mirrored file at http://SaturnianCosmology.Org/ For complete access to all the files of this collection see http://SaturnianCosmology.org/search.php ========================================================== Was Darwin Wrong? Home | Intro | About | Feedback | Prev | Next | Search new 22 Feb 2004 <#Homology> contents <#Contents> Independent Birth of Organisms? The Chromosomes Say /NO!/ A review /by/ Gert Korthof. 29 Dec 2002 (updated 28 Jan 2005 ) * The origin of life is an age-old problem. Mr Senapathy came up with an extraordinary solution: the independent origin of all organisms. A non-creationist solution, but a solution completely at odds with the Darwinian principle of common descent. How did he arrive at such an unorthodox solution? Senapathy did computer simulations and found that it was very difficult to find genes of bacteria in computer generated random DNA sequences. However, he found that it was easy to find genes interrupted with meaningless pieces of DNA or 'split genes'. All plants and animals have split genes. Therefore, the synthesis of random stretches of DNA would automatically contain split genes. Whole genomes could be automatically produced from the building blocks of DNA. Therefore, this new theory would not only explain the origin of life, but of all species of animals and plants in one strike. Darwinian mutation, natural selection and common descent would be unnecessary. However, it is difficult to say which biological facts are most fatal to this theory, because there are so many that make this theory highly implausible. * A computer simulation AVTQMOIBIYUTTYRXBVGHSFRETYPNMKJBZXCVBFGTWRWEDDFALH OILPMNKJUVBGHYFQSZVDFTRYOPMMJLAJSHJGFRTYQREFFGFBNBMI ALKEIUQJLJRYTWSDHTRHFMNZBXVCHQYTNVHSKFYWURIOPMCVHY HDFQIOREUYSKJGHADGLZXMNRBCNVYQNEUCBNRTYVBNFYUIRHJY NBBNZCXJKWOPIKIUQWYR*TO*HVBCNMZJSGHFGTWRERUUIOPPMKJH HGAWRYBCGDFHNXCYRQZCVNBIOVYZNSGHENMBKHJIYQXHFIAGHII YOPPZNCVJHFGJJMMBJHQOVNMZBXVTRRQEWFHKPLOIQAZSGJHUIO THKLPMLOK*BE*SICUBNJCGTQRWETRYIIPOCNMKSALIWTYTYHCBZVX ASPMQIZUXEMCCUVIEASRTTYPOIVLASFGUEYRTHNBCVXVAQWHGK JFGURYTOPZDFGKHLUITYWRERYVNGFASDFLJIWKERHVNXJWIWZAQ WSDDSXCMKOPLJHEDRFTGYHUBVFEWSXMUBTCWQA*OR*WAGJLNVX ZWSAQEDCBHYNMKOLPIUWQERVFCXNBMJHGFTIOLEWQAJUIMJTED WSAQZXCVBNMKIJHYTEWQSDFHLOPKYQAMOECIMTBUNHFSKOPMQ PMZALYBECMIQMXNCVHVKITUYQASLKJGNHVMCHFDZCERWTQYTU IOMBJGPOQWUNXGDFFHSYRTYAZNGHKITYTQRHSDNJHKLJPGKJFJHS LQEIWUZV*NOT*IHLOKIAFDJGDFKIUUTWTYERUJGHDNMHKJHKJKJKQ ZATMLPOKJIMNBVZXUYTRWDKJHGFAASOJHSAWQHJKLYVOFQWED FGHBVCDEWSQAZXMJIXOLPMYHTGRFEDSWQAZXCFRDIOPNJHGGVJ JFHJJYGHRTEDWQEXSSDXGFVOPLKMJHJJBHNGHQWSRFGGYUHIOKP OLMKJNBHVCZSSZWAWDFGOPNGYHY*TO*FFGVGBHWIYHGUHJQWSC FVBMNIYUTPIIERJDFHOIURTYIERUQOBMNZBXCBNCGHFTRYGJHJJGH GFGSOFSKSKHJJKTKMQIOYUTCBTREOPZWSETFBGJGNUJBDFEDLOPT EGJALJQEPBMNZWAXI*BE*CVBIYOYQWTREHJLMBNQACVIMJXKFGODR Fig 1. The wordsTO, BE, OR, NOT, TO, BE found in a random string of letters (p.226). In this figure from Senapathy's book a computer generated random sequence of the letters of the alphabet is shown and 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 <#Notes>). 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 statistical claim. 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 <#Notes>). Introns are pieces of DNA in the middle of a gene, which are eliminated when the gene is translated into protein and so the intron sequence does not end up in the protein. Introns are central to Senapathy's theory because the occurrence of genes in random DNA sequences depends on finding /split genes/: genes with introns. He correctly concludes that finding the uninterrupted gene sequences of today's prokaryotes in a computer-generated random DNA sequence is extremely unlikely. Therefore, in real life the random origin of current genes of prokaryotes must also be extremely improbable. Evolutionary biologists today have other ideas about the approach to the origin of life question (see also paragraph What is Life? <#Life>). This is crucial for Senapathy's thesis: if split genes cannot be found in a random DNA sequence with sufficient probability, then his whole thesis breaks down. In the figure above, the words are only 2-3 letters, otherwise we needed pages full of letters to demonstrate the effect. For longer words, we simply need longer sequences of letters. However, we can see from the figure that the meaningless pieces of letters are far greater than the real parts of the gene. This is exactly what is found in real genes of eukaryotes (organisms with a nucleus in their cells such as all animals and plants). Therefore, it is not very surprising that Senapathy became enthusiastic for the thesis of independent origin of organisms. However: is it plausible? Searching for exons, ignoring introns Senapathy searches for exons (protein coding DNA) and ignores introns ('non-coding DNA') in his random genomes. This strategy succeeds in eukaryotes, because eukaryotes have pieces of coding DNA interrupted with variable pieces of noncoding DNA. His search strategy fails in prokaryotes because prokaryotes have continuous genes. That's why prokaryotes in Senapathy's theory cannot spontaneously arise in the primordial pond. However, if one cannot ignore introns, Senapathy's strategy would fail. Are introns just random noise as he assumes in his computer simulations? Recently it has been discovered that introns do sometimes have identifiable functions (41 <#Notes>). In that case Senapathy is not justified in ignoring introns and they should be included in his computer simulation of virtual genomes. But then his search for genes (exons+introns) in random DNA certainly would fail just as it fails for prokaryotic genes. Eukaryotes with intronless genes Senapathy claims he can find eukaryotic genes in random DNA because they are interrupted with 'random' non-coding DNA (introns). What if eukaryotes have intronless genes too? Recently, intronless genes have been discovered in eukaryotes (45 <#Notes>). The process by which these genes are produced is called retroposition and the genes are called retrogenes. It is based on reverse transcription of RNA (see: Steele review). Retroposition is an important mechanism of gene copying and produced a large number of functional genes in mammalian genomes. For example, retroposition produced approximately 1000 functional intronless genes in humans. Intronless genes in eukaryotes are more widespread than previously thought and do not necessarily depend on retroposition. Nearly all the genes (99.5%) of a red alga species are intronless (49 <#Notes>). This means that the human genome cannot be found in a random piece of DNA using Senapathy's search strategy. Omitting these intronless genes results in an incomplete genome. 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 <#Notes>), but it nevertheless refutes his theory of independent origin of many eukaryotes. Furthermore, retroposition is a process which fits very well in an evolutionary paradigm, not in a paradigm with immutable genomes. Genes, genomes and beyond new 30 Nov 2003 The basic question is: When is a DNA sequence a genome? Any sequence could be a gene or genome, but * correct splicing sites, start and stop codons are necessary * meaningful expression characteristics of the gene * location of the gene on a chromosome * other genes in the genome that influence its function * specific genetic code (how 64 codons are translated into 20 amino acids) * laws of biochemistry (energy production, protein folds, catalysis) * a genome needs a cell (mitochondria, membrane, ribosomes, nucleus) (55,56 <#Notes>) * the physical conditions of the earth (temperature, atmosphere, gravity) The crucial question is /not/ what the probability is of finding many eukaryotic genes, /not/ what is the probability of finding an arbitrary collection of genes, but what is the probability of finding a *complete* genome? A complete genome with the right combination of genes is necessary but not sufficient to produce an organism. This is important: a genome is not a random 'collection of genes' (imagine an elephant with the legs of a giraffe, or a swallow with the wings of a swan). "When the number of random events are large enough, the unbelievable will certainly happen" (p.332) So even finding all eukaryotic genes of all species is not enough. The right genes (and there are up to 30,000 genes in a mammalian genome) must go in the nucleus of one cell in order to make a mammal. The key question for Senapathy is: how many trials does one need to produce the genome of a human being? Senapathy must show that the ratio of the /observed/ genomes to all /possible/ genomes is high enough to be realistic. Regrettably, the number of possible genomes is infinite. This is an important problem and it is not discussed at all by Senapathy. There are still more serious problems at a deeper level: * Senapathy in fact merges the problem of the origin of life (an unsolved problem), with the origin of species (solved in principle by Darwin). Darwin's /Origin of Species/ did not discuss the origin of life. 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? <#Life>). * 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 <#Notes>). 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! * Beyond the sequence: "The major problem, I think, is chromatin^1 . 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^2 ? You can inherit something beyond the DNA sequence. That's where the real excitement of genetics is now." (James D. Watson: 30 <#Notes>) 1) chromatin: the dynamic complex of DNA and histone proteins that makes up chromosomes. 2) epigenetics: chemical modification of the DNA that affects gene expression. However, Senapathy asks one interesting question: How would DNA of current organisms look like if it originated randomly, and especially how would the distribution of stopcodons look like? (see box). My point however is that 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 <#Notes>), 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: s e x. *A test for randomness (1)* An interesting question of Senapathy is: If DNA has directly arisen from random assembly of the building blocks in the absence of millions of years of selection, then the distribution of stopcodons should be random. Does it? Actually there are two questions: What do we observe? What do we expect? S does not state this clearly at the beginning. S produces plots to answer both questions, but they are difficult to read, not well explained and do not seem to support his theory. A stopcodon is the DNA code for the end of the protein. If the distribution of stopcodons in current genomes would match a purely random distribution, it would be strongly suggestive for the random origin of genomes. The frequency of stopcodons in a random computer generated DNA string must be calculated on the basis of the fact that 3 out of the 64 codons are stopcodons (4.7%) (assuming this holds for the origin of life also). So I would expect 47 stopcodons in 1000 codons (=3000 bases). Assuming all codons have equal probability, the average length of genes between two stopcodons would be 1000/47=21 codons (=63 bases) (my calculation, Senapathy does not show this). However, this is too small for a gene! Genes are hundreds or thousands bases long. According to Senapathy the expected length of genes in computer generated random sequences would vary from 0 (two stopcodons next to each other!) up to 500 bases or 600 bases, but "More than 95% of all random genes are shorter than 100 bases" (p.234). According to Senapathy genes in organisms are often 9000 bases (=3000 amino acids) long (p234). So this is far above the length of the genes found in the computer generated sequences. Therefore, I would conclude that typical eukaryotic genes could not be formed directly from randomly assembled DNA. Nevertheless, Senapathy does not seem to be discouraged by this result. He invokes a kind of processing of DNA that results in eliminating all the shorter DNA sequences and leaving all the longer sequences. This processing has to result in two things: eliminating pieces with too many stopcodons and producing precisely the genes we find today. However, these 2 goals do not automatically cooperate. Worse, there is no connection. The problem with this idea is that right from the start in his procedure he makes unwarranted assumptions, such as that the key sequences necessary for proper splicing are just there! One must not only find exons! This is not shown in the above computer simulation! So we should *not* search for: TO BE OR NOT TO BE, but something like: XYZTOXYZ XYZBEXYZ XYZORXYZ XYZNOTXYZ XYZTOXYZ XYZBEXYZ (XYZ being splicing recognition sites). How else can the words (exons) TO BE OR NOT BE be recognised? (26 <#Notes>) In reality the number of bases that are essential for proper splicing is unlikely to be less than 10 and is plausibly as high as 30 (39 <#Notes>). To be correctly processed to proteins, begin and end of exons need to be recognised. However, this would make the task of finding them in a random sequence far more difficult than Senapathy imagined. I see another problem with his data: he shows graphics showing that the shortest DNA sequences (down to zero length) are most frequent! Why is this? He does not explain. Why is there not a normal distribution around the mean length? Further questions: Senapathy does not tell us why there are only 3 stopcodons and not 1 or 2 or not more than 3. If only 1 stopcodon existed, that would produce longer sequences. Maybe there used to be only 1 stopcodon at the origin of life and later 2 were added. So Senapathy's assumption is unsubstantiated, and he could have used speculatively 1 stopcodon: 1,56% stopcodons = 156 stopcodons in 10.000 codons (=30.000 bases) = mean length = 64 codons = 192 bases (still too short). *A test for randomness (2)* The genetic code is redundant. The number of codons for amino acids varies from 1 up to six. However, the usage of synonymous codons is non random. Some are rarely used, others with high frequency. For the amino acid LEU the most frequntly used codon is used 140 times more often than the least frequenlty used codon (33 <#Notes>). This is a genome wide bias. There should be no such huge codon bias when genomes arose by chance from the primordial pond. In the independent birth scenario all codons for a amino acid are expected to occur on average with the same frequency. Furthermore, when the ratio of AT/CG is measured on the whole genome level, it appears that it is not 1:1. This conflicts with the random origin of genomes. While the A:T and C:G ratios are 1:1 (famous Chargaff ratio discovered before Watson and Crick model), the (C+G) percentage of a genome is free to vary. And it does. Already in 1952 C+G percentages as low as 34,8% have been discovered in the DNA of insect viruses (34 <#Notes>). In the bacterial kingdom the C+G percentage varies from 25% to 75% (35 <#Notes>). [17 Aug 03] *Paul Davies about genomes* /Paul Davies wrote a crystal clear analysis of the problem:/ "If genomes are information-rich, then they have to be random (or almost so). If biological organization is random, its genesis should be easy. [!] The vast majority of possible sequences in a nucleic-acid molecule are random sequences. Only a tiny, tiny fraction of all possible random sequences would be even remotely biologically functional. A functioning genome is a random sequence, but it is not just /any/ random sequence. It belongs to a very, very special subset of random sequences" (40 <#Notes>). So Senapathy is right about genomes being mathematical random, but its production is /not easy/ because only a /tiny, tiny/ fraction of the genomes are functional. [28 Nov 03] Everything you always wanted to know about s e x, (but were afraid to ask) Sexual reproduction is a most important fact against independent origin. The independent origin of a female and a male of the same species is extremely improbable. This applies to all sexual reproducing organisms. (Asexually reproducing organisms are a different matter). As a starting point, I list the following uncontroversial facts. One does not need to be an evolutionist to accept them. 1. Human body cells are diploid: one complete set of chromosomes from the father, plus one complete set from the mother. 2. sperm and egg cells are haploid: 1 incomplete set of chromosomes. 3. a diploid set consists of 23 pairs of chromosomes, 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 Fig. 2 below). 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. (we could call the mitochondrial genome 'human chromosome number 25' or the second genome) 8. The number of genes in the human genome is about 25,000 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. 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) This is astonishing and outrageously careless (an understatement). The first quote proves that Senapathy does not distinguish between 'haploid' and 'diploid' cells (18 <#Notes>). 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). Senapathy does not specify any details. Indeed, part of the trouble is that his scenario is extremely vague at crucial points. I will consider two possible scenarios. It must mean that either (1) a haploid or (2) a diploid cell must have originated in the primordial pond. Can a male or female arise from haploid cells? If the goal is to produce a male one needs an egg that is fertilised by a sperm carrying a Y-chromosome and for a female one needs and an egg that is fertilised by sperm carrying a X-chromosome. So one needs 4 cells in total to produce one male and one female. (3 <#Notes>) chromosome X chromosome Y X Y Fig 2. Human sex chromosomes (2 <#Notes>) What is the probability that those 4 cells arise from the primordial pond? Let us start with the production of one egg cell from random assemblage of genes in the primordial pond. A human egg cell contains approximately 32,000 genes (minus Y-specific genes) distributed over 23 chromosomes. For example chromosome 1 contains an estimated 2700 genes; X chromosome 1600 and Y chromosome 250. I will ignore a lot of complicating factors: a chromosome is more than naked DNA (19 <#Notes>), has a centromere, telomeres, and an egg cell is more than a bag of genes. All those genes have exact locations on the chromosomes characteristic for the species. For a given species, the same genes are on the same chromosomes and in the same order. Chromosomes themselves have no order (free floating). If one wants to produce a fertile individual that is able to reproduce then a requirement is that all genes on the corresponding chromosomes of the egg and the sperm are in exactly the same locations. Therefore, the probability of the genomes of one egg cell and one sperm cell equals *the probability of 32,000 genes ending up in exactly the same positions on 23 chromosomes in two independent trials*. Please note that I am not estimating the probability of random assembly of the human genome in one trial. I am estimating the *repeatability* of the event. In this scenario we need the repeatability because in the end we need 4 (haploid) genomes of the same species. The problem can now be formulated as: how many permutations are there of 32,000 genes? To get an idea of the magnitude of the problem: the number of permutations of only 29 genes exceeds 10^30 (which is the number of DNA sequences in Senapathy's primordial pond). It is clear from this that it's impossible that a *second* cell that matches the first, will be produced with this method, let alone that 4 genomes could be produced in this way. *Virgin birth?* Theoretically a haploid female cell could 'double' and 'divide' to produce two identical daughter cells. Although it is known for an egg to start developing without being fertilised in some insects and reptiles, fully parthenogenetic human embryos cannot develop to term (4 <#Notes>). 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 fetilisation by a father] in mammals (31 <#Notes>). 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 <#Notes>). 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. Period. 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 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 are not all species haploid?/ *possible objections* I suppose Senapathy could come up with the following objections: (1) maybe millions of different genomes could produce humans. - This is not relevant. What is relevant that any genome must be produced in a male and a female form. That makes it impossible. (2) genes do not need to be in same position as the current positions to produce a human, so the probability to produce a human genome from random DNA sequences is very much higher. - Theoretically it seems quite possible that genes which are ordered in a different way on the human chromosomes would still produce a human being. However, paternal and maternal genes (alleles) have identical positions on chromosomes. That situation must be explained. (3) there are many variations of a gene that produce the same protein and many protein sequence variants produce the same enzymatic function. - This is right but not relevant because I only considered the positions of genes on chromosomes. Those chromosomal positions must match. (4) sex organs are generated by genes just as all other organs, so it should not be difficult (p.353). - Of course sex organs are generated by genes. That is not the point. The point is: what is the probability that male-specific genes come together on chromosome Y AND that the sex-genes are expressed at the right time and the right place in the right sex, AND that both genomes are identical apart from sex-specific genes, AND both genomes are able to fuse and create a new individual? Can a male or female arise from diploid cells? A diploid cell (= a pair of each chromosome) must be somehow produced because human body cells are diploid. Theoretically, replicating each chromosome of a haploid cell and skipping cell division could produce a female diploid cell. This doubling method escapes the huge improbability of generating a human genome twice. However, the 'doubling method' fails to produce a diploid male cell because X and Y are quite different chromosomes. Without a male cell, this scenario fails to produce a male and a female. Therefore, it fails to produce what could be the start of a new species. *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* which creates haploid cells. Both processes are complex because they must guarantee that daughter cells receive the correct number of chromosomes. At the beginning of mitosis, the process of cell division, chromosomes are organised randomly - like /j/ i/ g/ s a w 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 <#Notes>). 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. 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 <#Notes>) 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. 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 <#Notes>). *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! *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 <#Notes>). 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! Conclusion: both the haploid and the diploid methods fail to produce the first male and female. It is impossible to produce humans from a pool of genes even if all the necessary human genes were swimming around /in duplicate/. The funny thing is that Senapathy /knows/ that 'eukaryotic organisms usually contain two of each gene, and a haploid genome contains only one copy of each gene' , but he does not realise that this is fatal to his theory. Diploidy and sexual reproduction are tightly interconnected. But even when one allows for the independent origin of diploid organisms, than it is still not necessary that they should have sexual reproduction with such a complicated process like meiosis. Indeed, why don't all diploid species use budding (like many plants) or some form of asexual reproduction? Why not produce diploid children directly from a diploid cell, thereby circumventing meiosis? In general: when there are two solutions for a problem in nature, the theory of independent origin should predict the most probable solution, that is the most simple, of the two alternatives. Did prokaryotes arise from eukaryotes? Senapathy's theory states that eukaryotes originated first because genes with introns can be found in computer generated random sequences of bases, whereas prokaryote intronless genes cannot. Did prokaryotes arise from eukaryotes? The standard textbook view is that the first organisms found in the fossil record are 3,500 million years old and are prokaryotes (bacteria). For the next 800 million years life on earth consisted of prokaryotes. Another source states that the first 1.5 billion years, life consisted of aquatic microbes (51 <#Notes>). The first indirect evidence of eukaryotes appeared 2,700 million years ago and the first fossil eukaryotes appeared 1,7000 million years ago. Another source states that eukaryotes emerged perhaps as many as 2 billion years later than prokaryotes. Senapathy claims eukaryotes emerged first. It's clear from these data: the fossils say NO! *Mitochondria* are organelles in all eukaryotic cells; they are crucial for eukaryotic life; they multiply independently within eukaryotic cells; 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 <#Notes>). 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 <#Notes>). 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). Senapathy only devotes two short paragraphs to an issue of crucial importance to his theory. In the quote he switches from the problem of mitochondria to another issue: the nucleus. He conveniently omits that mitochondria have their own DNA (which is present in John Maynard Smith, 1975). Clearly, he wants to get rid of the theory because it undermines his own theory. The main problem for his theory is that it is extremely unlikely that a dual genetic system originated /independently/ in a million eukaryote species. Additionally it is even more unlikely that the mitochondrial genome contains a non-random subset of genes (related to respiration). It is impossible that the mitochondrial genome of all higher animals got 13 mRNAs, 22 tRNAs and 2 rRNAs just by accident. The most plausible explanation is that the dual genetic system arose only once and was inherited from the first eukaryote. One of the most irritating facts in Senapathy book is that he dismisses a theory without a careful examination of the facts. The presence of mitochondria in eukaryotes is not an insignificant fact. It is now recognised that eukaryotic life on earth became the dominant form of life on earth because mitochondria caused gender (5 <#Notes>). Common descent versus independent origin Rejecting common descent comes at a huge cost: it equals reinventing the wheel a million times! All the combined adaptations that produce successful flight must be reinvented for each bird. All the combined adaptations that enable survival in the sea must be reinvented for each fish. It just seems crazy to reinvent a dog-like type repeatedly to explain wolf, fox and coyote (see also Independent origin and homology <#Homology>). Small modifications of a basic dog-like type would suffice. Creationists and other critics of common descent must have suspected this problem and proposed a limited form of common descent for similar organisms. Compare the two diagrams below. The first is from Senapathy and the second from intelligent design creationist Paul Nelson. Remarkably, both accept a limited form of common descent ('microevolution'). A dog-like 'basic type' produces the dog, hyena, fox, wolf, and coyote species. similar species of a distinct creature Senapathy millions of distinct independently-born creatures Fig 3. Senapathy, p.462 pheasants ducks dogs cats horses Nelson creation of basic types Fig 4. Paul Nelson (7 <#Notes>) Senapathy: "many species within a genus usually connectable by evolution and many families within an order are sometimes connectable by evolution" (p.461). However, this implies all the mechanisms for large-scale evolution such as mutation, selection, genetic drift, and the generation of new species! As the name of his theory suggests the 'independent birth' of organisms is the most important aspect of his theory. Unexpectedly, Senapathy's theory is not a theory of independent origin! Further evidence comes from the primordial pond: numerous creatures originated from "a common pool of genes in the same primordial pond" (p.455). A common pool of genes denies the /independent/ origin of genes. We have now a violation of independent origin at three levels: (1) common pool of genes, (2) microevolution (Fig 3), (3) prokaryotes evolved from eukaryotes. Therefore, it is misleading to label this theory as 'independent origin'. Apart from the label, the amount of common genes is left unspecified. Probably because he has no theoretical reasons for their existence. I am afraid that random origin of DNA sequences predicts unique sequences, not multiple occurrences of the same sequence. There is a practical implication of the hypothetical "common pool of genes": a *common* pool requires that there is only *one* pool on the earth. Where was it located? How big was it? How long ago? How long did exist? (25 <#Notes>) Was it fresh or salt water? All unanswered questions! Furthermore, both mechanisms (independent and dependent) can be arbitrarily invoked to explain any pattern of similarities and dissimilarities in nature. Similarly, it could 'predict' any pattern. Far from being an advantage of the theory, it is actually a disadvantage. It is an ad hoc explanation. The scientific value of his theory becomes still worse (but still more comfortable for Senapathy), when he allows for arbitrary *genome mixing*: "slightly changed creatures could also be produced in the primordial pond by mechanisms of genome mixing and genome alteration and or restructuring" (p.455). My objections are: (1) This is again contradicting /independent/ origin; (2) If 'genome mixing' completely mimics common descent, then there is no observational difference of his theory and common descent (3) 'genome mixing' is too vague, too 'cheap' and too 'easy'; (4) it does not make sense that anything goes at the moment that genomes originate and millions of years thereafter all genomes are frozen; (5) It is impossible to refute such a theory. When showing evidence that refutes independence, Senapathy always can claim 'my theory can explain this by a common pool of genes and genome mixing'. We do not learn anything new about nature. Finally, let us not forget that in Senapathy's theory prokaryotes /derived/ from eukaryotes, thereby contradicting /independent/ origin again. It is an odd aspect of Senapathy's theory that bacteria, the most simple living organisms, did not arise directly from the primordial pond, but from more complex organisms. The role of natural selection in Senapathy's theory Senapathy needs natural selection because not every assembled genome survives. There is nothing in Senapathy's theory that tells us how many genome trials are needed to produce a human genome. One trial? hundred? thousand? A million trials? Evolution needed 3 billion years to produce us. If selection is a negligible factor, then the origin of (human) life could be a matter of hours! The fundamental question here is how easy is it to produce a genome? (24 <#Notes>) The point of Fred Hoyle's Boeing-747 story (14 <#Notes>) is that building blocks are not enough to produce complex systems. Essentially Senapathy believes that a tornado in a junkyard produces a Boeing-747 (probably with a few selection steps). Creationists /and/ Darwinists reject the possibility that a complex system can arise by chance in one trial. According to evolutionary biologists, numerous selection steps are needed. According to creationists, 'intelligence' is needed. example1 Fig 5. example2 Fig 6. Strickberger (15 <#Notes>) compared the very low chance of getting the word 'EVOLUTION' in one trial (figure 5) with the high probability of getting it in successive small steps (figure 6). Although some details of Strickbergers illustrations are confusing, it is clear that the method of figure 5 is essentially Senapathy's method. Therefore, Senapathy chooses the most difficult method (20 <#Notes>). Senapathy's mechanism is a *whole-genome-test*. The Darwinian mechanism is a test of a small modification of a genome. Another important difference between the Senapahty type of selection and Darwinian selection is that Senapathy's selection applies to unique genomes, while Darwinian selection applies to individuals of a species. The death of a Senapathy genome equals extinction, while Darwinian selection means that very similar genomes of the same species survive and can be improved. The power of selection comes from endlessly repeated cycles of magnification of the successful genomes in populations of very similar individuals. Lucky accidents are magnified. This is crucial feature is completely absent in the theory of Independent Birth. Suppose a healthy human 'male' originated from the primordial pond, /but missing just one gene/: the SRY-gen, which makes the unlucky individual completely infertile. That means no descendants and 100% selection against that individual. It means that this extremely rare and nearly perfect genome is extinct forever. The odds that the same genome with an intact SRY-gene will arise for the second time are astronomically low. Compare this with an endlessly repeated cycle of small improvements based upon successful individuals of previous generations. It will become clear that the intensity of selection in Senapathy's scenario is huge when compared to selection in the Darwinian scenario. The power of common descent is the accumulation of inventions and the power of natural selection is selection of small variations of proven successful individuals. I only realised the powerful advantages of common descent and natural selection when I compared them with independent origin. Can we test whether genomes have a random origin? Of course. Senapathy should have given statistical tests of randomness of real genomes (they were available already in 1952, see box). For example, the frequencies of A,T,C and G should be equal if genomes have a random origin. Any deviation from randomness can only be explained by mutation and selection. As far as Senapathy is concerned, a genome could have originated yesterday. His genomes are timeless fixed creations. Senapathy genomes do not contain any history. Finally, /any/ amount of selection after the creation of a genome destroys the whole idea of organisms arising /directly/ and simultaneously from the primordial pond. Common descent and Natural Selection are both central theories of Darwinism. Senapathy smuggles in downgraded versions of both and at the same time triumphantly claims that Darwin's theory is 'fundamentally incorrect'. The role of mutation in Senapathy's theory "Mutations in a genome can only lead to normal individual variations, or to genetic defects, which are absolutely (28 <#Notes>) useless for organismal evolutionary change" (p.46) and having said something about the effects of mutations, he goes on to declare the *immutability* of organisms: "the genome of every independently born creature is unique and unchangeable into that of another unique creature, and therefore is essentially immutable." (p.6) and "a snail can give rise to many different snail varieties, but never to a crab or a sea star." (p.46). Senapathy's use of the concept 'immutability' is very confusing. He does not clearly distinguish between the existence and the possible effects of mutations. That hampers a clear discussion of the topic. To add to the confusion, he mixes well-defined scientific concepts such as 'species' with ill-defined concepts such as 'varieties', 'distinct creatures', 'organisms'. This can be compared with mixing up the physical concepts "atom", "molecule", "electron" with concepts such as "stuff". It makes reading his book hard. Apart from that, his immutability concept introduces a serious difficulty in his 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 ). However, many genes are not identical to many viable genomes. The role of adaptation: random perfection "At the time of the birth of organisms, "random perfection" of organisms filtered the meaningful organisms from among the myriad mostly meaningless independently-born organisms. Those creatures that fit well with the physical environment survived while others perished. Among the physically fit immutable organisms, ecological fitness occurred by chance." (p.204) 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. *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 <#Notes>) 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. 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). Senapathy's theory could be called internalism. All the creative power is in the assemblage of genomes and the environment plays a minor role. 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 that is an adequate characterisation of Senapathy-genomes. For Senapathy, life is a 'genome accident'. Independent origin and the clumpiness of morphospace What can be more curious than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should contain the same bones in the same relative proportions? Most organisms are well adapted to their immediate environments, but also built on anatomical ground plans that transcend any particular circumstance. Why should structures adapted for particular ends, root their basic structure in homologies that do not have a common function? Why should this be so, if all organisms arose independently? Why do animals take the forms they do, and not others? Why are all land vertebrates 'tetrapods', while none have six, eight, or many legs? Why does the domain of mammalian carnivores contain a large cluster of cats, another of dogs, a third of bears, leaving so much unoccupied morphological space between? This feature of life on earth is called 'the clumpiness of morphospace': the inhomogeneous occupation of all possible forms of extant or extinct animals. This clumpiness must be explained. In the theory of evolution, the cluster of cats exists primarily as a consequence of homology and historical constraint. All cat-like animals (lion, tiger, puma, leopard) share a basic morphology because they arose from the common ancestor of all cat-like animals. In a world of independent origin, a world without history, where all features of organisms express their initially created state, why does homology exist at all? If organisms arose independently, they would show more structural variation, and not be morphologically clustered as varied manifestations of 'archetypes' (47 <#Notes>). Senapathy cannot use historical developmental constraints, because Independent Origin is an unhistorical or even anti-historical theory. Senapathy can not use limitations of genome production either, because if genomes are random, then /any/ genome is possible. The primordial pond is a free lunch The primordial pond is the 'birthplace' of all species. Water is the natural home of fishes. Predatory fishes prey on other fishes. As soon as a predatory fish originates in the primordial pond, it starts eating. It swallows everything it can get. Therefore, predatory fish easily cause the extinction of every 'species' it can swallow, because the method of 'independent birth' does not produce species but single unique individuals of a species. Thus before a single unique individual can multiply and become a population, it has been swallowed by a predatory fish. Likewise, plankton feeders will exterminate all plankton. The primordial pond is a free lunch until the predators die of starvation when all prey has been eaten. That is why Darwin, Oparin and Haldane already argued that life could have emerged only on a sterile, lifeless planet (50 <#Notes>). All mammals require a mother A baby without a mother? Surely, you're joking, Mr. Senapathy! Could a human baby develop in a primordial pond? Could it survive? That would be a miracle! (29 <#Notes>). Would there be a constant supply of food and oxygen during nine months? How is this done if there is no umbilical cord and no mother? Does the primordial pond precisely have the temperature of the body of the mother? Is there no danger for bacterial and viral infections in the open primordial pond? Is there no competition for food and predation in the primordial pond? If the 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? 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. However, 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 chimpansees. The head of the fetus is still small enougn to pass through its mother's birth canal. One of the consequences is that humans at birth are utterly helpless (42 <#Notes>). Amazingly, in order to be a healthy individual, the first 'female' genome would not need hormones for ovulation, menstruation, pregnancy, and lactation. If no hormones are necessary, then genes for hormones are unnecessary. The genomes would be different. 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. 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 <#Notes>). 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 <#Notes>). 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. The final refutation Conserved chromosome segments between human and mouse are the final refutation of independent origin. If all genomes arose independently from the primordial pond and if the distribution of genes over chromosomes were random, then genes of related species should not have /the same linear order/ on their chromosomes. However, if a great number of genes appear in the same order in different species, this cannot be explained by pure chance. This is exactly what has been found when geneticists recently compared the genome of mouse and man (8,9,10 <#Notes>). A segment of roughly 90,5 million bases on human chromosome 4 is similar to mouse chromosome 5. (11 <#Notes>). Almost all human genes on chromosome 17 are found on mouse chromosome 11 (12 <#Notes>) and human chromosome 20 appears to be entirely orthologous to the bottom half of mouse chromosome 2, apparently in a single segment (13 <#Notes>). That means that thousands of genes are in the same order in mouse and man. A few genes might be expected to be in the same order by pure chance, but not thousands. This can only be explained by common descent of mouse and man. If all species were independently born, then the probability of finding similarities in a human-mouse comparison should equal the probability of finding it in, say, a human-turtle, a human-fish or a human-mushroom comparison. Of course, Senapathy could not have known all these facts in 1994, but conserved chromosome segments are now the most impressive refutation of independent origin. This evidence alone is sufficient to refute independent origin. No theory of independent origin can survive such a blow. Naked genomes Senapathy has a gene and genome centred approach to explaining life. There is nothing wrong with that approach if one knows its limitations. Indeed, genes determine most of the differences between humans and other species. But Senapahty does not know its limitations. The big mistake is to believe a naked genome is technically capable of creating a human being. This is succinctly described by the historian Jan Sapp as: "Critics of gene theory continue to emphasize that only a cell can make a cell, and that plant and animals emerge from eggs, not genes" (38 <#Notes>). It is an unremarkable fact of biology that all animals start life as a single cell and that animals and plants have two complete sets of chromosomes (diploid). In this context however, it is a highly significant fact, because that single cell resulted from the fusion of *two* (haploid) cells and the two sets of chromosomes directly came from *two* parents. In Senapathy's theory, there are no parents! Therefore, his theory must be wrong for technical reasons. I collected additional technical reasons from developmental biology, genetics and ecology on the page: Independent Origin and the facts of life . What is life? Senapathy claims to explain the origin of life. What is life? If one has a wrong idea of what life is, then the theory to explain 'life' is useless. So, what is life? According to chemical engineer Tibor Ganti (43 <#Notes>) life consists of 3 subsystems: 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 stable 3) an information-carrying subsystem (for example DNA) which enables reproduction of the 3 subsystems. Together these 3 subsystems are a living system. Senapathy's theory is concerned with the information-carrying subsystem (DNA) only. So he has a mistaken view of what life is. Therefore, his theory is useless. Furthermore, he got the order of origin of the 3 subsystems wrong. Generally it is believed that metabolism originated first, and that the information carrying subsystem arose later (as a by-product). The reason is that whereas the abiotic synthesis of amino acids is easy, the abiotic synthesis of nucleotides is difficult (44 <#Notes>). Rerun the tape of life There are more fundamental questions, which are not yet solved by any biological theory. If we would rerun the tape of life, or if life evolved on a million earth-like planets, would we see the same survival solutions? Would we see lions, mushrooms, eagles, and HIV again? Would we see the same animal body plans? Five-digits on each hand and leg? Again the same haemoglobin molecule to transport oxygen? The same genetic code? Photosynthesis? We do not know. However, if Senapathy is right and life originated really independently a million times on this earth, then the universal genetic code must be the predictable outcome of the laws of nature. Moreover, all genes and proteins common to all species on earth must be natural and inevitable. How else could they be common to all life? Evolution is a mix of accident and necessity. For Senapathy all common features of life must be the inevitable outcome of the laws of nature (including statistical laws). Summary & Conclusion Evolution is not necessarily true. Independent origin is not by definition false. The theory of Independent origin is wrong for technical-biological reasons. However, thanks to Senapathy there is now an alternative for evolution. Senapathy wrote a 600-page book to convince us that all life forms, from the most simple to the most complex, arose independently from a single primordial pond. Senapathy needs to be thanked for such a detailed non-religious alternative. However, his theory is /not/ a theory of independent birth of organisms. Furthermore, he invokes small-scale common descent and natural selection. Nevertheless, I am not convinced by the parts of his theory that do claim a truly independent origin. On the contrary. By whatever mechanism /higher/ life forms originated, it could not be by independent origin. Higher life forms /depend/ on previous generations and /depend/ on their ecological relations with other life forms so strongly that without them they could not come into being, develop, survive and reproduce. The origin of the /first/ forms of life is a different matter. They are closer to an independent life. However, Senapathy is wrong here too. He claims that the more complex life forms, the eukaryotes (all plants and animals), are the first forms of life. Additionally, that the most simple forms of life, the prokaryotes (bacteria) /evolved/ from the eukaryotes. It is difficult enough to understand how eukaryotes evolved from prokaryotes. It is far more difficult to imagine that they arose directly from a pool of DNA. The origin of the life is one the most difficult problems in biology. The best scientists in the world have not solved it. Senapathy proposed a mechanism that is highly improbable. Senapathy developed a non-religious alternative for evolution. His primary argument is a mathematical argument. His theory is not based on biochemistry. That is the difference with Christian Schwabe (16 <#Notes>), the only scientist in the world also defending independent origin. An important difference is that Schwabe proposes that both prokaryotes and eukaryotes arose independently from the primordial pond. Senapathy is a baffling personality: on the one hand he is the director of a high tech firm and published in scientific journals, but on the other hand he lacks basic biological knowledge and is a crank. In contrast to Darwin, Senapathy did not include a chapter 'Difficulties of the theory', which counts against him. Creationists William Dembski and Michael Behe are wrong for other reasons, but usually show more respect for the facts. Studying this and religious alternatives for evolution, convinced me that it is not easy to develop a consistent alternative for evolution and that evolution theory is certainly not an arbitrary paradigm in biology that is mindlessly defended by biologists due to conservatism, prejudice or atheism. I am impressed and a little bit surprised that evolution theory escapes so much of the traps Periannan Senapathy fell in. *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), 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. 30. A Conversation with James D. Watson , Scientific American, April 2003. 31. David Haig (2002) "Genomic imprinting and kinship", Rutgers University Press, p.11. 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 ] *Further Reading* * Senapahty's company Genome Technologies . * Senapathy's new home site . * Senapahty's immodest autobiography . * contents Independent Birth of Organisms - A New Theory That Distinct Organisms Arose Independenlty From the Primordial Pond Showing That Evolutionary Theories Are Fundamentally Incorrect (1994). Genome Press, Madison, 635 pages. The book is free available as an Adobe pdf file (3 MB!). Fast internet connection recommended. The pdf file is full-text searchable, which is extremely handy for research purposes (recommended for any book! Each book should also be published on CDROM!) * A layman's summary of the new theory by Jeffrey Mattox. With many links (some dead links). Mattox is an electrical engineer who discovered Senapathy * Double helix: 50 years of DNA (from /Nature /), containing a collection of overviews celebrating the historical, scientific and cultural impacts of the discovery of the double helix. All content is free * A Chemist's View of Life: Ultimate Reductionism & Dissent . A review of Schwabe's book * Independent Origin and the facts of life by Gert Korthof. [updated 13 Feb 2004]. Reasons from developmental biology, genetics and ecology (please note that I skipped reasons from evolution biology!) * Review of /The principles of Life/ by Tibor Gánti. (the origin of life) * Lynn Margulis and Dorion Sagan (2002) /Acquiring Genomes. A theory of the origin of species/. Recommended reading. If anything contradicts independent origin then it is Margulis' now well established symbiosis theory. WDW home: www.*w*asdar*w*in*w*rong.com http://home.planet.nl/~gkorthof/korthof58.htm Nedstat Basic - Free web site statistics Copyright ©G.Korthof 2002/2003 First published: 29 Dec 2002 Updated: 28 Jan 2005 Notes/FR: 25 Dec 2004