definitions they gave were rather variable and not very specific. The word 'species' conveyed the idea of a class of objects, members of which shared certain defining properties. Its definition distinguished a species from all others. Such a class is constant, it does not change in time, all deviations from the definition of the class are merely "accidents," that is, imperfect manifestations of the essence (eidos). Mill in 1843 introduced the word 'kind' for species (and John Venn introduced 'natural kind' in 1866) and philosophers have since used the term natural kind occasionally for species (as defined above), particularly after B. Russell and Quine had adopted it. However, if one reads a history of the term 'natural kind' (Hacking 1991) one has the impression that no two authors understood quite the same thing by this term, nor did they clearly discriminate between a term for classes of inanimate objects and biological populations of organisms. There is some discussion among philosophers whether there are several types of natural kinds. But I will refrain from entering that discussion. The traditional species concept going back to Plato's eidos is often referred to as the typological species concept.

The current use of the term species for inanimate objects like nuclear species or species of minerals reflects this classical concept. Up to the 19th century this was the most practical species concept also in biology. The naturalists were busy making an inventory of species in nature and the method they used for the discrimination of species was the identification procedure of downward classification (Mayr 1982, 1992a). Species were recognized by their differences, they were kinds, they were types. This concept was usually referred to as the morphological or typological species concept.

Even though this was virtually the universal concept of species, there were a number of prophetic spirits who, in their writings, foreshadowed a different species concept, later designated as the biological species concept (BSC). The first among these was perhaps Buffon (Sloan 1987), but a careful search through the natural history literature would probably yield quite a few similar statements. Darwin unquestionably had adopted a biological species concept in the 1830s in his Transmutation Notebook even though later he largely gave it up (Kottler 1978, Mayr 1992b). Throughout the 19th century, quite a few authors proposed a species definition that was an approach to the BSC (Mayr 1957).

Late in the 19th century and in the first quarter of the 20th century, taxonomists like K. Jordan, E. Poulton, L. Plate, and E. Stresemann were among those who most clearly articulated the biological species concept, as will be shown below.

As long as the inventory taking of kinds of organisms was the primary concern of the students of species, the typological species concept was a reasonably satisfactory concept. But when species were studied more carefully, all sorts of properties were discovered that did not fit with a species concept that was strictly based on morphology. This was particularly true for behavioral and ecological properties. Most damaging was the discovery of the unreliability of morphological characters for the recognition of biological species.

Morphological difference had traditionally been the decisive criterion of species. Population A (e.g., continental North American savanna sparrows) was determined to be a different species from population B (e.g., savanna sparrows from Sable Island, Nova Scotia), if it was deemed to be sufficiently different from it by morphological characters. This definition was very useful in various clerical operations of the taxonomist such as in the cataloguing of species taxa and their arrangement in keys and in collections. However, for two reasons it was inadequate if not misleading for a study of species in nature. The first one is that, as is now realized, there are many good biological species that do not differ at all morphologically or only very slightly. Such cryptic species have been designated sibling species. They occur at lesser or greater frequency in almost all groups of organisms (Mayr 1948). They are apparently particularly common among protozoans. Sonneborn (1975) eventually recognized 14 sibling species under what he had originally considered a single species, Paramecium aurelia. Many sibling species are genetically as different from each other as morphologically highly distinct species. A second reason why a morphological species concept proved unsatisfactory is that there are often numerous different morphological types within a biological species, either due to individual genetic variation or due to different life history categories (males, females, immatures) which are morphologically far more different from each other than are the corresponding morphological types in different species.

The morphological difference between two species fails to shed any light on the true biological significance of species, the Darwinian why question. So-called "morphological species definitions" are in principle merely operational instructions for the demarcation of species taxa. The realization of these deficiencies of the typological species concept led, in due time, to its almost complete replacement among zoologists by the so-called biological species concept (BSC).

Many of the authors who profess to adhere to the morphological species concept do not seem to realize that unconsciously they base their decisions ultimately on the reproductive community principle of the BSC. They combine drastically different phenotypes into a single species because they have observed that they were produced by the same gene pool. This was already done by Linnaeus when he synonymized the names he had given to the female mallard and the immature goshawk.

6. Insufficient or erroneous species criteria.

6.1 Characterized by its Evolutionary Potential. Some 50 years ago the fact that species are not constant but the product of evolution and still potentially continuing to evolve was included by several authors in the species definition. For instance, in 1945 A.E. Emerson defined the biological species as follows: "a species is an evolved or evolving genetically distinctive, reproductively isolated, natural population." Indeed, nothing distinguishes a biological species better from a natural kind than its capacity to evolve. Yet, this is not a sufficient criterion. Everything else in living nature also has the capacity to evolve. Every population, every structure and organ is the product of evolution and continues to evolve, genera and higher taxa evolve, and so do faunas and floras. Most of all, the capacity for evolving is not the crucial biological criterion of a species, which is the protection of its gene pool. It is for this reason that I and most adherents of the biological species concept omit "evolving" from the species definition. Those authors who still emphasize the evolutionary aspect of the species have never made it clear what the real significance of species is.

The paleontologist Simpson attempted to make evolution the basis of a species concept: "An evolutionary species is a lineage (an ancestral-descendant sequence of populations) evolving separately from others and with its own unitary evolutionary role and tendencies." (1961, 153). He replaced the clear-cut criterion (reproductive isolation) of the biological species concept with such undefined vague terms as "maintains its identity" (does this include geographical barriers?), "evolutionary tendencies" (what are they and how can they be determined?). and "historical fate." What population in nature can ever be classified by its "historical fate" when this is entirely in the future?

Furthermore, as I pointed out previously (Mayr 1988a. 323-324), this concept encounters three additional major difficulties: (1) it is applicable only to monotypic species and every geographical isolate would, by implication, have to be treated as a different species; (2) there are no empirical criteria by which either evolutionary tendency or historical fate can be observed in a given fossil sample (Simpson 1961, 154-l60): and (3) the definition does not help in the lower or upper demarcation of chronospecies, even though the main reason why the evolutionary species concept was apparently introduced, was in order to deal with the time dimension, which is not considered in the non-dimensional biological species concept. Indeed, Simpson's definition is essentially an operational recipe for the demarcation of fossil species.

6.2 Other Unsatisfactory Species Concepts. The so-called phylogenetic species concept (Wheeler, 1996) is actually nothing more than the revival of a purely morphological species concept (Mayr 1996). The so-called ecological species concept, based on the niche occupation of a species, is for two reasons not workable. In almost all more widespread species there are local populations which differ in their niche occupation. An ecological species definition would require that these populations be called different species even though, on the basis of all other criteria, it is obvious that they are not. More fatal for the ecological species concept are the trophic species of cichlids (A. Meyer 1990) which differentiate within a single set of offspring from the same parents. Finally, there are the numerous cases (but none exhaustively analyzed) where two sympatric species seem to occupy the same niche, in conflict with Gause's rule. All this evidence shows not only how many difficulties an ecological species concept faces but also how unable it is to answer the Darwinian why? question for the existence of species.

Perhaps Templeton's (1989, 1994) cohesion species concept should be mentioned here. It attempts to combine the best components of several other species concepts but fails to escape the resulting conflicts. It emphasizes the presence of gene flow, but fails to distinguish between the internal (isolating mechanisms) and external (geographic isolation) barriers to gene flow; it stresses cohesion through gene flow, but claims also to be "applicable to taxa reproducing asexually," which have no gene flow. It attempts to characterize an evolutionary lineage, but does not indicate how to delimit such an open ended lineage at either end: and he does not state how to deal with the geographic variation of demographic-ecological attributes in widespread polytypic species. I do not see any advantages of this concept over the BSC.

6.3 Two Origins of Species. Normally one calls a population a species when it has acquired isolating mechanisms, protecting its gene pool against its parental or a sister species. In other words, such a species is the product of the process of multiplication of species. However, the paleontologist encounters also cases where a phyletic lineage changes over time to such a degree that sooner or later it is considered to be a different species. The occurrence of the origin of such phyletic species is usually ignored when non-paleontologists speak of speciation. Phyletic evolution does not produce an additional entity, it merely modifies an existing one. Nevertheless, the changes are sometimes sufficiently pronounced so that the paleontologist gives a new species name to the modified phyletic lineage. Gingerich (1979), in particular, has called attention to the relative infrequency of such cases. Such new species differ usually only in size and proportions, but not in the acquisition of any notable innovations. Such phyletic speciation must be mentioned because it is what a paleontologist usually seems to have in mind when he speaks of speciation. It is for such species that Simpson proposed the evolutionary species definition. It has been impossible so far to discover any criteria by which a phyletic species can be demarcated against ancestral and descendent "species." It is for this reason that Hennig (1966) rejects the recognition of new species without branching.

In his discussion of the origin of species, Hennig (1966) only considers the case of a phyletic lineage splitting by dichopatric speciation into two daughter species. He considers both daughter species as new species. He ignores the more frequent case where by budding from a phyletic lineage a new daughter species originates through peripatric speciation. By his definition, Hennig is forced to call the phyletic lineage after the budding point a new species, even though it has not changed at all. Hennig's species definition results also in difficulties when a phyletic lineage gradually changes into a new species, even though there has been no splitting of the lineage nor any budding. Hennig is forced to ignore such phyletic speciation no matter how conclusive the indirect (morphological) evidence for the origin of a new species may be. On the whole, whenever a biologist speaks of species, he has in mind the product of the process of multiplication of species, not the product of phyletic evolution.

6.4 Multidimensional Species Taxa. Species taxa ordinarily have an extension in space (geography) and in time. They are composed of local or temporally circumscribed populations which differ slightly from each other. Such populations, when they are considered to be conspecific, are combined into a polytypic species. The major species problem in species level taxonomy is to decide which local populations to combine into polytypic species. Since this decision is based on inference, it is always somewhat uncertain. The paleontologist encounters in the time dimension the same problem which the student of the geographic variation of species encounters in the spatial dimension. During the period when the typological species concept was dominant, almost any isolated population that differed by a morphological character was called a different species. Since the rise of the biological species concept, the question is always asked whether or not such a population would interbreed with other populations differing in space or time if they would meet in nature.

The widespread use of polytypic species has several advantages for information conveyance as pointed out by Mayr and Ashlock (1991.41). Conspecific populations that differ from each other morphologically are called subspecies. If such subspecies are part of a series of contiguous populations, they are a purely taxonomic device. However, they are incipient species if such subspecies are geographically isolated. They may in due time acquire the needed isolating mechanisms to function as well separated species. Owing to the gradualness of the process of speciation, every incipient species at one time in its cycle goes through the subspecies stage.

7. A major criticism of the biological species concept. The biological species concept is least vulnerable to criticism in the non-dimensional situation, as I have emphasized in numerous previous papers. When two populations (in reproductive condition) meet at the same place at the same time, they either interbreed because they are conspecific or they do not do so because they are different reproductive communities (different species). In that case, their isolating mechanisms keep them apart.

A geographically isolated population also has the isolating mechanisms of the species to which it belongs, but they are, so to speak, invisible, since they do not need to be activated. In some of my earlier species definitions I said of isolated populations that they might be "potentially" reproductively isolated. If in the future any contact with a different species population was going to be established, the isolating mechanism would at once spring into action, thereby documenting their existence.

Speciation, as Darwin has shown, is normally a gradual populational phenomenon. Sudden, saltational speciation as in the case of' allopolyploidy, seems to be virtually absent in most groups of sexually reproducing organisms. Owing to the gradualness of the speciation process one should find in nature populations that are on the way to becoming separate species, but have not yet quite completed the process. Such "semi-species" are indeed found. They are documented, for instance, by the so-called zones of secondary hybridization. Here two incipient species, usually expanding from a Pleistocene refuge, hybridize along a more or less long contact line, but the hybrid zone stays narrow, often less than 100 km wide, even though this contact zone may have existed for 5-10,000 years. Both of the two semi-species discriminate against introgressing genes of the other semi-species, as documented by the lowered fertility of hybrid pairs. Hybridization is too indiscriminate in the contact zone to permit a selection for isolating mechanisms, as Darwin already remarked. The effects of continuing hybridization completely override the counterselection against inferior hybrids and introgressing genes so that it does not come to any parapatric speciation. Isolating mechanisms, however, can be further improved after speciation between overlapping species has been complete (Bullin 1989: Lion and Price 1994)

During a period of geographic isolation the presence of species specific isolating mechanisms can only be inferred. Curiously, there are large numbers of taxonomists who seem to be unaware how frequent the need is for inference making in scientific theorizing. The most helpful inference on the species status of isolated populations is greater morphological difference as compared to other populations that are seemingly conspecific. To be able to use degree of morphological difference in order to be able to infer species status, one must have a "yard stick," which determines which of the isolated populations already have reached species status and which others have not. Constructing such a yard stick requires a thorough knowledge of related species and subspecies and is a rather technical procedure. It is described in Mayr and Ashlock 1991, 100-105.

What must be emphasized, because this is so often misunderstood, is that this procedure is not a falling back on a morphological species concept, but simply uses the degree of morphological difference as an indication of the underlying degree of reproductive isolation. This procedure is very much the same as that described so perceptively by G.G. Simpson (1961) for identical twins: an individual is an identical twin not because he is so similar to another individual, but rather, he is so similar to it because he is its identical (monozygotic) twin. Analogously, an individual belongs to species X not because it has the same species specific characters as other individuals of species X, but it has these species specific characteristics because, like other conspecifics, it is part of the species.

Curiously, Mahner (1994) has reversed the roles of the concept of reproductive community and species-specific characters. For a Darwinian to determine the significance of a biological process one always starts with the Darwinian why question. As far as the species is concerned, the answer clearly is protection of the gene pool through establishment of a reproductive community. The next question is how, and here the answer is isolating mechanisms and other species-specific attributes. These are indicators of species status, but do not constitute the basic meaning of species. I have pointed this out as the reason why isolation is the primary and recognition (the answer to the how question) the secondary aspect of the species (Mayr 1988b). When I used morphological inferences (Mayr 1992a) to determine which nominal species of plants in the township of Concord (Massachusetts) were good biological species, I did not shift to a morphological species concept, as Whittemore (1993) seemed to think.

8. The ontology of the species taxon. A considerable clarification of the status of species taxa was achieved when it was realized by some taxonomists that species taxa are not classes but particulars or "individuals" or biopopulations, or by whatever other term you may want to characterize this difference. Much of the argument on this issue seems to be semantic, and this is not the place to deal once more with this problem. The belief that species are concrete particulars was recently rediscovered by Ghiselin and Hull, but it has actually been the view of many, if not most naturalists for more than one hundred years, as I have shown (Mayr 1988a). As early as 1866, Haeckel said "die art ist ein individuum." For a detailed discussion of this conclusion, see papers by Ghiselin (1971-1972), Hull (1975), and Mayr (1987, 1988a).

One could also say that organisms that belong to sexually reproducing species have two sets of characteristics. First, those that serve as isolating mechanisms and are jointly responsible for the fact that this population of individuals constitutes a biological species, and, second, all other properties of the species. Organisms which belong to two related species usually share a large number of characteristics but this does not make them conspecific. The important thing is that they differ by a certain limited number of attributes, their isolating mechanisms, which prevent them from interbreeding and thus prevent the destruction of the integrity of their gene pool. To repeat, certain individuals are part of a certain species not because they have certain characteristics in common but they share these characteristics because they belong to a single reproductive community, a biological species. And this is the reason why we must rely on the biological meaning of species in articulating the BSC.

9. Difficulties in delimiting species taxa. There are a number of evolutionary processes that make the delimitation of species taxa from each other and the determination of their rank often very difficult. The most important is so-called mosaic evolution. This means that certain characters may evolve much more readily than others. this results in a discord between the message provided by various characters. In particular, reproductive isolation and morphological difference often do not evolve in parallel with each other. This is why sibling species exist; they are reproductively isolated but morphologically indistinguishable. There is no simple recipe by which the problem posed by mosaic evolution can be solved. The decision has to be made in each case on the basis of the totality of information as well as the usefulness of the proposed classification.

What is often the basic problem is an insufficiency of needed information. This is why the decision about the status of isolated populations has to be based on inference, it is not given directly by the available data. This is as true for populations that are geographically isolated as for stages in the evolution of a single phyletic lineage.

The basic message which emerges from this account of the numerous difficulties of the species problem is that the definition of the biological species must be based on its biological significance, which is the maintenance of the integrity of well balanced, harmonious gene pools. The actual demarcation of species taxa uses morphological, geographical, ecological, behavioral, and molecular information to infer the rank of isolated populations.

Notes

1 I am not aware of a single major feature of living nature of which this claim could be refuted.

2 By "superior" I meant would be rewarded by leaving a greater number of viable descendants.

Tuesday, May 25, 2010

Is it impossible to design an importer protein that can selectively import certain molecules without using energy? If not, why?

Ans.:
Cell has high concentration of different substances, it requires energy (we have to do it forcibly, and will not occur spontaneously by itself) so it has some energy stored in this way.
One of the fundamental principles of physics is that entropy of the universe never decreases. To continue living, cell has to concentrate some definite substances inside the cell; this process leads to a decrease in entropy. So according to aforesaid principle, entropy must increase in some other processes. Entropy can increase by simultaneous diffusion of some other substances or simply by dissipation of energy- namely heat. So in principle, it is impossible to design an importer protein that can selectively import certain molecules without using energy of any form (energy can be stored in concentration gradient which can also be harnessed in active transport process).

Tuesday, May 18, 2010

transpiration

Chain of water molecule – evaporating at one end.
The evaporating molecule must move up, with an upward drag. To make the drag more efficient it will be good idea to make a vacuum tube. But even vacuum tube has a limit because after reaching certain height two opposing process gravity and transpiration-drag will reach equilibrium. Solution is adhesion of water molecule to xylem vessel, transferring weight of the water column to the tree itself. Now we have got rid of gravity.
What we'll do when gas bubbles breaks the chain. Answer is make new fibre. Simple!

Wednesday, April 7, 2010

Are recombination random events?

If they are and not because of an existing signal, we should expect the following :

If e.coli is infected by two bacteriophage one functional other not functional, the plague forming unit formed in a given time will be less than when e.coli is infected by only functional bacteriophage (same titer as used in previous experiment). It is because unnecessary recombination event forming some non-functional virus.

Monday, April 5, 2010

What is spin of an electron?

Spin is a quantum number. Quantum number is used to define the state of an electron in an atom.

Quantum numbers:
  1. Principle quantum number indicates distance of the electron from the nucleus
  2. Azimothal quantum number indicates angular momentum of the electron orbiting.
  3. When electron orbits in the orbital it creates a magnetic field which is expressed by magnetic quantum number.
  4. Spin quantum number is an intrinsic magnetic field which arise from the spinning of the electron on it's own axis.
Things written above can't be taken literally. It's only poor analogy drawn between quantum and classical mechanics. From classical theory and experiment we know that moving charge (macroscopic) produce magnetic field. Charge is a fundamental property of matter, there is no question about it's existence. Now the question is whether it is true for fundamental particles like electron or proton. Do moving electron produce magnetic field? I think it does. Because magnetic field is a fundamental thing, if it is not produced by some fundamental action it can't arise at all. From that we can be sure that moving electron must produce magnetic field.

But there is a difficulty in saying that the spin of electron arise from rotating on it's own axis. To produce observed magnetic moment the equatorial region of the electron must rotate at speed more than that of light. And another point that electron don't spin in classical sense is that - to complete a period or make a complete revolution it must rotate 4 pi radian as opposed to 2 pi.

So here are the safe things to say -
1 . Electron has two magnetic field separate from each other.
2. One is associated with the shape of orbital and other is intrinsic.
3. Both of the them are quantized,
4. Spin quantum number can only take two values - +1/2 and -1/2.
5. Electrons in the same orbital must have different spin quantum number.
6. Because spin quantum number can take only two values associated magnetic moment has also two values. If set in a magnetic field it can either align with or against the magnetic field but can't do otherwise (say align in a direction 60 degree with the magnetic field). I don't know the answer why??

Sunday, April 4, 2010

amplification of signal (biological signals)

Fire: Fire is an example of one sort of amplification. Naively amplification of heat, we give a little heat and it get's amplified. Heat is one kind of energy so it's wrong to say amplification of energy. We can think of it as one kind of signal amplification. The existence of fire indicates the existence of initial activation energy. Flammable substances are systems for amplifying a signal namely activation energy. Initial activation energy may be very low to notice but it is transformed to fire which contain large amount of things and light to be noticed.
Production of fire involves chain reaction as shown below.
















In every step the energy released is not completely used in transforming substrate to product, the extra energy is added as the reaction goes on and it gets hot and bright.

Enzymes: Enzymes transform one type of substance to other. One enzyme molecule can easily transform a large amount of substances. This is one sort of amplification.


In biological system one excited enzyme molecule can transform thousands of other molecule in small time. This way signal which excite or activate a single molecule can be amplified. Fire usually amplifies in uncontrolled way but biological signal amplification is controlled.

Finding optimum solution

Enzyme catalysis:
Specificity is about binding. When we say that an enzyme is exclusively specific to a particular substrate it only binds with that substrate and in a sense repel other substances. For being strictly specific correct form of binding must be strictly necessary for catalysis.
This specificity will also result in strong binding. There is a problem with strong binding because if so after the reaction or chemical transformation, product will not easily leave the enzyme and make it available for new substrate. This will slow the actual rate of transformation of substrates. So good enzymes should give only marginal time for reaction to occur and release the product. This is about enzyme affinity for substrate which is directly related to binding. Strong binding (high specificity) will oppose quick release.
Rate of transformation inside the enzyme is also a function of binding. Releasing is also a function of binding. If they were separate event one would say that for a good enzyme, the binding affinity for substrate (of an enzyme) will be such that to match the average time of transformation.
But the reality is that rate and binding affinity is not independent from each other so that they can move freely to be adjusted to an optimum. They are connected - changing binding affinity inconsiderately can effect rate. Rate is not only dependent on substrate binding but also with the binding with transitional state, so there may be ways in which we can change binding affinity still not changing the rate.

Thursday, April 1, 2010

vomitting

There is a place in brain called vomiting center.
Why an organism would like to kick out ingested food?
Because the food may contain poison, pathogen etc.

There may be several signals which tells the brain that the food contain harmful material, then the brain send a signal to vomit.

spinning also induce vomiting. Why?
May be there are some harmful thing which cause the brain to feel spining , that's why spinning feeling is interpretted as harmful thing inside the stomach (I just speculate).

Monday, March 15, 2010

Immune system (innate and adaptive immune system)

Innate immune system work by detecting pathogen associated molecular pattern (PAMP). Pathogen can't escape innate immune system easily because it detect whole structure like LPS, double stranded rna etc. and variation inside them actually don't count. So the only option the pathogen has is to discard the whole structure.

Adaptive immune system helps the body to detect pathogen which body has never even encountered in evolutionary history. It is capable of detecting every non-self structure
very specifically. It is this specificity that characterize adaptive immune system. Like a species can adapt itself to changing condition through natural selection, there is a part of immune system which can adapt itself with the invader (theoretically any invader). That part of immune system is called adaptive immune system. Adaptive immune system has other important property which can be called memory. It can recognize a previously encountered entity and this recognition bring more rapid and strong response than virgin encounter.
Invader's can escape and confuse adaptive immune system by slightly changing their antigenic molecule but not innate immune system. So adaptive immune system confer lasting immunity against a pathogen it has encountered before but this immunity is a specific one- which can be beaten by mutating the corresponding antigenic molecule.

T cells recognize MHC 1 bound antigen.
B cells recognize antigen and the antigen don't have to be bound with MHC protein.

Cytotoxic T cells is specialized to kill infected cells so it must make sure it binds with infected cell. Simultaneous binding with MHC and antigen ensure this.

Innate and adaptive immune system work together. When a macrophage binds with microbial component it release soluble proteins which stimulate and direct adaptive immune response. Adaptive immune system also secrete substance that increase the sensitivity of macrophage and their ability to kill the digested microbes.

Innate immunity can only detect pathogen specific molecular pattern. It can't distinguish say, variation in the same species. So the phenomenon of tissue rejection in tissue transplant is not due to innate immunity but because of adaptive immunity.
Actually the different individual in the same species are likely to have different MHC(major histocompatibility factor) molecules. This leads to tissue rejection.

MHC 1
MHC class I molecules are loaded with peptides generated from the degradation of ubiquitinated cytosolic proteins in proteasomes. As viruses induce cellular expression of viral proteins, some of these products are tagged for degradation, with the resulting peptide fragments entering the endoplasmic reticulum and binding to MHC I molecules. In this way, the MHC class I-dependent pathway of antigen presentation is the primary way for a virus-infected cell to signal T cells that abnormal proteins are being synthesized as a result of infection.

The fate of the virus-infected cell is almost always induction of apoptosis through cell-mediated immunity, reducing the risk of infecting neighboring cells. As an evolutionary response to this method of immune surveillance, many viruses are able to down-regulate or otherwise prevent the presentation of MHC class I molecules on the cell surface. In contrast to cytotoxic T lymphocytes, Natural killer (NK) cells are normally inactivated upon recognizing MHC I molecules on the surface of cells. Therefore, in the absence of MHC I molecules, NK cells are activated and recognize the cell as aberrant, suggesting they may be infected by viruses attempting to evade immune destruction. Several human cancers also show down-regulation of MHC I, giving transformed cells the same survival advantage of being able to avoid normal immune surveillance designed to destroy any infected or transformed cells

Class switching in B cells:

usually IgM to IgG
variable region (so the antigen specificity) does not change but the constant region of the heavy chain change
class switching occurs at DNA level

Saturday, March 6, 2010

Molecular nature of cell signals


Cells usually communicate with each other by sending signals. These signals are not like any signal we are used to send. They are not electromagnetic or they don’t flow through a cable. Signals are in the form of molecules and the process they are transmitted is diffusion. These molecules reach their target through diffusion. The process of diffusion requires a continuous liquid medium from source to target.

Diffusion is a passive process, molecules don’t know where they are going- actually they go to every possible direction. In this aspect they are like electromagnetic wave and become weaker (less concentrated) as distance increases.