Mathematically Measuring Evolution.

by towerwatchman 205 Replies latest watchtower beliefs

• 

  Coded Logic

  If we really do want to measure evolution we're going to have to be willing to do the math. Not sure how deep you want to get into this but the information is readily available for anyone who wants to take a stab at it.
  

  Also, I agree with Caedes. It would be nice if you could provide the source for your OP and the mathematics you used to reach your conclusion.

  Of the four methodologies I provided to look at our DNA here are some of the calculations we can use -

  1.) Mitochondrial DNA:
  

  

  The variable RW above is the average fraction of wild-type nucleoid among mitochondria (i.e. the average of (1−RM,imito)) in a cell. The sigmoidal function is motivated by the activity data of cytochrome c oxidase (COX) as a function of the relative proportion of wild-type and mutant mtDNA in cybrid cells (see Fig. 1B) [38]. COX is an enzyme complex involved in the mitochondrial ATP production and its activity is used as an indicator of mitochondrial respiration function. Based on the equation above, the maximum amplification of mtDNA replication by retrograde signaling (at RW = 0) is rmax +1, which has been reported to be ∼16 times the basal rate [39]. A linear function can also be used in place of the sigmoidal function above, without changing the general trend and conclusions from the model simulations

  
  

  (A) During a mitochondrial fusion, the nucleoid information (W and M) of the precursor mitochondria is retained and a fission site is created (bold line). During fission of a previously fused mitochondrion, a fission site is randomly chosen from the possible sites in the mitochondrion selected for fission. The redistribution of nucleoid contents between the two daughter mitochondria is determined randomly according to a Binomial distribution, while the particular nucleoids to be transferred are randomly taken from a Hypergeometric distribution. During fission of a primary mitochondrion, i.e. mitochondrion without any fission site, nucleoids are randomly distributed between two daughter mitochondria. (B) Steady state distribution of mitochondrial size as a function of mitochondrial size. In the figure inset, the fission propensity is shown as a function of mitochondrial size (number of nucleoids). (C) Mitochondrial fusion-fission and nucleoids mixing rate. Mitochondrial heterogeneity in each cell is represented by the mean coefficient of variation (COV) of RMmito. The mean COV of RMmito is scaled such that the steady state value is −100%. In this case, the mixing time τ is defined as the time for the scaled COV of RMmito to reach −63.2%. A faster decrease in the mean COV of RMmitoindicates a faster mixing and hence is indicated by a smaller mixing time constant τ.
  
• 

  Coded Logic

  2.) X Chromosome

  This one's a little easier to figure out as it's practically a Fibonacci number. Here are the numbers we need:
  

  
  

  Though I do prefer this chart as it's a little more intuitive:
  
  
  
• 

  Coded Logic

  3.) Alelle Frequencies:

  We can start off with the Hardy-Weinberg equation which is expressed as follows

  p2 + 2pq + q2 = 1

  where p is the frequency of the "A" allele and q is the frequency of the "a" allele in the population. In the equation, p2 represents the frequency of the homozygous genotype AA, q2 represents the frequency of the homozygous genotype aa, and 2pq represents the frequency of the heterozygous genotype Aa. In addition, the sum of the allele frequencies for all the alleles at the locus must be 1, so p + q = 1.

  
  

  Or, if we want to look more broadly at the genotype - we'd need to use a multinomial distribution in which genotype frequencies are f(AA) = p2 for the AA homozygotes, f(aa) = q2 for the aa homozygotes, and f(Aa) = 2pq for the heterozygotes.

  
  

  
  

  
  

  
  
• 

  GrreatTeacher

  Oh, sweet Jesus; Mathematics is beautiful!
• 

  towerwatchman

  Coded Logic

  Hahaha, well I suppose I should be happy that you've changed your position from Archeopteryx is "just a bird" all the way to Archeopteryx is "just a bird with unique features". I guess that's progress. But, if we're being honest, it's NOT just a bird with unique features is it? It's a "bird" with features that are inherently reptilian. It's a "bird" with the exact sort of features we would expect to see during a speciation event in which "birds" were much more like their dinosaur precursors. Not only that, if you'll recall, you were the one to bring up morphological and anatomical differences. I'm not sure it's really fair to cry foul (or perhaps, in this case, fowl) now that it's "too subjective" a topic since you've decided you don't like where the evidence is leading.

  Yes Archaeopteryx is truly unique, and appears to exhibit a tapestry of characters, sharing some in common with the class Aves and some with the class Reptilia. What is it suited for? A life of crawling on the ground or under rocks? Or suited for a lifestyle of short flights and agile crawling in trees? The features which make it unquestionably a bird for classification purposes are uniquely and completely present and perfect. If it was transitional the feathers would be half way between scales to feathers, but it is not. Just this would disqualify it as a transitional form. A bat is not a transitional form between bird and mammal, nor is a platypus transitional between duck and mammal, even though it exhibits some features of both.

  ‘… we are not even authorized to consider the exceptional case of Archaeopteryx as a true link. By link, we mean a necessary stage of transition between classes such as reptiles and birds, or between smaller groups. An animal displaying characters belonging to two different groups cannot be treated as a true link as long as the intermediary stages have not been found, and as long as the mechanism of transition remains unknown. [Human Destiny (N.Y. 1947)] Evolutionist Lecomte du Noüy.

  These are each independent methods of studying various aspects our DNA to determine hierarchy. For example, evolution predicts that our closest cousins are chimpanzees', followed by guerrillas and then orangutans. And when we look at our mitochondrial DNA (this is what's used in paternity and ancestry tests) we observe the exact same thing. The same is true when we look at the family lines along the x-chromosome. We find that human's closest cousins are chimpanzees followed by guerrillas and then orangutans. Next, we can do something very different. We can see what endogenous retrovirus' (ERVs) we share with other animals. According to evolution, we should expect that any ERVs we share with orangutans we'd also share with guerrillas and chimpanzees since orangutans are our most distant ape cousins. And, conversely, we'd expect that there would be some ERVs we'd share with chimpanzees and guerrillas that we don't share with orangutans. Guess what? This is exactly what we observe! Lastly, we can look at allele frequencies (or, more broadly, genotype frequencies). And the species with which humans have the lowest number of genetic variants is . . . you guessed it, chimpanzees! Wow, what a stunning surprise. Want to wager which species might be next closest? Or next closest after that? Why guerrillas and orangutans of course!

  Let’s talk about chimp to man. Evolutionist say that the difference between man and chimp is 1.5 %. Does not seem much. What we need to find out is how much is much. When we hear that there is a 1 ½ % difference between man and chimp it seems not to be much. But we must take into account what 1 ½% exactly means. If there are three billion base pairs in a human 1 ½% calculates to 45 million base pairs or 15 million codons. It is estimated that it would take 10X10^21 mutations to get five condons to mutate in the right order. One and half percent does not look like much but when analyzed, it becomes overwhelming evidence against man ever evolving from a chimp.
• 

  towerwatchman

  To Cofty

  The sequences are remarkably similar across species, especially at certain positions.
  For example, every one has a phenylalanine at position 10, a histidine at 18, a proline at 30 and a methionine at 80. Clearly, evolution selects against any change at these positions. In addition, numerous sites display a limited number of changes, in most cases allowing only residues with similar properties. For example, residue 98 can be only leucine, isoleucine, or valine - all lipophilic residues.
  Likewise, His18 (shown in the graphic above), which coordinates to the heme iron, is conserved throughout.The implication is that the strongly conserved residues contribute significantly to the structure and function of the protein. Other positions contribute very little and are highly variable; evolutionary drift randomizes these residues. Note that human and chimpanzee sequences are identical, and macaque and spider monkey are very similar to the human/chimpanzee sequence. This implies a common and relatively recent evolutionary divergence...

  Let’s use your evolutionary tree as an example of evolutionary hierarchy, with the bottom being the common ancestor and the end branches being the creatures alive now. You are measuring the difference horizontally, across the branches, I am measuring vertically [over time.]

  If the evolutionary line such as Chordates to Tetrapods to Mammals to Primates to Hominidae to Homo were true, including the multitude of transitional forms, we should see an ever widening gap in portage from the simplest to the most complex. But we do not.

  Again the difference between a cyclostome and fish [75%], amphibian [81%], bird [78%], marsupial [76%] and mammal [73%]. Notice mammals are closer to cyclostome than a fish.

  When we look deeper into the nucleotide sequences then we find an even greater example of evidence for common ancestry. Humans and chimps differ by 4 DNA letters but the very same amino acid sequence. The same pattern is repeated throughout life demonstrating gradual evolution over millions of years.

  Let’s talk about chimp to man. Evolutionist say that the difference between man and chimp is 1.5 %. Does not seem much. What we need to find out is how much is much. When we hear that there is a 1 ½ % difference between man and chimp it seems not to be much. But we must take into account what 1 ½% exactly means. If there are three billion base pairs in a human 1 ½% calculates to 45 million base pairs or 15 million codons. It is estimated that it would take 10X10^21 mutations to get five condons to mutate in the right order. One and half percent does not look like much but when analyzed, it becomes overwhelming evidence against man ever evolving from a chimp.
• 

  Anony Mous

  Wow, the stupidity of this guy.

  To get 5 codons to mutate in the "right order" it can mathematically take no more than 125 mutations.

  1.5% of 3B is the same ratio even if there were more base pairs. But that's also not how evolution works and mutations happen all the time, it's how you age and develop cancer. You can make mutations to species in a lab for crying out loud in a matter of hours.
• 

  towerwatchman

  Caedes

  You keep on using those figures and still haven't actually stated a source for them, if you had any understanding of basic scientific principles you would understand why they are being dismissed.

  Apologize for the amount of time it took to find it. It is from “Evolution A Theory In Crisis” by Michael Denton. His source is ‘Dayhoff Atlas of Protein Structure and Function [1972 edition]’.

  However you are looking at one protein, and it is being coded by a ubiquitous gene. What that means is that it is coding for a very basic function, one that is common to all life. Since there are lots of ways of functionally coding for this protein (as I mentioned before) then if life were unrelated then you would expect that there would be a wide variety in how it is coded.

  It is not that simple. It is estimated that it takes 10x10^21 mutations to get five codons to mutate in the right order to fold in the right form to accomplish the function.

  What we actually see is that it is coded in a very similar way and that the small differences reflect how related any two organisms are. The more closely related the the two organisms are then the coding will be increasingly similar.

  They aren't radically different because they are related! Your figures are still incorrect!
  

  But that is not what we see. The difference between a cyclostome and fish [75%], amphibian [81%], bird [78%], marsupial [76%] and mammal [73%]. Notice mammals are closer to cyclostome than a fish. What this leads to is that all living things appeared at the same time.

  All species are transitional in regards to moving along a particular branch of the evolutionary tree. The first part of your sentence shows that you still have no real understanding of how fossilisation works or how evolution works. I'll sum up the key points, fossilisation is rare, fossilisation of rare species is even rarer. The evolution of species happens to groups of organisms not individuals, for a strong selection mechanism to be happening then lots of that group are dieing and a small number are surviving. So we wouldn't expect to see a lot of fossilisation but we do see it.

  Why don’t you see large amounts of fossilization? What happens when a fish or sea creature dies today? We have all seen the results, the body floats on the surface of the water or sinks to the bottom where it is devoured quickly by other fish. Or how does a dead fish lie on the bottom of a lake for hundreds of years until it is fossilized? Of course, that does not happen in real life, only in the fertile and desperate minds of evolutionists. But the fossil fish are often found very well preserved in sedimentary rocks. What we do have are many creatures, when alive, did not share the same environment, yet they were buried together. They seem to all have died in one cataclysmic event.

  Let's assume your figures for the differences between man and chimp are correct for a moment, so what you are saying is that we need a method to sieve out all the useless mutations that are harmful. Let's then look at the title of Darwin's book On the origin of species by means of natural selection. What does the second part of that title tell you about what happens? That's right, the successful genes are naturally 'selected' (by not being in a dead organism) so there you have your method to sieve out the harmful mutations. Then all you need is a population breeding like rabbits and you have evolution.

  The theory of Natural Selection promotes that the species that survives is the fittest, and the fittest is the species that survives. What does Natural Selection identify as the determining factor of the survival of the fittest? Whatever gave the surviving form the edge over the extinct on is the determining factor[s]. Since Natural Selection has become an all-purpose explanation of anything and everything, it becomes an explanation of nothing. Just about any characteristic can be either advantageous or dis advantageous depending upon the surrounding environmental conditions the subject is found.

  Based on the species thriving we can assume a characteristic to be advantageous to it, but in most cases it is impossible to identify the advantage independently of the outcome; therefore any advantage can also be a disadvantage. Simply put, the historical record only confirms one advantage, success in reproduction. Following Natural Selection, the individual which reproduce the most offspring must have the qualities required for producing the most offspring, or the fittest individuals in a population [identified as these which leave the most offspring] will leave the most offspring.

  No, you are incorrect, modern birds do not show the reptilian features shown in primitive birds like archeopterix and archeopterix shows bird like features not seen in true reptiles. That is not speculation, you can see the fossils for yourself.

  Yes Archaeopteryx is truly unique, and appears to exhibit a tapestry of characters, sharing some in common with the class Aves and some with the class Reptilia. What is it suited for? A life of crawling on the ground or under rocks? Or suited for a lifestyle of short flights and agile crawling in trees? The features which make it unquestionably a bird for classification purposes are uniquely and completely present and perfect. If it was transitional the feathers would be half way between scales to feathers, but it is not. Just this would disqualify it as a transitional form. A bat is not a transitional form between bird and mammal, nor is a platypus transitional between duck and mammal, even though it exhibits some features of both.

  ‘… we are not even authorized to consider the exceptional case of Archaeopteryx as a true link. By link, we mean a necessary stage of transition between classes such as reptiles and birds, or between smaller groups. An animal displaying characters belonging to two different groups cannot be treated as a true link as long as the intermediary stages have not been found, and as long as the mechanism of transition remains unknown. [Human Destiny (N.Y. 1947)] Evolutionist Lecomte du Noüy.

  
  
  
• 

  towerwatchman

  Coded logic

  If we really do want to measure evolution we're going to have to be willing to do the math. Not sure how deep you want to get into this but the information is readily available for anyone who wants to take a stab at it.

  Impressive.
  
  
• 

  towerwatchman

  Anony Mous

  Wow, the stupidity of this guy. To get 5 codons to mutate in the "right order" it can mathematically take no more than 125 mutations. 1.5% of 3B is the same ratio even if there were more base pairs. But that's also not how evolution works and mutations happen all the time, it's how you age and develop cancer. You can make mutations to species in a lab for crying out loud in a matter of hours.

  One thing I learned a long time ago. You cannot fix stupid. So let’s see how stupid this post is. You are arguing against Intelligent Design and for blind evolution. But notice you cite intelligence as proof that intelligence had nothing to do with it. “You can make mutations to species in a lab for crying out loud in a matter of hours.” Notice you doubt not only the institution you denounces but the very thing you denounces it with.

  But let see if it takes only 125 mutations without any guidance.

  "To construct even one short protein molecule of 150 amino acids by chance within the prebiotic soup there are several combinatorial problems – probabilistic hurdles- to overcome. First, all amino acids must form a peptide bond when joining with other amino acids in the protein chain. If the amino acids do not link up with one another via a peptide bond, the resulting molecule will not fold into a protein. In nature many other types of chemical bonds are possible between amino acids. In fact, when amino acid mixtures are allowed to react in a test tube, they form peptide and none peptide bonds with roughly equal probability. Thus, with each amino acid addition, the probability of it forming a peptide bond is roughly ½. Once four amino acids have become linked, the likelihood that they are joined exclusively by peptide bonds is roughly [1/2]^4. The probability of building a chain of 150 amino acids in which all linkages are peptide linkages is {1/2}^149, or 1 chance in 10^45.

  Second in nature every amino acid found in proteins [ with one exception] has a distinct mirror image of itself, there is one left handed version, or L form, and one right handed version, or D form. These mirror image forms are called optical isomers. Functioning proteins tolerate only left handed amino acids, yet in abiotic amino acid production the right handed and left handed isomers are produced with roughly equal frequency. Taking this into account further compounds the improbability of attaining a biologically functioning protein. The probability of attaining, at random only L amino acids in a hypothetical peptide chain 150 amino acids long is [1/2]^150 or roughly 1 chance in 10^45. Starting from mixtures of D and L form the probability of building a 150 amino acid chain at random in which all bonds are peptide bonds and all amino acids are L form is, therefore, roughly 1 chance in 10^90.

  Amino acids link together when the amino group of one amino acid bonds to the carboxyl group of another. Notice that water is the byproduct of the reaction. [Condensation reaction].

  Functional proteins have a third independent requirement, the most important of all, their amino acids, like letters in a meaningful sentence, must link up in functionally specified sequential arrangements. In some cases, changing even one amino acid at a given site results in the loss of protein function. Moreover, because a there are 20 biologically occurring amino acids, the probability of getting a specific amino acid at a given site is small 1/20 [actually the probability is even lower because in nature, there are also may none protein forming amino acids.] On the assumption that each site is a protein chain requires a particular amino acid, the probability of attaining a particular protein 150 amino acids long would be [1/20]^150 or roughly 1 chance 10^195. 1chance in 10^195.

  Taking this into account only causes the improbability of generating the necessary proteins by chance or the genetic information to produce them, to balloon beyond comprehension. In 1983 distinguished British cosmologist Sr. Fred Hoyle calculated the odds of producing the proteins necessary to service a simple one celled organism by chance at 1 in 10^40K.

  [There are 10^65 atoms in our galaxy]”

  [Stephen C. Meyer]