new:
PLOS publication

new:
Senapathy and
the Greek philosophers

updated:
Conclusion

A seductive computer experiment

Highlighted are the pieces of Shakespeare's phrase "To be or not to be". Senapathy admits that it is hopeless to search for an uninterrupted simple phrase "To be or not to be". That is why he allows for the words being separated by strings of an arbitrary number of arbitrary letters. The phrase is present completely by accident, but it occurs with predictable frequency in a random sequence of letters of about 3500 characters long. So far so good: this is uncontroversial. For practical reasons, the example phrase contains only 2 and 3 letter words. If longer words are needed, then the distance between the individual words would be larger. So would the whole string of letters. However, it would be nearly always possible to find the words in the right order, says Senapathy. Furthermore, any sentence and indeed the complete works of Shakespeare (interrupted by nonsense words) can be found when the random sequence is long enough (22). Senapathy does not tell how long. This is not just a game with words. What is possible with words is possible with genes according to Senapathy. Just substitute 'words' for 'exons', the nonsense between the words with 'introns' and you have Seanapthy's theory! Please note that this is essentially a mathematical theory. It is a claim about probabilities.
His central idea is:

1. split genes (genes with introns) are easy to find in computer generated random DNA sequences. Genes without introns are impossible to find.
2. so when in real life DNA sequences are randomly assembled from their building blocks, genes with introns will easily be formed by accident
3. since split genes are only found in eukaryotes (plants and animals), eukaryotes must have originated first and
4. prokaryotes (which don't have introns) must have evolved from eukaryotes by losing introns (23).

Searching for exons, ignoring introns

Junk DNA
What fraction of the non-coding DNA is real junk? It has been found that introns account for at least 30% of the human genome and may be a significant, perhaps major, source of regulatory noncoding RNAs (116).
An experiment concerning the relationship between introns and coded proteins provided evidence that some non-coding DNA is just as important as coding DNA. This experiment consisted of damaging a portion of noncoding DNA in a plant which resulted in a significant change in the leaf structure because structural proteins depended on information contained in introns (113).
Senapathy is searching for protein coding genes in random DNA. However, the majority of functionally important DNA sequences in mammals do not code for proteins. For example, a considerable fraction of the junk DNA could be involved in chromatin structure maintenances and remodeling such as scaffold/matrix attachment regions (SARs/MARs) (117).
Senapthy's theory of random origin of genomes does not predict that organisms with comparable sizes of the gene sets and levels of organizational complexity, such as insects, on the one hand, and mammals, on the other hand, differ so dramatically in terms of gene density and the amount of the apparent genomic junk.

Searching for exons, ignoring regulatory sequences

Eukaryotes with intronless genes

Furthermore, if he would accept intronless genes in eukaryotes, he must also accept it for prokaryotes. The same holds for all eukaryotic species that have intronless genes. Of course, Senapathy could not have known the extent of this phenomenon when he wrote his book (46), but it nevertheless refutes his theory of independent origin of many eukaryotes. Furthermore, retroposition is a process which does not fit very well in an immutable genomes paradigm.

How does Senapathy explain the existence of intron-poor eukaryotic genomes such as unicellular eukaryotes? Nearly all the genes (99.5%) of a red alga species are intronless (49).

A static versus a dynamic genome

A DNA sequence is not a genome, not a cell, not an organism

• A DNA sequence is not a genome
  1) The universal genetic code is the strongest argument against independent origin I can think of.
  A DNA sequence itself is just a polymer. Most importantly, a sequence of DNA is meaningless without a genetic code. The genetic code specifies how DNA is translated into proteins. Given that there are 4 different bases in DNA and that they are read in triplets, it follows that there are 64 different triplets. Those 64 triplet codons are translated into 20 amino acids. The most remarkable fact is that all living creatures on earth have the same genetic code! The most profound question one can ever ask is: Why is there a nearly universal genetic code when there are millions of possible codes?
  1. Did this universal code arise randomly or is it a chemical necessity?
  2. Why 4 bases A, T, C, G? (111) and why precisely those 4?
  3. Why are 20 amino acids used? Why exactly those 20 amino acids and not others?
  4. Why 3 bases (triplet) as the unit of the genetic code?
  5. Why are there 3 stopcodons? why exactly those 3?
  6. Combining 2+3+4+5 results in a redundant code: 64 triplet-codons coding 20 amino acids and 3 stopcodons. Given a redundant code, why is there a codon usage bias for the 18 of the 20 amino acids which are coded by more than one triplet? Codon usage should be random.
  The universal genetic code is the strongest argument against independent origin I can think of. Under the random and independent origin scenario there should be millions of different genetic codes even when the code is restricted to triplets of A,T,C,G. If this restriction is rejected many millions of alien genetic codes are possible above those. This very profound objection to independent origin occured to me only 7 years after I started this review. Crucially, the code is encoded in DNA itself! (82). Without a consistent genetic code, only meaningless proteins would be produced, if anything at all. This fact alone destroys the random origin of a genome. The rest of this page constitutes additional evidence.
  2) A genome is more than a sequence of 4 bases. A complete DNA-methylation map of the human genome is required. Methylated cytosine, often referred to as DNA's fifth base, makes up a subset of nucleotides in the mammalian genome (121). It can regulate tissue-specific gene transcription, without affecting the genetic blueprint. Cytosine methylation may function as a memory module of cell identity and developmental state.
• A string constructed with 4 different letters is not DNA
  A string constructed with 4 different letters like A,T,C,G is not DNA because DNA is a double stranded helix. DNA has two strands. In nature only one strand (sense strand) is translated into proteins, the other non-sense or antisense strand is not translated. Senapathy's example in figure 1 is a virtual single-stranded DNA. If Senapathy's computer DNA model is correct, why is DNA in reality not single-stranded? If his computer DNA-string were doublestranded, he could search both strands for 'TO', 'BE', 'OR', 'NOT', 'TO','BE', which would be much easier. So, why are not both strands sense strands? Logically, boths strands can be translated into proteins, using the same genetic code, so why does this not happen in nature? Alternatively, if only one strand is sense strand, how is decided which strand is the sense strand? Senapathy's theory needs to solve this problem, which is logically connected to the genetic code problem above. (added 7 Dec 2009)
  Related to the above issue: why should DNA be able to replicate? "All organisms, from bacteria to humans, face the daunting task of replicating, packaging and segregating up to two metres (about 6 × 10⁹ base pairs) of DNA when each cell divides." (Nature 28 Jan 2010)
• A DNA sequence is not a chromosome.
  A random DNA sequence is not a chromosome because important chromosomal structures are required: telomeres, centromeres and nucleosomes. At least these structures are present in linear chromosomes in eukaryotes, not in the circular chromosomes of most bacteria. Although linear chromosomes probably have advantages, they come with problems. Telomeres are needed to protect the ends of linear chromosomes and prevent their fusion. Without telomeres, the chromosomes would be shortened during each cell division, because DNA polymerase is unable to copy to the very end of one of the two DNA strands it is replicating. The protection conferred by telomeres is a fundamental biological mechanism present in nearly all animals and plants (119). Centromeres are essential for equal chromosome separation during mitosis. Mammalian centromeres are typically complex structures characterized by the presence of satellite tandem repeats. Nucleosomes form the fundamental repeating units of eukaryotic chromatin, which is used to pack the large eukaryotic genomes into the nucleus while still ensuring appropriate access to it.
  Here is the fundamental problem for the theory of independent origin: why should the most complex chromosome type, the linear chromosome, with all its problems, arise spontaneously in stead of the circular chromosome? For example: why do humans not have 46 circular chromosomes? On the other hand, evolution theory needs to explain the evolution of the linear chromosome (120).
  Cell division: Chromosomes do not only create an organism, they are duplicated just before each cell division. Why do cells divide in the first place? Does it follow necessary from the proporties of spontaneously synthesized DNA? "Chromosome segregation must be executed with high fidelity so that the mother cell and the daughter cell that arise from division receive precisely the same DNA content". "To understand the physical problems that segregating a genome presents, consider that the DNA in a cell is orders of magnitude longer than the cell itself. Therefore, central to the problem of segregation is the issue of packaging." Nature 28 Jan 2010.
• A DNA sequence is nothing without proteins: histones, polymerases, telomerases, topoisomerases, spliceosome.
• A DNA sequence is nothing without a cell: a sequence of DNA is useless without a cell (membrane, mitochondria, ribosomes, nucleus, nuclear membrane, centrosome) (55,56). The ribosome is an RNA-protein complex performing protein synthesis in all living cells. The emergence of the ribosome constituted a pivotal step in the evolution of life. This event happened nearly four billion years ago. The centrosome is inherited from a mother cell. Upon cell division, each daughter cell receives one centrosome.
  A DNA sequence with introns needs splicing sites, the splicing out of introns requires a spliceosome, which is a complex structure.
• A DNA sequence is nothing without an organism: parts of the DNA sequence (genes) must be expressed at the right time and place in the right quantities in order to develop an adult from one cell and maintain life als an adult. To achieve this, proteins that control such processes have to bind to specific places in the genome. There is evidence that ageing entails a gradual drift towards more random patterns of gene expression, which might cause organ/tissue failure. There are millions of ways to express genes at the wrong time, place, quantity or sex. Furthermore:
  • other genes in the genome influence the function of a gene
  • the function of the gene product must be in accord with the laws of biochemistry (energy production, protein folding, catalysis, prevention of protein aggregation). Some proteins cannot fold without the help of other proteins, called chaperones, so that means: genes cannot function in isolation, they need other genes.
  • DNA must be protected from damage: right from the start DNA must be protected from damage (mutation). Indeed: a very complicated DNA-repair system exists. Furthermore, DNA must be faithfully duplicated (replication) with the help of specialised enzymes. It is highly improbable that they arose by chance.
  • a sequence of DNA is meaningless without the correct ecological context, that is biological and nonbiological (the physical conditions of the earth: temperature, atmosphere, climate, gravity, water). See: The genome is blind.
• A DNA sequence is not an organism: an eukaryotic organism contains multiple separate genomes. See: here. Explaining the nuclear genome is not enough.
• A computer generated DNA string is a virtual thing. See: here.
• See also: par 7: Genome-centred approach

• Origin of life: Senapathy merges the problem of the origin of life (an unsolved problem), with the origin of species (solved in principle by Darwin). Senapathy knows that Darwin did not address the question of the origin of life in his Origin of Species (p.199). Following Darwin, evolutionary biologists focus on the origin of species, and leave the origin of life to specialists (chemists). Senapathy has to solve both problems at the same time! However, he does not have the necessary expertise. Even worse, he does not even begin to analyse what the very problem of the origin of life is (see also paragraph What is Life?).
• Senapathy does not distinguish between the origin of an individual and a species. Suppose, the primordial pond produced an individual, how to proceed to a population of interbreeding individuals? Only a few genes can prevent interbreeding of individuals of the same species (incompatibility genes, hybrid sterility, reproductive isolation). Self-incompatibility is of special importance because of obligate outcrossing.
• Next he reduces both problems to finding the Sequence. Next he reduces that problem to a statistical problem, without ever calculating the probability of any genome. He cannot do this because one has to know the proportion of random sequences that have biological meaning. "Any theory postulating that genes [!] may have emerged randomly and then waited to be used are fundamentally wrong, especially in a world dominated by the deleterious effects of the second law of thermodynamics. Genes had to have a functional meaning from the very beginning or they would have vanished soon after they emerged." (53). Please note, this applies to genes. Let alone to genomes. Therefore, the origin of life is a chemical problem and the origin of species is a biological problem. I am afraid that he thinks that as soon as he has solved finding the Sequence, he has solved all the problems of biology! However, a sequence without cellular machinery is like software without a computer! (please note Senapahthy is a computer scientist!)
• Epigenetics: beyond the sequence. "The major problem, I think, is chromatin. What determines whether a given piece of DNA along the chromosome is functioning, since it's covered with the histones? What is happening at the level of methylation and epigenetics? You can inherit something beyond the DNA sequence. That's where the real excitement of genetics is now." (James D. Watson: 30). Chromatin is defined as the dynamic complex of DNA and histone proteins that makes up chromosomes. Epigenetics is defined as the chemical modification of DNA that affects gene expression but does not involve changes to the underlying DNA sequence. As the emphasis in biology is switching away from genetic sequence and towards the mechanisms by which gene activity is controlled, epigenetics is becoming increasingly popular (104).

Epigenetic processes are essential for packaging and interpreting the genome, are fundamental to normal development and are increasingly recognized as being involved in human disease. Epigenetic mechanisms include, among other things, histone modification, positioning of histone variants, nucleosome remodelling, DNA methylation, small and non-coding RNAs. (Nature, 7 Aug 2008).

A computer simulation of DNA is a virtual world

    Senapathy asks one interesting question about the real world: How would the DNA sequence of current organisms look like if it originated randomly, and especially how would the distribution of stopcodons look like? (see box 'A test for randomness').
However, whatever the amount of arguments for independent origin, if independent origin predicts that eukaryotes originated first and prokaryotes later, then the theory is inherently improbable. If Senapathy had known that there are 30 differences between eukaryotes and prokaryotes (17), he would never dared to propose his theory in the first place. It is improbable simply because eukaryotes are far more complex than prokaryotes. One reason is: sex. See also:

• Did prokaryotes arise from eukaryotes?.
• The role of time: the chronological order of life.

Genome-centred approach

cell membrane

Not by genes alone Do genes code the organismal form? Not quite, says evolutionary biologist Massimo Pigliucci. "Genes by themselves do literally nothing. Organisms do not begin with a bunch of genes that generate everything else: they need a set of environmental conditions, as well as the inheritance of materials and extra-genetic information from the previous generation. From the point of view of causal analysis, genes may be said to be a necessary but far from sufficient condition for the development (and evolution) of organisms."

A DNA sequence is meaningless "A DNA sequence, by itself, is meaningless. The information in the double helix is interpreted through its interactions with the rest of the cell." Barton et al (2007), p.381. [added: 6 Dec 08]

Every gene needs an environment "We now know that there is no such thing as a gene that acts in isolation and that every gene needs an environment --whether the environment is the presence of molecules made by other genes, signals generated internally within the developing nervous system, or electrical activity transduced from the external world. The genes of brain development are impressively environment- and experience-dependent." Mriganka Sur (2008) NEUROSCIENCE: The Emerging Nature of Nurture, Science 12 December 2008: Vol. 322. no. 5908, p. 1636

The logic of the genome-centred view

Conclusion:
Shortcomings of genome-centred approach are: it ignores cell and cell membrane, cell arises from fertilization, and genes need to be regulated and true understanding of gene regulation requires the study of epigenetics. Therefore, any gene- and genome-centred theory of the origin of life is incomplete and wrong. I collected additional technical reasons from developmental biology, genetics and ecology on the page: Independent Origin and the facts of life.

Even within the genome-centred view two different views are possible: 'the regulatory code' versus 'the protein code'. Senapathy exclusively pays attention to protein-coding sequences (introns, exons). However, many of the observed differences between species likely stem from when and where the products of the genes are made, in other words: 'the regulatory code'.

Everything you always wanted to know about s e x, but were afraid to ask

1. Human body cells are diploid: one complete set of chromosomes from the father, plus one complete set from the mother. (95)
2. sperm and egg cells are haploid: 1 incomplete set of chromosomes.
3. humans have a diploid set of 23 pairs or 46 chromosomes in total
4. females have 23 identical pairs, including a X-chromosome pair, excluding the Y-chromosome
5. males have 22 identical pairs and one non-identical pair of a X-chromosome and a Y-chromosome. The Y-chromosome is about 1/5 the size of an X-chromosome (see photograph, and diagram: Fig. 2).
6. Egg cells have always one X chromosome and sperm cells have either one X or one Y chromosome.
7. additionally female egg cells contain many mitochondria each containing 37 genes. The mitochondria are transmitted exclusively via the female egg cell.
8. The number of genes in the human genome is about 22,000 genes (estimates vary, but that is not relevant for my argument). The DNA in the human genome that does not code for protein is ignored.

So far the facts of life. Now Senapathy's claims that "The genomes were directly assembled into single seed cells, analogous to the fertilized eggs of sexually reproducing organisms" (p.5) "male and female 'seed cells' lead to male and female individuals"; "Both male and female seed cells can be assembled"; "One can infer that it is not difficult to segregate the genes for a male or a female into a specific chromosome and in two different sex cells". (p.358)
"Not difficult"! This is an astonishing and outrageously careless statement. The first quote proves that Senapathy does not distinguish between 'haploid' and 'diploid' cells (18). This is fatal for his theory. Although he knows about X and Y chromosomes in another context (p.588), in this context he forgets about it. Just look how different the X- and Y-chromosome are! (Fig 2) He just flatly states that it is "not difficult" without any evidence! Senapathy jumps from genes to genomes, thereby completely ignoring that chromosomes exist and have a structure. However, when he criticises evolution, he knows about chromosome structure and histones (p.125,143). He ignores the problem of anisogamy versus isogamy, internal versus external fertilization, hermaphroditism versus separate males and females, egg-laying versus live birth, etc. Senapathy does not specify any details. Indeed, part of the trouble is that his scenario is extremely vague at crucial points. See the following quote for an entertaining, charming and unscientific scenario:

Can a male or female arise from haploid cells?

X     Y Fig 2. Human sex chromosomes (2)

      Degenarate polyploid genomes  

The situation is even worse. Many plant species are polyploid, having duplicated genomes. For example: yeast Saccharomyces cerevisiaea is a tetraploid and its genome consists of four roughly identical genomes (the diploid number is 4N). Because of the accumulation of mutations during the history of the species the original identical genomes start to differ. These are called degenerate tetraploids. Is is highly unlikely that degenerate tetraploids originated spontaneously from a pool of random DNA segments (especially all mutations being neutral).

      Virgin birth?  

Male bees, wasps, and ants develop from unfertilized haploid eggs, so are haploid. Would that help Senapathy's theory? No, because a diploid female has to produce the egg. Although it is known for an egg to start developing without being fertilised (parthenogenesis) in some insects, snakes, lizards, and Komodo dragons, and parthenogenesis has been reported in about 70 vertebrate species (roughly 0.1%) and even in sharks (75), fully parthenogenetic human embryos cannot develop to term (4). The embryos die after a few days. Maternal and paternal genomes are both necessary for normal development in mice, and this is believed to account for the absence of parthenogenesis [=development without fertilisation by a father] in mammals (31). An embryo that did not have a sperm involved in its formation cannot make a placenta (the organ that keeps the fetus alive) and so cannot be born (54). In plants the formation of asexual seeds is called apomixis and it leads to populations that are genetically uniform maternal clones (apomixis is found in more than 400 species of flowering plants). Even if parthenogenesis would work in humans, this only produces females, so would not explain the origin of males. This does apply to all animal species with an XX-female/XY-male sex-chromosome system. There is no Y-chromosome in a female cell, therefore a male cannot be produced parthenogenetically.
    Apart from the Y-chromosome, all sexually reproducing animals, simply have two parents. Asexually reproducing species (making clones of themselves) like bacteria, only have one parent.

    Conclusion: Senapathy's computer experiment shows a single sequence (Fig 1). The analogy with a haploid genome is obvious. I guess he based his theory of independent birth on the idea of a haploid genome and assumed it was no problem to produce diploid organisms. Regrettably, the haploid method fails to produce the first human male and female. The haploid method can only produce asexually reproducing bacteria and other prokayotes. The funny thing is that Senapathy knows about X and Y chromosomes when he wants to refute neo-Darwinism, but does not realise that they are an insurmountable obstacle for his own theory. Nobody would deny that simple genomes have a higher probability than complex genomes. Therefore, a haploid organism should be the expected outcome of the primordial pond. Multicellular haploid organisms do exist: males of the honeybee are haploid. Senapathy is confronted with the amazing but inevitable question: why on earth are not all species haploid?

Can a male or female arise from diploid cells?

      two kinds of cells - two kinds of cell division  

From a genetic point of view all animals and plants have two different kinds of cells: diploid body cells and haploid sex cells. These cells are created by two fundamentally different processes: mitosis which creates diploid cells and meiosis (91) which creates haploid cells. Both processes are complex because they must guarantee that daughter cells receive the correct set of chromosomes. At the beginning of mitosis, the process of cell division, chromosomes are organised randomly - like jigsaw puzzle pieces spread out on the floor. During the process of mitosis the two halves must be oriented such that they will be pulled in opposite directions into two newly forming doughter cells. Mechanisms must exist to eliminate wrong configurations while selecting the right ones (52). Meiosis is even more complex and is controlled by meiosis-associated genes. In normal female meiosis in plants and animals, only one of the four products forms an egg nucleus while the other three are discarded into polar bodies. Why? Even the loss of a single chromosome can be lethal and can contribute to birth defects and cancer. Explaining these two highly complex and highly conserved processes with randomness, explains precisely nothing.
    Then there is a third process called fertilization which is the fusion of a haploid sperm and a haploid egg. Fertilization creates the first diploid cell of an individual. After that, mitosis takes care of creating the rest of the body cells. Fertilization is 'simplier' than meiosis, because it is just adding two genomes together. However, things can go wrong too. The fusion must add precisely two and not three or more genomes. Furthermore, it appears that many highly specific proteins are involved in fertilization (71), and these proteins must be encoded by the genome. So the fertilization process is not much simpler than meiosis.

Plants have a double fertilization: one sperm fertilizes the haploid egg cell, which becomes the diploid embryo, and the other sperm fertilizes the diploid central cell, generating the triploid endosperm. It is extrremely unlikely that these complicated processes occur by chance. The endosperm nourishes the embryo during seed development. That is another clue that plant seeds need a mother plant. The endosperm genome is not transmitted to the next generation.

    Evolutionary theory starts with relatively simple haploid cells which reproduce without sex and without meiosis. They are in fact clones. On the other hand diploid sexually reproducing organisms are much more complicated, because they use both mitosis and meiosis. The transition from asexual clones to sexual reproduction is one of the 8 major transitions of life (John Maynard Smith, 32) and Senapathy lets them originate just as easy as single celled organisms by random forces.
    Senapathy claims that his theory predicts eukaryotic genomes. I don't see how his theory could predict diploid organisms in the first place. Given the fact that there are less complicated and therefore more likely ways to reproduce, his theory certainly would not predict a complicated process like meiosis (37). However, meiosis is even more complicated than that. Meiosis produces in the end four haploid germ cells. In males, all four give rise to sperm. In the female however, only one of those four develops into an egg cell, while the other three eventually die. So, additionally, there is also a sex difference in the meiosis process.

      A hermaphrodite?  

Could the first organism be a hermaphrodite? In a hermaphrodite species all individuals have both male and female reproductive organs. The possible advantage would be that there is no need to produce two individuals (males and females) which differ in the DNA that determines sexual characteristics, but have otherwise equal genomes. Therefore, the origin of the hermaphrodite species could start with just one self-reproducing individual. The problem with this idea is that hermaphrodites need two individuals to reproduce. Consequently, the problem remains, to produce two exactly the same genomes. This is only slightly less difficult than producing a species with males and females. Apart from this, if successful, it would only explain hermaphrodite species, not the majority of species with males and females! If a transformation is assumed from the hermaphrodite status to females and males, it means evolution or mutation of the genome. And Senapahty forbids mutation.

      A male without a Y chromosome?  

Males of grasshoppers and aphids ('plant bugs') do not have a Y chromosome, they are described as XO. Females of those species have two X-chromosomes; they are XX (36). Are females of grasshoppers and aphids perhaps candidates for independent origin? Theoretically they could produce a species. However, apart from the absence of the Y-chromosome problem, the problem of producing a female and male version of the same genome still exists. Furthermore, the production of males requires a rather unusual form of meiosis. Apart from this, if successful, it would only explain XO species, not the majority of species with a Y-chromosome!

Did prokaryotes arise from eukaryotes?

Endosymbiosis theory refutes Senapathy
    Mitochondria are organelles in all eukaryotic cells; they are crucial for eukaryotic life; they multiply independently within eukaryotic cells in a simple asexual fashion (just like bacteria); have their own DNA (37 genes in humans) which is autonomously copied; their DNA is circular (just like bacteria!); and all genes are intronless (just like bacteria, but unlike eukaryotes!). These facts support the hypothesis that mitochondria were once free living single-celled prokaryotes. This hypothesis is called endosymbiosis theory and was proposed by Lynn Margulis in 1970 (Senapathy knows this). Initially rejected by biologists as too speculative, the theory was accepted by evolutionary biologist John Maynard Smith in 1975 in his The Theory of Evolution. That was 19 years before Senapathy published his book. The theory is now the standard view in biology and evolution textbooks (5). Nobel Prize winner Christian de Duve said about the proofs for the bacterial origin of mitochondria: "In the opinion of the vast majority of investigators, these proofs are conclusive." (6). Grauer and Li (2000) in Fundamentals of Molecular Evolution state "the molecular evidence is now overwhelmingly in favor of the endosymbiotic theory". What Senapathy has to say is this:

Some scientists have suggested that eukaryotes were formed by "endosymbiosis"... Although there exists some resemblance between mitochondrion and bacterial cells, the origin of the nucleus in the eukaryotic cell is still considered to be a total mystery. (p. 231).

Mitochondria "Take the enzyme cytochrome oxidase, for example, which handles the final step of cell respiration. In mammals, the complex is composed of 13 subunits, 3 of which are encoded by mitochondrial DNA, and 10 by nuclear genes. If the subunits of cytochrome oxidase don't work together properly, electrons are not passed to oxygen and respiration fails, triggering the death of the cell." "The mitochondrial and nuclear genes adapt to each other within a population, and the process must happen quickly because the mutation rate is so high in mitochondrial DNA." Nick Lane, Nature 19 Nov 2009

    To complicate matters further, the Woesian revolution established that that prokaryotes, far from being a homogeneous group, actually consists of two genetically very different groups: Bacteria and Archaea (73, 114). Although Archaea superficially resembled bacteria (being single-celled and lacking a nucleus), Archaea have a distinctively different metabolism, cell wall, and transcription machinery. That means in Senapathy's theory both Bacteria and Archaea are supposed to have originated from eukaryotes. This is very unlikely.

All mammals require a mother

© Lennart Nilsson (1990) Human embryo with umbilical cord. The umbilical cord is the link between mother and embryo.

viviparity

Viviparity means the embryo develops inside the body of the mother. The best example is placental mammals. Another group is the pouched marsupials like the kangaroos and koalas of Australia. At birth, the baby kangaroo is no larger than a peanut, a blind, pink, hairless fetus-without-a-whomb that must crawl on its own through the mother's fur into the pouch. It drinks milk from a teat (122). However, scorpions, some sharks, some snakes, and velvet worms also are viviparous. Roughly 20% of non-avian reptile species (lizards, snakes) give birth to live offspring (viviparity).

birth

Other problems: if the human embryo is in the water of the primordial pond during nine months, how does the sudden transition to air breathing (usually called: 'birth') happen? Who helps the baby out of the water to prevent death by drowning? After normal birth fetal haemoglobin (a crucial oxygen-carrying protein) drops off and the adult version kicks in. How is this regulated? Timing?
Babies have average birth weights around 7.5 pounds. In the primordial pond, the baby could grow to any size before 'birth', because it does not have to pass the birth canal of its mother. Females have wide hips and a large enough pelvic opening that enable babies with big brain sizes to be born. A real genome 'knows' to start the delivery at the right size of the baby. How does a human genome in the primordial pond know about the nine months? Does the mouse genome know that it is sitting in smaller animal and needs to deliver in a shorter time?
    The human baby is born premature when compared with chimpanzees. The first teeth appear only after 6 - 12 months. The head of the foetus is still small enough to pass through its mother's birth canal. One of the consequences is that humans at birth are utterly helpless (42). The human brain doubles in size in the first year of life and achieves 95% of its adult size by the age of 5 (although white matter grows at least to age 18). Big brains are so metabolically expensive that primates must postpone the age of reproduction in order to build them. High fecundity requires at least an extended family with fathers and grandmothers around to help provision and care for the young (109).
    Amazingly, in order to be a healthy individual, in Senapathy's scenario the first female genome would not need hormones for ovulation, menstruation, womb, pregnancy, and lactation. If no hormones are necessary, then genes for hormones are unnecessary. The genomes would be different.

sex organs

The fetus has internal and external sex organs which are useless in the Womb. Furthermore, sex organs would be unnecessary for survival of the first individual. There is no reason to expect that the primordial pond would produce complete male and female genomes. Sex organs simply do not contribute to the health and survival of the first individual.
Furthermore, why should the first female have a pair of breasts which grow considerably after puberty? A pair of breasts does not contribute in any way to the health and survival of the individual possessing them. They are a burden and a risk (breast cancer). Additionally, how does Senapathy explain that only 50% of the individuals have breasts? The first individual needs food, needs to escape disease and predation to survive, not sex. So why is the primordial pond not producing sexless individuals forever? (25).

complete genomes

Returning to the issue of complete genomes: what is a complete genome? If spontaneous generation of genomes were nature's method for producing animals and plants, then a healthy sexless individual is viable and complete. As an illustration: only one missing gene can make healthy male or female mice sterile (27). On the other hand one needs a few hundred genes, I guess, to add maleness and femaleness. To evaluate 'independent birth' we need to eliminate our deeply rooted prejudices about the necessity of sexual reproduction. Senapathy should take his primordial pond serious and reason from the point of view of the primordial pond, and resist relying on the benefit of hindsight.

altricial species

In general, in bird and mammal biology altricial species ("requiring nourishment") are those whose newly hatched or born young are relatively immobile, have closed eyes, lack hair or down, and must be cared for by the adults. Altricial young are born helpless and require care for a comparatively long time. Among birds, these include, for example, herons, hawks, woodpeckers, owls and most passerines. Rodents and marsupials are altricial, as are cats, dogs and humans.

imprinting

The best known form of imprinting is filial imprinting, in which a young animal learns the characteristics of its parent.

©Antal Festetics, 1983

Common descent versus independent origin

The role of randomness and improbability

The role of natural selection

The role of mutation

    His 'immutability' concept introduces two more serious difficulties for his own theory. Mutations are steps in genome space. If mutations are worthless, then steps in genome space are worthless. This makes individuals isolated islands in genome space. If genomes are essentially fixed, and cannot use mutations to explore genome space, then how does the primordial pond find those rare viable genomes? How does it avoid those unsuccessful genomes? Furthermore, if there are no viable intermediates in 'genome space' and viable genomes are rare, then this is a problem for both independent origin and gradual evolution. There is only one world, therefore both theories have to deal with the same genome space. Senapathy needs either a huge amount of luck or a huge amount of selection. A huge amount of luck is unsatisfactory and a huge amount of selection contradicts his own claim that selection is unimportant. Senapathy postulates a very resourceful primordial pond ("The number of genes in it must have been several times more than that contained in all creatures that ever have lived on earth", p. 312 ). Several times? Could you be more precise? You are a computer scientist!

The role of adaptation: random perfection

Fig. 8. Is the match between the extreme long spur of the orchid and the extreme long tongue of the moth an accident? © image Sinauer 2005 (60)

One of the main functions of flowers is to attract animals. Why? How did this happen? Even Goethe felt compelled to explain the origins of floral structures. For Senapathy the answer is: Random perfection! Why would anybody opt for such a desperate 'explanation'? If all adaptations are the direct result of randomly assembled genomes, then we can not ask any further questions about those adaptations. We can not make any progress in our understanding of adaptation. 'Random perfection' caused by random genomes is the final answer. Don't ask any further questions. In fact, every property of an organism must be explained by random genomes according to Senapathy's theory, since mutation and natural selection are excluded (81). This implies that we never will understand the big questions in biology: the origin of adaptations like the brain, eye, ear, nose, hart, lung, digestion, photosynthesis, meiosis, respiration, blood circulation, warm-bloodedness, sexual dimorphism, parental care and bird migration, let alone the interrelations between them (61). This is an unacceptable drawback for a professional biologist. Senapathy is forced to accept 'random perfection'. He has no alternative. He has no choice.
    Senapathy misses a number of crucial points here: a few trials are not enough to determine if an individual is 'ecological fit'. Genomes cannot be tested in isolation from other species, because species are each other's environments! (See this page). Senapathy's theory reduces organisms to isolated individuals. We need a theory that let species originate, evolve and adapt to their local environments including other species. Additionally, the origin of species is completely unconnected to the geological context (geographical differences, continental drift, ice ages, meteorite impacts, climate changes, etc). In Darwinism the environment is an important external causal factor (externalism). Furthermore, genomes cannot be tested at one point in time only, because that leaves unexplained how species are able to adapt to ever changing environments.

Her response was: "Do you really think that an insect or a rat simply came about as it is?" I simply answered "Yes, I do!". (1)

    Senapathy describes in several pages the complexities and the diversity of the eye in the animal world and claims Darwinism can not explain this. He ignores that his theory implies that the eye has to be reinvented a thousand times in mammals which all have the same type of eye. According to his theory, the eye has been independently produced by the genomes of the rabbit, squirrel, mouse, bat, tiger, lion, leopard, deer, bear, giraffe, buffalo, dolphin, rhinoceros, elephant, monkey, ape, human, etc, etc.
    Creationists frequently claim that evolution relies exclusively on randomness, but in fact randomness is an adequate characterisation of Senapathy-genomes. For Senapathy, life is a 'genome accident'.

The genome is blind
"The genome is blind and cannot visualize the existing niches and environments. Therefore, millions of bizarre phenotypes must be produced in a species for the selection of one useful structure. (p. 89, see also p.75).

The role of time: the chronological order of life

Figure 11.1. The chronology and time table of the independent birth of organisms. Chapter 11: 'A New Look at The Fossil Record', page 497.

first humans did appear 6-7 million years ago first bats, dogs, weasels, elephants: 30 - 40 million years ago first placental mammals (rabbits, whales, rodents): 60 - 65 million years ago first mosquitoes, honeybees: 65 - 70 million years ago first turtles: 65 - 190 million years ago first butterflies (Lepidoptera): 150 million years ago first birds: 155 million years ago first frogs, crabs: 135 - 190 million years ago first flowering plants appeared about 135 million years ago; grasses appeared around 94 million years ago first sex chromosomes (XY) appeared some 200 million - 300 million years ago first amphibians: 360 million years ago first tetrapods: 375 - 363 million years ago reptiles did not appear before 416 million years ago plants did not appear before 465 million years on land; plant with leaves appear with a delay of 40 million years fish with jaws appeared: 416 - 359 million years ago jawless fish appeared: 500 - 435 million years ago eukaryotes: 1.78 - 1.68 billion of years ago cyanobacteria: 2.15 billion years ago The reader is advised to have a look at: TimeTree: The Timescale of Life

The reader will search in vain for human fossils in chapter 11 A New Look at The Fossil Record. Senapathy forgot to discuss human fossils. That's a pity, because I would like to learn why there are no human fossils known from the Cambrian period and the whole primordial pond period. If a human fossil was found in the Cambrian period the theory of evolution would be falsified.

Furthermore, many forms of life appeared in the fossil record before the start of Senapathy's primordial pond (600 Mya). There is solid evidence that life was present on the earth more than 3 billion years ago. Conclusion: life appeared 2400 million years before the start, and 500 million years after the end of Senapathy's primordial pond. Secondly: the first fossil animals found in the oldest layers were creatures that lived in the sea (trilobites, brachiopods), only later animals and plants living on land are found. Why? The first animals on land were amphibians and reptiles. Reptiles dominated the earth before mammals appeared. Mammals appeared much later. This was known before Darwin (1859). There was little overlap between "the age of reptiles" and "the age of mammals". Traces of humanity did not appear until the very end of the record. Anyone proposing a non-evolutionary explanation for the origin of life and species must start with explaining the fossil record as known in 1859 and everything that has been learned since then. Senapahty forgot to do this. This fossil record cannot be explained by a primordial pond that produces creatures in a random order.

Fact: plants The first plants on land were small and leafless. Plants with leaves appeared 40 million years later (72). Why don't leafless and leaved plants appear randomly in the fossil record? Why were green algae present in oceans 500 million years before plants colonized the land? Why the chronological order of appearance? In Senapathy's genome-centred view the chronological and environmental context is absent. There is no possibility to answer questions why certain fossils are where they are.

Fact: photosynthesis There ares two photosynthesis methods: C3 and C4 (used by 7500 plant species, mostly subtropical grasses, maize, sugarcane). The C3 method is optimal for high atmospheric carbon dioxide levels (100x today) and the C4 is optimal for low carbon dioxide levels. However, there is only one atmosphere and one primordial pond in Senapathy's scenario. Data support the view that the C3 system arose 3 billion years ago under high carbon dioxide levels, the C4 system arose as an adaptation to low carbon dioxide levels about 30 million years ago (72). If both systems were produced by the primordial pond, then the primordial pond must have existed from 3 billion years ago up to 30 million years ago. Unlikely as it is, it still does not explain why it produced the systems in that chronological order and why with such a huge time interval. (see also: Incompatible primordial ponds).

Fact: sex Why on earth was there no sexual reproduction in the first half of the history of the earth? These are facts from the geological record. One does not need to be an evolutionist to accept them. On the theory of independent origin such groups of organisms should appear randomly in the history of the earth or why not all at the same time?

How many primordial ponds?

Why not propose thousands or millions of primordial ponds in stead off one? It could make independent origin much and much more easier! Maybe Senapathy needs "a common pool of genes in the same primordial pond"? (see: §13). Why not propose a primordial pond that lasts millions of years? Amazingly, Senapathy did all this! He claimed that there exists a single primordial pond (p.8), two distinct ponds (p.500), many (p.502) and 'millions of small and large ponds must have existed on the primitive earth' (p.214). That is really a powerful theory!

Extinctions and recoveries

The role of place: the biogeography of the origin of species

Independent origin and the clumpiness of morphospace

The primordial pond is a free lunch

Incompatible requirements for a primordial pond

      Furthermore, if born, why and how do organisms migrate from the primordial pond to all those different locations? Some organisms only survive at deep sea, hydrothermal vent communities are found at depths ranging from 1,500 to 3,200 m. Giant tube worms (chemoautotrophs), in the absence of sunlight, subsist on hydrogen sulfide found in the warm waters surrounding vent communities. There is evidence for living prokaryotic cells in 1626 meters below the sea floor sediments that are 111 My old and at 60° to 100°C (79). The bacterium D. audaxviator lives at 2.8 kilometer depth in a South African gold mine and is lacking a complete system for oxygen resistance, suggesting the long-term isolation from O₂. That means it is damaged by oxygen (102).

Eggs incompatible with water

In the primordial pond organisms develop from 'egg cells'. Please, have a look at the cover illustration again: not accidently, there is no bird or mammal creeping out of the primordial pond. Bird eggs do not survive in water (apart from the requirement of incubation). Saltwater crocodiles, marine iguanas and sea turtles, although marine, lay eggs on land. Reptiles cannot successfully lay eggs under water because gas exchange across the eggshell is much slower in water than in air.

Bar-headed goose. © Chalto Digital Images

On the other extreme are bar-headed geese - the world's highest-altitude migrants - fly from their winter feeding grounds in the lowlands of India, sometimes even directly above Mount Everest (29,000 feet), on their way to their nesting grounds on the Tibetan plateau (only a third of the oxygen available at sea level). They have a special type of hemoglobin that absorbs oxygen very quickly when the birds are at high altitudes; as a result, they can extract more oxygen from each breath of rarefied air than other birds can. The most plausible explanation for this migratory behaviour is the geological history of the region (80). How do these geese, if born in the primordial pond anywhere in the world, -ignoring all other problems-, know to fly to the Tibetan plateau?

The origin of life

      The origin of life  
In modern science the Origin Of Life field has grown into a separate research field with strong connections to astrobiology, organic chemistry and geochemistry. According to the most recent textbook of Evolution (89) there are seven criticial steps in the origin of life:

1. the generation of simple organic molecules from inorganic molecules
2. chemcial "evolution" to produce more complex organic molecules and primitive metabolic netwerks
3. the origin of self-replication and the creation of "genotypes"
4. compartimentalization and the creation of cells
5. the linking of genotype and phenotype
6. the origin of the genetic code
7. the takeover of early replication systems by one involving DNA

The final refutation of independent origin

What is life?

1. a chemical motor (metabolism) that supplies energy to synthesise compounds necessary for the other 2 subsystems and is stable;
2. a membrane which keeps the other 2 subsystems together, protects against dilution and is itself stablel;
3. an information-carrying subsystem (for example DNA) which enables reproduction of the 3 subsystems.

Rerun the tape of life

PLOS ONE article

I tried to decipher the logic of his argument in the PLOS article. Despite I studied his argument for years, it is not easy. I guess, he does not want to defend the idea that the present-day human genome as a whole is random. No scientist would want to do that. A random genome could not produce a human being. On the other hand, nobody can argue against the claim that "The presence of three stop-codons for every 64 codons limits the average ORF length to about 60 bases in random DNA" ('random DNA' is a computer generated random string of four different symbols; ORF = Open Reading Frame). What he seems to argue is that, despite the predominant non-random nature of present-day genomes, exon length still has a random signature.

Figure 7A. The ROSG model. ORF = Open Reading Frame

When

Senapathy does not distinguish clearly between the timing of the different events: 1) the origin of the very first DNA sequences, 2) the processing of those sequences, 3) subsequent genome evolution during 2 billion years. But prebiotic environments are completely different from those of a living organism. Irrespective of when (106) this processing occurred, after 'splicing together short coding pieces', exons lengths, gene lengths and genomes are not random anymore. Any selective processing of random DNA makes it non-random. Any non-random removal of stopcodons change the statistical properties of the sequence. If present-day exons are a combination of shorter pieces joined together, than by definition current exon lengths are not random.

The mechanism

His figure shows the combination of 4 small exons into one large exon, but any exon length can be explained in this way. An arbitrary number of exons with arbitrary lengths can be joined to an arbitrary number of new exons with arbitrary lenghts. Also, an arbitrary number of exons may stay unmodified. Exon length distribution is the main thing Senapathy wants to explain and he introduces a mechanism that changes them in an unspecified way. Why do introns still exist? Why are there still so many introns in our genes? Why did his mechanism not eliminate all introns? Senapathy observes present-day exon lengths and postulates a hypothetical mechanism that produces exactly the exon sizes of today. That does not add anything to our knowledge.
My own suggestion would be: it is true that stopcodons would limit gene length, but a far more simpler solution would be elimination of stopcodons by a one-base mutation of the stopcodon in the context of living organisms. That is a far more simple because it does not require complicated splicing machinery. Certainly under prebiotic conditions where no functional enzymes are present. He did not give evidence that this complicated processing is possible in prebiotic chemistry. He stated that functional proteins cannot be encoded in genes with average ORF length of about 60 bases.

Facts

In addition to the contradiction of his own model with his own data (called 'non-confirming' data by Senapathy), two types of evidence are contradicting his hypothesis: too many short exons and too many long exons. Humans have 170 exons of length up to 25 bp (107) which is significantly lower than the expected size of 60 and exon sizes up to 2087 bp exist (108) which is much outside the predicted maximum.

Summary and Conclusion

Fig. 9. Which genome originated first: the humming bird genome or the flower genome? How could they survive and reproduce without each other? Is this mutual adaptation merely a genome accident? © image Sinauer 2005 (60)

    Studying this and religious alternatives for evolution, convinced me that it is extremely hard to develop a consistent and original alternative for evolution which does not contradict the facts of life. Further, that evolution theory is certainly not an arbitrary paradigm in biology that is mindlessly defended by biologists due to conservatism or atheistic prejudice. I am impressed and a little bit surprised that evolution theory escapes so much of the traps Periannan Senapathy fell in. I am equally surprised and amused how thousands of seemingly neutral facts turn out to be evidence against Independent Origin and evidence for common descent. This flow of evidence continues to inspire and give me deep insights into the fundamental properties of life on earth and the structure of the theory of evolution. Evolutionary biologists should learn from Senapathy that it is always wrong to say: it's easy!.

      Notes  

1. Senapathy: "When I initially tried to explain my theory to my wife, I said, All the organisms could have come about just as they are, independently from the primordial pond. Her response..." (p.295). Please note, she forgot to ask about humans.
2. Source of chromosomes. These chromosomes are not from Senapathy's book. There are no chromosomes in his book. That is the point.
3. Only male honeybees hatch from unfertilized eggs [are haploid], but female honeybees hatch from fertilized eggs [are diploid], therefore that won't help independent origin theory very much. See: Olivia Judson(2002) Dr. Tatiana's sex advice to all creation, p.18 . Hermaphrodites (organism with both female and male sex organs) usually need another individual to reproduce.
4. Helen Pearson: Human genetics: "Dual identities", news feature, Nature 417, 10-11 (2002), 2 May 2002.
5. See for a full exposition for the non-specialist Mark Ridley(2000) Mendel's Demon. Gene Justice and the Complexity of Life (review), Chapter 6 "Darwinian merger and acquisition" is about the far reaching implications of having mitochondria in the cell.
6. Christian de Duve (2002) Life Evolving, Oxford Univeristy Press, p. 141.
7. Robert Pennock (2001) Intelligent Design Creationism and its Critics, p. 685.
8. S.G. Gregory et al (2002) A Physical map of the mouse genome. Nature AOP, published online 4 August 2002.
9. Carina Dennis and Richard Gallagher (2001), The Human Genome, p.120: "The largest apparently contiguous conserved segment in the human genome is on chromosome 4, including roughly 90,5 Mb of human DNA that is orthologous to mouse chromosome 5."
10. Similarities found in mouse genes and human's. Nicholas Wade, NewYork Times Science, 5 Dec 2002.
11. Comparision of Human chromosome 4 and Mouse chromosome 5.
12. Comparision of Human chromosome 17 and Mouse chromosome 11.
13. Comparision of Human chromosome 20 and Mouse chromosome 2.
14. A memorable misunderstanding on this site.
15. Evolution (Third Edition) on this site.
16. A Chemist's View of Life: Ultimate Reductionism & Dissent on this site.
17. Ernst Mayr (2001) What Evolution is, p.46. See also: Lynn Margulis(1998) Five Kingdoms. An illustrated guide to the phyla of life on earth, third edition. p.12.
18. Senapathy has a short paragraph What is a "seed cell"? (p.307), in which he uses 'haploid' and 'diploid', but there he neither explains what a seed cell is, nor how a diploid cell arises out of the primordial pond.
19. Portrait of a molecule by Philip Ball. This is a good article for those who think that a genome is just naked DNA. Nature 421, 421 - 422 (2003) (free). Have a look at the beautiful diagram of the 3-D structure of the chromosome showing that a genome is more than just the sequence of the bases! Looking at this image it is clear that Senapathy's discovery about split genes in random DNA is almost irrelevant. He did not explain the massive amounts of highly specialised proteins (histones), which form the complex 3-D structure of the eukaryotic chromosome.
20. Richard Dawkins used the now famous weasel computer experiment to demonstrate the difference between one-step and cumulative selection in The Blind Watchmaker, chapter 3. See also Spetner review.
21. David Foster attributed this argument to Thomas Huxley (see review of Foster's book).
22. Senapathy states (p.222) that the occurrence of the uninterrupted text of Shakespeare is improbable.
23. Senapathy easily contradicts his own theory: "Thus it is possible for the prokaryotic genome to have been derived directly from contiguous genes in the open primordial pond". (p.238)
24. In fact, this question is wrong. There is no such a thing is "the human genome". Only female and male human genomes exist.
25. "the primordial pond could have been productive for a very long geological time" (p.345).
26. "indentifiying exon-intron borders is a notoriously difficult task", Antoine Danchin(2002) "The Delphic Boat", p.238.
27. Charles Spruck (2003) Requirement of Cks2 for the first metaphase/anaphase transition of mammalian meiosis. Science 300 (5619):647. 25 Apr 2003.
28. Whenever Senapthy is uncertain, he says "absolutely". The word occurs 138 times in his book!
29. Even Jesus, the son of God, had a mother. Significantly, this is claimed by people who otherwise accept miracles. However, Adam and Eve did not have a mother and father, but were created as adults. Senapthy's creatures also did not have a father and mother, but at least did not start as adults!
30. A Conversation with James D. Watson, Scientific American, April 2003.
31. David Haig (2002) Genomic imprinting and kinship, Rutgers University Press, p.11. A further reason for the absence of parthenogenesis in animals is that the sperm also contributes the centrosome to the egg which is essential for initial divisions of the fertilized egg (Christiane Nüsslein-Volhard, 2006, p.15).
32. John Maynard Smith & Eörs Szathmáry (1999) The Origins of Life. From the Birth of Life to the Origin of Language. Furthermore, the members of higher levels are composed out of members of lower levels.
33. Graur and Li (2000) Fundamentals of Molecular Evolution. Second edition. p. 136.
34. Donald Forsdyke (2001) The Origin of Species Revisited, p. 103. (see review on this site).
35. Syozo Osawa (1995) Evolution of the Genetic Code, p. 45.
36. Michael Majerus (2003) Sex wars. - Genes, bacteria, and biased sex ratios, p.63,66.
37. Actually, meiosis is more complex. In males, the products of meiosis are four sperm, each sex chromosome in the original diploid cell being present in two of the products. In females of most species, however, only one egg is produced for each parent cell that undergoes meiosis, the other three haploid products together giving rise to the yolk of the ensuing egg. See also review of Mendel's Demon (Unexpected predictions and explanations).
38. Jan Sapp (2003) Genesis. The Evolution of Biology, Oxford University Press, paperback, p.x (Prefeace). This is elaborated in the chapter "Beyond the Genome".
39. M. Lynch, Proc. Natl. Acad. Sci. U.S.A. 99, 6118 (2002)
40. Paul Davies (1999) The Fifth Miracle. The Search for the Origin and Meaning of Life". p.119. Very important book!
41. What is known about the function of introns? , Scientific American, Ask the experts/Biology, 1999.
42. Louis Berman (2003) "The Puzzle. Exploring the evolutionary puzzle of male homosexuality", p.478
43. Tibor Ganti (2003) The Principles of Life, Oxford University Press. Furthermore, Ganti writes: "A living organism can never be developed from genetic material alone", "An egg, a seed, or a spore must always contain the substances of the cytoplasm". p.126.
44. Freeman Dyson (1999) "Origins of Life", second edition. p.18.
45. J.J. Emerson et al (2004) "Extensive Gene Traffic on the Mammalian X Chromosome", Science 303, nr 5657, 23 Jan 2004, pp. 537-540.
46. However, retrogenes are known for a long time. Examples of intronless retrogenes are: PGK (1987), calmodulin gene (1987), globin gene (1987), actin gene (1985). See Wen-Hsiung Li (1997), p.347.
47. S. J. Gould (2002) "The Structure of Evolutionary Theory", pp 252-253, 325, 527-528, 1174 (slightly adapted).
48. Solving the origin of life without the origin of species is difficult enough. However, even the origin of life itself is difficult enough because it commonly includes the origin of the genetic code. Hungarian chemist Gánti simplified the question by distinguishing between the origin of life an the origin of the genetic code.
49. Motomichi Matsuzaki et al (2004) Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D, Nature, 428, 653-657. 08 Apr 2004. This species has 5331 genes, only 26 genes have introns.
50. Iris Fry (2000) The emergence of life on earth, p.56, 170.
51. Paul G. Falkowski and Colomban de Vargas (2004) Shotgun Sequencing in the Sea: A Blast from the Past? Science, 304, 58-60, 2 Apr 2004.
52. Iain Cheeseman and Arshad Desai (2004) Cell division: Feeling tense enough?, Nature, 428, 32-33, 4 March 2004.
53. Radu Popa (2004) "Between Necessity and Probability: Searching for the Definition and Origin of Life", p. 95-96. [ 18 June 2004 ]
54. David Bainbridge (2000) Making babies. The science of pregnancy, page 35-36.
55. Philip Ball (2004) "Synthetic Biology: starting from scratch", Nature, 431, 624-626 (7 Oct 2004). "Bacterial genomes are within the range of current DNA-synthesis technology" says John Mulligan, president of the DBA-synthesizing company Blue Heron Technology. But bacterial genomes must be embedded within a cell and its attendant biochemical machinery, making them much harder to synthesize than viruses.". [ 9 Oct 2004 ]
56. Why are stem-cells so important? Stem-cell biology is the second pillar of twenty-first-century biology. If a genome were enough, why are stemm cells so important for medicine? See: Ann Parson (2004) The Proteus Effect: Stem Cells and their Promise for Medicine. [ 24 Oct 2004 ]
57. Mark T. Ross et al (2005) "The DNA sequence of the human X chromosome.", Nature, 434, 17 Mar 2005, 325-337.
58. Christian de Duve (2002) Life Evolving, p.38.
59. Gil Ast (2005) The Alternative Genome. Scientific American April 2005 pp40-47.
60. Douglas Futuyma (2005) Evolution, Sinauer Associates, page 53 and 440. (figures adapted for the web).
61. This is similar to explaining everything by saying 'God created the perfect fit between organism and environment'.
62. Large genomic differences explain our little quirks, Nature, 19 May 2005, 252.
63. Patrick Forterre (France) argues "that bacteria probably evolved more recently, and that LUCA was in fact a eukaryote", NewScientist 3 Sept 2005, p.28. (LUCA=Last Universal Common Ancestor). So Forterre seems to suggest that bacteria evolved from eukaryotes, but the difference with Senapathy is that Forterre does not claim that all eukaryotes arose independently. So although Forterre's view is highly unorthodox and implausible, Senapathy's view is a million times more unlikely.
64. Nick Lane (2005) Power, Sex, Suicide. Mitochondria and the Meaning of Life, p.143.
65. Asexual reproduction in animals is rare: the freshwater polyp Hydra reproduces by budding and some insects like aphids show life phases of quick multiplication through diploid eggs that form large, genetically identical clones. But in difficult times, even these animals reproduce sexually. (Christiane Nüsslein-Volhard, 2006, p.21).
66. Please note that the primordial pond illustration on the cover shows a turtle, a frog, a crab, a butterfly, a worm, but no mammal! No human being for that matter.
67. Blowing In The Wind. Seeds & Fruits Dispersed By Wind. (a beautifully illustrated page about all kinds of seed dispersal).
68. Robert Shapiro (2007) 'A simpler Origin for Life', Scientific American, june 2007, page 28.
69. Alec Panchen (1993) Evolution, p.175.
70. Reduced fitness in individuals due to homozygous deleterious alleles is known as "inbreeding depression". See: Scott Freeman and Jon Herron (2007) 'Evolutionary Analysis', page 270. See also: "the analysis found more than 4 million variants between Venter's maternal and paternal chromosomes. This suggests that humans differ by 0.5%, not 0.1%, as suggested by earlier estimates." Jon Cohen (2007) Venter's Genome Sheds New Light on Human Variation, Science, 7 Sep 2007. On the other hand inbreeding (of dogs) can result in extremely long stretches of identical DNA common in different individuals of the same breed -millions of bases long compared to the typical tens of thousands of bases in humans. This is artificial selection with probably high costs (Science 21 September 2007). It is no accident that DNA of dog breeds are now investigated for genes for 18 diseases including four cancers, four inflammatory disorders, and three heart diseases.
71. Catherine Jessus & Olivier Haccard (2007) 'Fertilization: Calcium's double punch', Nature 449, 297-298 (20 September 2007).
72. David Beerling (2007) 'The Emerald Planet: How Plants Changed Earth's History', pp.180-183. There are regions on earth (Athi Plains in Kenya) were C₃ and C₄ plants coexist, so that would be the place for Senapahty's primordial pond!
73. See: Carl Woese (review).
74. Catherine Brady (2007) Elizabeth Blackburn and the Story of Telomeres: Deciphering the Ends of DNA, The MIT Press.
75. Erika Check Hayden (2008) 'Evolution: Scandal! Sex-starved and still surviving', Nature, 10 april 2008. " "Bdelloid rotifers reproduce entirely without males: females package a complete copy of their DNA into eggs that develop, sans fertilization, into the next generation. Asexual reproduction certainly isn't unheard of in the animal world: parasitic bacteria force some insects to reproduce without males and female sharks kept alone in captivity have surprised their keepers by giving birth to baby sharks."
76. Vaclav Smil Energy in Nature and Society, MIT Press: 2008. 512 pp. reviewed in Nature, 10 april 2008.
77. David A. Wheeler et al (2008) 'The complete genome of an individual by massively parallel DNA sequencing', Nature, 452, 872-876 (17 April 2008)
78. Elliott Sober (2008) Evidence and Evolution. The logic behind the science, p.116.
79. Erwan G. Roussel et al (2008) 'Extending the Sub-Sea-Floor Biosphere', Science, 23 May 2008.
80. For this amazing story see: Audubon Magazine. For a map see here. If the primordial pond is at sea level, do these geese survive at that level? How does the bizar migratory behaviour originate? Random? That's a helpful explanation! Senapathy never tells us when, and where the primordial pond existed!
81. In fact when one looks closely to the quote from page 204, Senapathy is describing random mutation followed by natural selection!!!
82. See for explanation 'Vicious circle' box in my review of Hubert Yockey. This is a devastating obstacle for Independent Origin for the same reason that any mutation in the tRNA genes is lethal. See also: 'Does life look unlike evolution?' in my review of Walter Remine. Additional surprise: this genetic code is the same for all organisms! How is this possible in the independent origin scenario?
83. "RNA nucleotides have never been synthesized from scratch, in spite of decades of focused effort" (Robert M. Hazen (2005) Genesis. The scientific quest for life's origin, p.219. Also: "Nucleotides, the building blocks of DNA have never been produced in any prebiotic synthesis experiment" (Barton, p.95). Senapathy can never solve this problem by supposing that nucleotides where synthesised under genome control, because without nucleotides no genomes!
84. But not impossible. It is quite funny that Senapathy did not claim that with enough time prokaryote genomes could originate.
85. Gordon Campbell in: M.R. Wright (2000) 'Reason and necessity'.
86. Pier Luigi Luisi (2006) The Emergence of Life. From chemcial origins to synthetic biology, page 208.
87. Sheref S. Mansy et al (2008) 'Template-directed synthesis of a genetic polymer in a model protocell', Nature, 3 Jul 2008.
88. "Neo-Darwinism is in fact falsifiable, for there are many empirically testable claims made, for example within modern genetics which currently explains the core principle of inheritance. However, if it were to be falsified a new theory would have to replace it, in order to explain design in a non-theological fashion, and this would have very many features in common with neo-Darwinism simply because of the explanatory burden such a theory would have to carry." Thomas E. Dickins in: Evolutionary Psychology, 2005. 3: 79-84. This is very interesting: not only any alternative to evolution needs to explain the same set of facts, it also is expected to have much in common with neo-Darwinism. This is exactly what Senapathy is doing: he copies natural selection and common descent into his theory!!! What he does not do is use the same set of data as neo-Darwinism. Furthermore, Intelligent Design theorist Michael Behe incorporates natural selection and common descent into his ID theory!
89. Nicholas H. Barton, Derek E.G. Briggs, Jonathan A. Eisen, David B. Goldstein, Nipam H. Patel (2007) Evolution, Cold Spring Harbor Laboratory Press, hardback 833 pp. (review).
90. See for the probability of the spontaneous origin of a well-designed body: Richard Dawkins (1991) The Blind Watchmaker, Penguin books 1991 paperback edition, page 146.
91. Additionally, meiotic recombination shuffles the genome, so each generation inherits a new combination of parental traits. How does Senapathy's theory explain the origin and continued existence of such a widespread, complex and costly proces as meiotic recombination? Meiotic recombination contradicts the idea that genomes are essentially fixed. What is the purpose of a recombination of parental genomes?
92. John Maynard Smith (1999) The Origin of Life, page 3.
93. John Maynard Smith (1997) The Theory of Evolution, Cambridge University Press paperback. p.110.
94. I overlooked this figure and his claim that the primordial pond coincides with the Cambrian explosion. However, it only makes my argument stronger and clearer.
95. Senapathy appears to know that chromosomes occur in pairs. On pag 588 in note 109 he mentions homologous chromosomes. He even knows that one chromosome of a homologous pair of chromosomes is from the father, the other from the mother.
96. However, he seems to adopt an infinite universe of DNA sequences which does the trick for him.
97. Of the myriad problems of this scenario I mention a simple error: "Only those individuals with the absolutely right organs will survive" is not correct for reproductive organs! The situation is not analogous. One does not need sex organs to survive, while one does need hart, lungs, kidney, liver, mouth, teeth, stomach, intestines, and anus to survive. Infertile people don't die. See: 'The female and male genome' on this page.
98. A good overview is: chapter 17 in: Stephen Stearns and Rolf Hoekstra (2005), second edition.
99. page 8. This is a revealing and charming description of his naive way of thinking.
100. Daniel Fairbanks (2007) Relics of Eden. The powerful evidence of evolution in human DNA, p.154.
101. John Allman (2000) Evolving Brains, Scientific American Library, page 86
102. Dylan Chivian et al (2008) 'Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth', Science 10 October 2008.
103. Science Daily (2003) Ultra-low Oxygen Could Have Triggered Die-offs, Spurred Bird Breathing System, Oct. 31, 2003.
104. Helen Pearson (2008) 'Outcry at scale of inheritance project', Nature, 10 October 2008
105. Periannan Senapathy et al (2008) 'Origination of the Split Structure of Spliceosomal Genes from Random Genetic Sequences', Plos One, October 20, 2008. Open Access.
106. When did this processing occur? Some evidence suggests that Senapathy means prebiotic processing, because he writes: "Stop codons occurred too frequently to allow functional proteins to be encoded in random DNA" (my emphasis). Life could not have started with too short genes and proteins, that would be incompatible with life. Life requires functional proteins. On the other hand, Senapathy also provides evidence that a substantial amount of processing occurred after the origin of random DNA: "The average exon length from the intron-rich genomes is about 170 bases whereas that expected from random ORF lengths is 60 bases. This may indicate that there has been a selection for longer exons within the allowed maximum ORF length of 600 bases for optimizing the frequency of suitable exon lengths." (my emphasis) Further evidence supports this interpreatation: "mRNA splicing evolved to overcome the problem of the frequent occurrence of stop codons in primordial random DNA"; "RNA splicing evolved to circumvent the problem of short ORFs"; "According to the ROSG model, mRNA splicing evolved to overcome the problem of the frequent occurrence of stop codons in primordial random DNA that severely restricted ORF lengths." This is vague. Senapathy is not clear about it. A good scientific theory should be clear.
107. Computational Discovery of Internal Micro-Exons
108. Stewart Scherer (2008) A Short Guide to the Human Genome, p.32.
109. Ann Gibbons (2008) 'The Birth of Childhood', Science 14 November 2008.
110. Henry Nicholls (2008) 'Darwin 200: Let's make a mammoth', Nature 456, 310-314 (2008). Let's make a mammoth from its DNA is a perfect analogy with Senapathy's project to create an animal from its genome! All the problems and obstacles to create a mammoth from its DNA appear in Senapathy's scenario!
111. Organisms could do with only CG pairs or only AT pairs. Furthermore, it is chemically possible to have 3 different base pairs and 6 bases, or 4 base pairs and 8 bases Nicholas Barton et al (2007) Evolution, page 561. Information in DNA can still be coded with one base pair. Each strand would have a sequence such as GCCGGGGC..., and each amono acid could be coded by four or five bases instead of three.
112. In an interview Jerry Coyne says: "I don't know of any challenge to evolution that's ever come from a non-religious person. Personally I've never experienced one.". Senapathy is such a non-religious critic of evolution.
113. Noncoding DNA
114. Actually Carl Woese showed that 'Prokaryotes' must be replaced with 'Archaea' and 'Bacteria' or alternatively with 'microorganisms'. See also: Norman R. Pace (2009) 'It's time retire the prokaryote', Microbiology Today, May 2009, 85-87.
115. Kurland CG, Collins LJ, Penny D (2006) Science 312:1011-1014. Quoted by Lynch
116. John S. Mattick and Igor V. Makunin (2006) 'Non-coding RNA', Human Molecular Genetics 2006 15.
117. Eugene V. Koonin (2009) Darwinian evolution in the light of genomics, Nucleic Acids Research, 2009, Vol. 37, No. 4 1011-1034.
118. Henrik Kaessmann (2009) More Than Just a Copy, Science.
119. Carol Greider, Elizabeth Blackburn and Jack Szostak received the Nobel prize 2009 for their work on telemeres. Nature
120. Fuyuki Ishikawa and Taku Naito (1999) 'Why do we have linear chromosomes? A matter of Adam and Eve', Mutation Research/DNA Repair Volume 434, Issue 2, 23 June 1999, Pages 99-107: "Bacterial circular chromosomes have sporadically become linearised during prokaryote evolution".
121. Dirk Schübeler (2009) 'Epigenomics: Methylation matters' Nature 462, 296-297 (19 November 2009)
122. Dennis McCarthy (2009) 'Here be dragons. How the study of animal and plants distributions revolutionzied our views of life and Earth', p.100.
123. Dennis McCarthy (2009) 'Here be dragons', p.186 and 191.
124. See also: "As Simpson himself pointed out, -any event that is not absolutely impossible ... becomes probable if enough time elapses" (Nature, 4 Feb 2010) about Madagascar species. What we need is quantification.