Comparison of Meyer 2004b to Meyer 2004a

Param a = 6
Param k = 4
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Param s = 4
Param w = 0.75
Thu Sep 23 12:29:29 GMT 2004
There are 230 lines in meyer2004_html_nonref.txt
There are 1352 lines in mdd02.txt
There are 13533 words in meyer2004_html_nonref.txt
There are 8267 words in mdd02.txt
Match 1 (1): Reference (000209 .. 000219, of 13533): Subject (007728 .. 007738, of 8267):
of phylogenesis the ultimate origination of new biological forms during the of the origin of biological information exposes a deficiency in the
Match 2 (1): Reference (000857 .. 000868, of 13533): Subject (000838 .. 000847, of 8267):
biological form and information during the history of life the Cambrian explosion biological information during the history of life the Cambrian explosion
Match 3 (1): Reference (000925 .. 000936, of 13533): Subject (006913 .. 006920, of 8267):
an adequate causal explanation of the origination of biological form in the an adequate explanation of the origin of the
Match 4 (1): Reference (000974 .. 001013, of 13533): Subject (000882 .. 000918, of 8267):
The Cambrian Explosion The Cambrian explosion refers to the geologically sudden appearance of many new animal body plans about 530 million years ago At this time at least nineteen and perhaps as many as thirty five phyla of forty total The Cambrian explosion refers to the geologically sudden appearance of many new animal body plans about 530 million years ago At this time at least nineteen and perhaps as many as thirty five phyla of forty total
Match 5 (1): Reference (001018 .. 001035, of 13533): Subject (000920 .. 000935, of 8267):
made their first appearance on earth within a narrow five to ten million year window of geologic time made their first appearance on Earth within a narrow five million year window of geologic time
Match 6 (1): Reference (001112 .. 001157, of 13533): Subject (001080 .. 001125, of 8267):
To say that the fauna of the Cambrian period appeared in a geologically sudden manner also implies the absence of clear transitional intermediate forms connecting Cambrian animals with simpler pre Cambrian forms And indeed in almost all cases the Cambrian animals have no clear morphological antecedents To say that the fauna of the Cambrian period appeared in a geologically sudden manner also implies the absence of clear transitional intermediate forms connecting Cambrian animals with simpler pre Cambrian forms And indeed in almost all cases the Cambrian animals have no clear morphological antecedents
Match 7 (1): Reference (001238 .. 001249, of 13533): Subject (001126 .. 001137, of 8267):
debate now exists about the extent to which this pattern of evidence Debate now exists about the extent to which this pattern of evidence
Match 8 (1): Reference (001408 .. 001423, of 13533): Subject (001171 .. 001184, of 8267):
can generate the form and information necessary to produce the animals that arise in the Cambrian can generate the information necessary to produce the animals that arise in the Cambrian
Match 9 (1): Reference (001789 .. 001909, of 13533): Subject (001198 .. 001315, of 8267):
information In classical Shannon information theory the amount of information in a system is also inversely related to the probability of the arrangement of constituents in a system or the characters along a communication channel Shannon 1948 The more improbable or complex the arrangement the more Shannon information or information carrying capacity a string or system possesses Since the 1960s mathematical biologists have realized that Shannon s theory could be applied to the analysis of DNA and proteins to measure the information carrying capacity of these macromolecules Since DNA contains the assembly instructions for building proteins the information processing system in the cell represents a kind of communication channel Yockey 1992 110 Further DNA conveys information via specifically arranged sequences of in biology In classical Shannon information theory the amount of information in a system is inversely related to the probability of the arrangement of constituents in a system or the characters along a communication channel Shannon 1948 The more improbable or complex the arrangement the more Shannon information or information carrying capacity a string or system possesses Since the 1960s mathematical biologists have realized that Shannon s theory could be applied to the analysis of DNA and proteins to measure their information carrying capacity Since DNA contains the assembly instructions for building proteins the information processing system in the cell represents a kind of communication channel Yockey 1992 110 Further DNA conveys information via specifically arranged sequences of
Match 10 (1): Reference (001911 .. 001920, of 13533): Subject (001330 .. 001341, of 8267):
bases Since each of the four bases has a roughly a linear array Since each of the four bases has a roughly
Match 11 (1): Reference (001911 .. 002016, of 13533): Subject (001330 .. 001438, of 8267):
bases Since each of the four bases has a roughly equal chance of occurring at each site along the spine of the DNA molecule biologists can calculate the probability and thus the information carrying capacity of any particular sequence n bases long The ease with which information theory applies to molecular biology has created confusion about the type of information that DNA and proteins possess Sequences of nucleotide bases in DNA or amino acids in a protein are highly improbable and thus have large information carrying capacities But like meaningful sentences or lines of computer code genes and proteins are also specified with respect to function a linear array Since each of the four bases has a roughly equiprobable chance of occurring at each site along the spine of the DNA molecule biologists can calculate the probability and thus the information carrying capacity of any particular sequence n bases long The ease with which information theory applies to molecular biology has created confusion about the type of information that DNA and proteins possess Sequences of nucleotide bases in DNA or amino acids in a protein are highly improbable and thus have a large information carrying capacity But like meaningful sentences or lines of computer code genes and proteins are also specified with respect to function
Match 12 (1): Reference (002018 .. 002032, of 13533): Subject (001440 .. 001454, of 8267):
as the meaning of a sentence depends upon the specific arrangement of the letters in as the meaning of a sentence depends upon the specific arrangement of the letters in
Match 13 (1): Reference (002018 .. 002054, of 13533): Subject (001440 .. 001479, of 8267):
as the meaning of a sentence depends upon the specific arrangement of the letters in a sentence so too does the function of a gene sequence depend upon the specific arrangement of the nucleotide bases in a as the meaning of a sentence depends upon the specific arrangement of the letters in the sentence so too does the function of a gene sequence depend upon the specific arrangement of the nucleotide bases in the gene Thus as
Match 14 (1): Reference (002057 .. 002080, of 13533): Subject (001483 .. 001508, of 8267):
molecular biologists beginning with Crick equated information not only with complexity but also with specificity where specificity or specified has meant necessary to function molecular biologists beginning with Francis Crick have equated information not only with complexity but also with specificity where specificity or specified has meant necessary to function
Match 15 (1): Reference (002162 .. 002178, of 13533): Subject (001371 .. 001388, of 8267):
function The ease with which information theory applies to molecular biology has also created confusion about the n bases long The ease with which information theory applies to molecular biology has created confusion about the
Match 16 (1): Reference (002406 .. 002440, of 13533): Subject (001553 .. 001584, of 8267):
The Cambrian explosion represents a remarkable jump in the specified complexity or complex specified information CSI of the biological world For over three billions years the biological realm included little more than bacteria and algae The Cambrian explosion represents a remarkable jump in the specified complexity or CSI of the biological world For over three billion years the biological realm included little more than bacteria and algae
Match 17 (1): Reference (002453 .. 002471, of 13533): Subject (001589 .. 001607, of 8267):
mya the first complex multicellular organisms appeared in the rock strata including sponges cnidarians and the peculiar Ediacaran biota mya the first complex multicellular organisms appeared in the rock strata including sponges cnidarians and the peculiar Ediacaran biota
Match 18 (1): Reference (002488 .. 002518, of 13533): Subject (001616 .. 001646, of 8267):
The emergence of the Ediacaran biota 570 mya and then to a much greater extent the Cambrian explosion 530 mya represented steep climbs up the biological complexity gradient One way to The emergence of the Ediacaran biota 570 mya and then to a much greater extent the Cambrian explosion 530 mya represented steep climbs up the biological complexity gradient One way to
Match 19 (1): Reference (002544 .. 002580, of 13533): Subject (001669 .. 001707, of 8267):
Valentine 1995 91 93 Studies of modern animals suggest that the sponges that appeared in the late Precambrian for example would have required five cell types whereas the more complex animals that appeared in the Cambrian e Valentine 1995 91 3 Studies of modern animals suggest that the sponges that appeared in the late Precambrian for example would have required five cell types whereas the more complex animals that appeared in the Cambrian such as representatives
Match 20 (1): Reference (002582 .. 002635, of 13533): Subject (001709 .. 001766, of 8267):
arthropods would have required fifty or more cell types Functionally more complex animals require more cell types to perform their more diverse functions New cell types require many new and specialized proteins New proteins in turn require new genetic information Thus an increase in the number of cell types implies at a minimum a Arthropoda would have required fifty or more cell types Functionally more complex animals require more cell types to perform their more diverse functions New cell types require many new and specialized proteins New proteins in turn require new genetic information Thus an increase in the number of cell types implies at minimum a considerable increase in the amount
Match 21 (1): Reference (002582 .. 002675, of 13533): Subject (001709 .. 001801, of 8267):
arthropods would have required fifty or more cell types Functionally more complex animals require more cell types to perform their more diverse functions New cell types require many new and specialized proteins New proteins in turn require new genetic information Thus an increase in the number of cell types implies at a minimum a considerable increase in the amount of specified genetic information Molecular biologists have recently estimated that a minimally complex single celled organism would require between 318 and 562 kilobase pairs of DNA to produce the proteins necessary to maintain life Koonin Arthropoda would have required fifty or more cell types Functionally more complex animals require more cell types to perform their more diverse functions New cell types require many new and specialized proteins New proteins in turn require new genetic information Thus an increase in the number of cell types implies at minimum a considerable increase in the amount of specified genetic information Molecular biologists have recently estimated that a minimally complex single celled organism would require between 318 and 562 kilobase pairs of DNA to produce the proteins necessary to maintain life Koonin
Match 22 (1): Reference (002677 .. 002716, of 13533): Subject (001803 .. 001845, of 8267):
More complex single cells might require upward of a million base pairs Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require orders of magnitude more coding instructions The genome size of a More complex single cells might require upward of a million base pairs Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require orders of magnitude more coding instructions The genome size of the modern fruitfly Drosophila
Match 23 (1): Reference (002677 .. 002724, of 13533): Subject (001803 .. 001850, of 8267):
More complex single cells might require upward of a million base pairs Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require orders of magnitude more coding instructions The genome size of a modern arthropod the fruitfly Drosophila melanogaster is approximately More complex single cells might require upward of a million base pairs Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require orders of magnitude more coding instructions The genome size of the modern fruitfly Drosophila melanogaster an arthropod is approximately
Match 24 (1): Reference (002737 .. 002823, of 13533): Subject (001861 .. 001947, of 8267):
Transitions from a single cell to colonies of cells to complex animals represent significant and in principle measurable increases in CSI Building a new animal from a single celled organism requires a vast amount of new genetic information It also requires a way of arranging gene products proteins into higher levels of organization New proteins are required to service new cell types But new proteins must be organized into new systems within the cell new cell types must be organized into new tissues organs and body parts Transitions from a single cell to colonies of cells to complex animals represent significant and in principle measurable increases in CSI Building a new animal from a single celled organism requires a vast amount of new genetic information It also requires a way of arranging gene products proteins into higher levels of organization New proteins are required to service new cell types But new proteins must be organized into new systems within the cell new cell types must be organized into new tissues organs and body parts
Match 25 (1): Reference (002824 .. 002931, of 13533): Subject (001952 .. 002059, of 8267):
These in turn must be organized to form body plans New animals therefore embody hierarchically organized systems of lower level parts within a functional whole Such hierarchical organization itself represents a type of information since body plans comprise both highly improbable and functionally specified arrangements of lower level parts The specified complexity of new body plans requires explanation in any account of the Cambrian explosion Can neo Darwinism explain the discontinuous increase in CSI that appears in the Cambrian explosion either in the form of new genetic information or in the form of hierarchically organized systems of parts We will now examine the two parts of this question These in turn must be organized to form body plans New animals therefore embody hierarchically organized systems of lower level parts within a functional whole Such hierarchical organization itself represents a type of information since body plans comprise both highly improbable and functionally specified arrangements of lower level parts The specified complexity of new body plans requires explanation in any account of the Cambrian explosion Can neo Darwinism explain the discontinuous increase in CSI that appears in the Cambrian explosion either in the form of new genetic information or in the form of hierarchically organized systems of parts We will now examine the two parts of this question
Match 26 (1): Reference (002936 .. 003114, of 13533): Subject (002064 .. 002243, of 8267):
Many scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins Such skepticism often derives from consideration of the extreme improbability and specificity of functional genes and proteins A typical gene contains over one thousand precisely arranged bases For any specific arrangement of four nucleotide bases of length n there is a corresponding number of possible arrangements of bases 4n For any protein there are 20n possible arrangements of protein forming amino acids A gene 999 bases in length represents one of 4999 possible nucleotide sequences a protein of 333 amino acids is one of 20333 possibilities Since the 1960s some biologists have thought functional proteins to be rare among the set of possible amino acid sequences Some have used an analogy with human language to illustrate why this should be the case Denton 1986 309 311 for example has shown that meaningful words and sentences are extremely rare among the set of possible combinations of English letters especially as sequence length grows The ratio of meaningful Many scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins Such skepticism often derives from consideration of the extreme improbability and specificity of functional genes and proteins A typical gene contains over one thousand precisely arranged bases For any specific arrangement of four nucleotide bases of length n there is a corresponding number of possible arrangements of bases 4 n For any protein there are 20n possible arrangements of protein forming amino acids A gene 999 bases in length represents one of 4999 possible nucleotide sequences a protein of 333 amino acids is one of 20333 possibilities Since the 1960s biologists have generally thought functional proteins to be rare among the set of possible amino acid sequences of corresponding length Some have used an analogy with human language to illustrate why this should be the case Denton for example has shown that meaningful words and sentences are extremely rare among the set of possible combinations of English letters especially as sequence length grows The ratio of meaningful
Match 27 (1): Reference (002936 .. 003224, of 13533): Subject (002064 .. 002355, of 8267):
Many scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins Such skepticism often derives from consideration of the extreme improbability and specificity of functional genes and proteins A typical gene contains over one thousand precisely arranged bases For any specific arrangement of four nucleotide bases of length n there is a corresponding number of possible arrangements of bases 4n For any protein there are 20n possible arrangements of protein forming amino acids A gene 999 bases in length represents one of 4999 possible nucleotide sequences a protein of 333 amino acids is one of 20333 possibilities Since the 1960s some biologists have thought functional proteins to be rare among the set of possible amino acid sequences Some have used an analogy with human language to illustrate why this should be the case Denton 1986 309 311 for example has shown that meaningful words and sentences are extremely rare among the set of possible combinations of English letters especially as sequence length grows The ratio of meaningful 12 letter words to 12 letter sequences is 1 1014 the ratio of 100 letter sentences to possible 100 letter strings is 1 10100 Further Denton shows that most meaningful sentences are highly isolated from one another in the space of possible combinations so that random substitutions of letters will after a very few changes inevitably degrade meaning Apart from a few closely clustered sentences accessible by random substitution the overwhelming majority of meaningful sentences lie probabilistically speaking beyond the reach of random search Denton 1986 301 324 and others have argued that similar constraints apply to genes and proteins They have questioned whether an undirected search via mutation and Many scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins Such skepticism often derives from consideration of the extreme improbability and specificity of functional genes and proteins A typical gene contains over one thousand precisely arranged bases For any specific arrangement of four nucleotide bases of length n there is a corresponding number of possible arrangements of bases 4 n For any protein there are 20n possible arrangements of protein forming amino acids A gene 999 bases in length represents one of 4999 possible nucleotide sequences a protein of 333 amino acids is one of 20333 possibilities Since the 1960s biologists have generally thought functional proteins to be rare among the set of possible amino acid sequences of corresponding length Some have used an analogy with human language to illustrate why this should be the case Denton for example has shown that meaningful words and sentences are extremely rare among the set of possible combinations of English letters especially as sequence length grows The ratio of meaningful Metter words to Metter sequences is 1 10 the ratio of 100 letter sentences to possible 100 letter strings is roughly 1 10100 Further Denton shows that most meaningful sentences are highly isolated from one another in the space of possible combinations so that random substitutions of letters will after a very few changes inevitably degrade meaning Apart from a few closely clustered sentences accessible by random substitution the overwhelming majority of meaningful sentences lie probabilistically speaking beyond the reach of random search Denton and others have argued that similar constraints apply to genes and proteins 1986 301 24 They have questioned whether an undirected search via mutation selection would have a
Match 28 (1): Reference (002936 .. 003246, of 13533): Subject (002064 .. 002373, of 8267):
Many scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins Such skepticism often derives from consideration of the extreme improbability and specificity of functional genes and proteins A typical gene contains over one thousand precisely arranged bases For any specific arrangement of four nucleotide bases of length n there is a corresponding number of possible arrangements of bases 4n For any protein there are 20n possible arrangements of protein forming amino acids A gene 999 bases in length represents one of 4999 possible nucleotide sequences a protein of 333 amino acids is one of 20333 possibilities Since the 1960s some biologists have thought functional proteins to be rare among the set of possible amino acid sequences Some have used an analogy with human language to illustrate why this should be the case Denton 1986 309 311 for example has shown that meaningful words and sentences are extremely rare among the set of possible combinations of English letters especially as sequence length grows The ratio of meaningful 12 letter words to 12 letter sequences is 1 1014 the ratio of 100 letter sentences to possible 100 letter strings is 1 10100 Further Denton shows that most meaningful sentences are highly isolated from one another in the space of possible combinations so that random substitutions of letters will after a very few changes inevitably degrade meaning Apart from a few closely clustered sentences accessible by random substitution the overwhelming majority of meaningful sentences lie probabilistically speaking beyond the reach of random search Denton 1986 301 324 and others have argued that similar constraints apply to genes and proteins They have questioned whether an undirected search via mutation and selection would have a reasonable chance of locating new islands of function representing fundamentally new genes or proteins within the time available Many scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins Such skepticism often derives from consideration of the extreme improbability and specificity of functional genes and proteins A typical gene contains over one thousand precisely arranged bases For any specific arrangement of four nucleotide bases of length n there is a corresponding number of possible arrangements of bases 4 n For any protein there are 20n possible arrangements of protein forming amino acids A gene 999 bases in length represents one of 4999 possible nucleotide sequences a protein of 333 amino acids is one of 20333 possibilities Since the 1960s biologists have generally thought functional proteins to be rare among the set of possible amino acid sequences of corresponding length Some have used an analogy with human language to illustrate why this should be the case Denton for example has shown that meaningful words and sentences are extremely rare among the set of possible combinations of English letters especially as sequence length grows The ratio of meaningful Metter words to Metter sequences is 1 10 the ratio of 100 letter sentences to possible 100 letter strings is roughly 1 10100 Further Denton shows that most meaningful sentences are highly isolated from one another in the space of possible combinations so that random substitutions of letters will after a very few changes inevitably degrade meaning Apart from a few closely clustered sentences accessible by random substitution the overwhelming majority of meaningful sentences lie probabilistically speaking beyond the reach of random search Denton and others have argued that similar constraints apply to genes and proteins 1986 301 24 They have questioned whether an undirected search via mutation selection would have a reasonable chance of locating new islands of function representing fundamentally new genes or proteins within the time available
Match 29 (1): Reference (002936 .. 003274, of 13533): Subject (002064 .. 002401, of 8267):
Many scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins Such skepticism often derives from consideration of the extreme improbability and specificity of functional genes and proteins A typical gene contains over one thousand precisely arranged bases For any specific arrangement of four nucleotide bases of length n there is a corresponding number of possible arrangements of bases 4n For any protein there are 20n possible arrangements of protein forming amino acids A gene 999 bases in length represents one of 4999 possible nucleotide sequences a protein of 333 amino acids is one of 20333 possibilities Since the 1960s some biologists have thought functional proteins to be rare among the set of possible amino acid sequences Some have used an analogy with human language to illustrate why this should be the case Denton 1986 309 311 for example has shown that meaningful words and sentences are extremely rare among the set of possible combinations of English letters especially as sequence length grows The ratio of meaningful 12 letter words to 12 letter sequences is 1 1014 the ratio of 100 letter sentences to possible 100 letter strings is 1 10100 Further Denton shows that most meaningful sentences are highly isolated from one another in the space of possible combinations so that random substitutions of letters will after a very few changes inevitably degrade meaning Apart from a few closely clustered sentences accessible by random substitution the overwhelming majority of meaningful sentences lie probabilistically speaking beyond the reach of random search Denton 1986 301 324 and others have argued that similar constraints apply to genes and proteins They have questioned whether an undirected search via mutation and selection would have a reasonable chance of locating new islands of function representing fundamentally new genes or proteins within the time available Eden 1967 Shutzenberger 1967 Lovtrup 1979 Some have also argued that alterations in sequencing would likely result in loss of protein function before fundamentally new function could arise Many scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins Such skepticism often derives from consideration of the extreme improbability and specificity of functional genes and proteins A typical gene contains over one thousand precisely arranged bases For any specific arrangement of four nucleotide bases of length n there is a corresponding number of possible arrangements of bases 4 n For any protein there are 20n possible arrangements of protein forming amino acids A gene 999 bases in length represents one of 4999 possible nucleotide sequences a protein of 333 amino acids is one of 20333 possibilities Since the 1960s biologists have generally thought functional proteins to be rare among the set of possible amino acid sequences of corresponding length Some have used an analogy with human language to illustrate why this should be the case Denton for example has shown that meaningful words and sentences are extremely rare among the set of possible combinations of English letters especially as sequence length grows The ratio of meaningful Metter words to Metter sequences is 1 10 the ratio of 100 letter sentences to possible 100 letter strings is roughly 1 10100 Further Denton shows that most meaningful sentences are highly isolated from one another in the space of possible combinations so that random substitutions of letters will after a very few changes inevitably degrade meaning Apart from a few closely clustered sentences accessible by random substitution the overwhelming majority of meaningful sentences lie probabilistically speaking beyond the reach of random search Denton and others have argued that similar constraints apply to genes and proteins 1986 301 24 They have questioned whether an undirected search via mutation selection would have a reasonable chance of locating new islands of function representing fundamentally new genes or proteins within the time available Schuetzenberger 1967 Lovtrup 1979 Berlinski 1996 Some have also argued that alterations in sequencing would likely result in loss of protein function before fundamentally new function could arise
Match 30 (1): Reference (003285 .. 003407, of 13533): Subject (002407 .. 002532, of 8267):
genes and proteins are sensitive to functional loss as a result of sequence change nor the extent to which functional proteins are isolated within sequence space has been fully known Recently experiments in molecular biology have shed light on these questions A variety of mutagenesis techniques have shown that proteins and thus the genes that produce them are indeed highly specified relative to biological function Bowie Sauer 1989 Reidhaar Olson Sauer 1990 Taylor et al 2001 Mutagenesis research tests the sensitivity of proteins and by implication DNA to functional loss as a result of alterations in sequencing Studies of proteins have long shown that amino acid residues at many active positions cannot vary without functional loss Perutz Lehmann 1968 More recent protein studies genes and proteins to functional loss as a result of sequence change nor the extent to which functional proteins are isolated within sequence space has been fully known Recently experiments in molecular biology have shed light on these questions A variety of mutagenesis techniques have shown that proteins and thus the genes that produce them are indeed highly specified relative to biological function Bowie and Sauer 1989 Reidhaar Olson and Sauer 1990 Taylor et al 2001 Mutagenesis research tests the sensitivity of proteins and by implication DNA to functional loss as a result of alterations in sequencing Studies of protein mutations have long shown that amino acid residues at many active site positions cannot vary without functional loss Perutz and Lehmann 1968 More recent protein studies
Match 31 (1): Reference (003285 .. 003435, of 13533): Subject (002407 .. 002560, of 8267):
genes and proteins are sensitive to functional loss as a result of sequence change nor the extent to which functional proteins are isolated within sequence space has been fully known Recently experiments in molecular biology have shed light on these questions A variety of mutagenesis techniques have shown that proteins and thus the genes that produce them are indeed highly specified relative to biological function Bowie Sauer 1989 Reidhaar Olson Sauer 1990 Taylor et al 2001 Mutagenesis research tests the sensitivity of proteins and by implication DNA to functional loss as a result of alterations in sequencing Studies of proteins have long shown that amino acid residues at many active positions cannot vary without functional loss Perutz Lehmann 1968 More recent protein studies often using mutagenesis experiments have shown that functional requirements place significant constraints on sequencing even at non active site positions Bowie Sauer 1989 Reidhaar Olson Sauer 1990 Chothia genes and proteins to functional loss as a result of sequence change nor the extent to which functional proteins are isolated within sequence space has been fully known Recently experiments in molecular biology have shed light on these questions A variety of mutagenesis techniques have shown that proteins and thus the genes that produce them are indeed highly specified relative to biological function Bowie and Sauer 1989 Reidhaar Olson and Sauer 1990 Taylor et al 2001 Mutagenesis research tests the sensitivity of proteins and by implication DNA to functional loss as a result of alterations in sequencing Studies of protein mutations have long shown that amino acid residues at many active site positions cannot vary without functional loss Perutz and Lehmann 1968 More recent protein studies including mutagenesis experiments have shown that functional requirements place significant constraints on sequencing even at nonactive site positions Bowie and Sauer 1989 Reidhaar Olson and Sauer 1990 Chothia
Match 32 (1): Reference (003438 .. 003529, of 13533): Subject (002564 .. 002654, of 8267):
1998 Axe 2000 Taylor et al 2001 In particular Axe 2000 has shown that multiple as opposed to single position amino acid substitutions inevitably result in loss of protein function even when these changes occur at sites that allow variation when altered in isolation Cumulatively these constraints imply that proteins are highly sensitive to functional loss as a result of alterations in sequencing and that functional proteins represent highly isolated and improbable arrangements of amino acids arrangements that are far more improbable in fact than would be likely to arise by chance 1998 Axe 2000 Taylor et al 2001 In particular Axe 2000 has shown that multiple as opposed to single amino acid substitutions inevitably result in loss of protein function even when these changes occur at sites that allow variation when altered in isolation Cumulatively these constraints imply that proteins are highly sensitive to functional loss as a result of alterations in sequencing and that functional proteins represent highly isolated and improbable arrangements of amino acids arrangements that are far more improbable in fact than would be likely to arise by chance
Match 33 (1): Reference (003566 .. 003578, of 13533): Subject (002669 .. 002681, of 8267):
Of course neo Darwinists do not envision a completely random search through the Of course neo Darwinists do not envision a completely random search through the
Match 34 (1): Reference (003591 .. 003782, of 13533): Subject (002689 .. 002881, of 8267):
natural selection acting to preserve small advantageous variations in genetic sequences and their corresponding protein products Dawkins 1996 for example likens an organism to a high mountain peak He compares climbing the sheer precipice up the front side of the mountain to building a new organism by chance He acknowledges that his approach up Mount Improbable will not succeed Nevertheless he suggests that there is a gradual slope up the backside of the mountain that could be climbed in small incremental steps In his analogy the backside climb up Mount Improbable corresponds to the process of natural selection acting on random changes in the genetic text What chance alone cannot accomplish blindly or in one leap selection acting on mutations can accomplish through the cumulative effect of many slight successive steps Yet the extreme specificity and complexity of proteins presents a difficulty not only for the chance origin of specified biological information i e for random mutations acting alone but also for selection and mutation acting in concert Indeed mutagenesis experiments cast doubt on each of the two scenarios by which neo Darwinists envisioned new information arising from the mutation selection mechanism natural selection acting to preserve small advantageous variations in genetic sequences and their corresponding protein products Richard Dawkins 1996 for example likens an organism to a high mountain peak He compares climbing the sheer precipice up the front side of the mountain to building a new organism by chance He acknowledges that this approach up Mount Improbable will not succeed Nevertheless he suggests that there is a gradual slope up the backside of the mountain that could be climbed in small incremental steps In his analogy the backside climb up Mount Improbable corresponds to the process of natural selection acting on random changes in the genetic text What chance alone cannot accomplish blindly or in one leap selection acting on mutations can accomplish through the cumulative effect of many slight successive steps Yet the extreme specificity and complexity of proteins presents a difficulty not only for the chance origin of specified biological information i e for random mutations acting alone but also for selection and mutation acting in concert Indeed mutagenesis experiments cast doubt on each of the two scenarios by which neo Darwinists envision new information arising from the mutation selection mechanism
Match 35 (1): Reference (003788 .. 003956, of 13533): Subject (002882 .. 003052, of 8267):
For neo Darwinism new functional genes either arise from non coding sections in the genome or from preexisting genes Both scenarios are problematic In the first scenario neo Darwinists envision new genetic information arising from those sections of the genetic text that can presumably vary freely without consequence to the organism According to this scenario non coding sections of the genome or duplicated sections of coding regions can experience a protracted period of neutral evolution Kimura 1983 during which alterations in nucleotide sequences have no discernible effect on the function of the organism Eventually however a new gene sequence will arise that can code for a novel protein At that point natural selection can favor the new gene and its functional protein product thus securing the preservation and heritability of both This scenario has the advantage of allowing the genome to vary through many generations as mutations search the space of possible base sequences The scenario has an overriding problem however the size of the combinatorial space i e For neo Darwinists new functional genes either arise from noncoding sections in the genome or from preexisting genes Both scenarios are problematic In the first scenario neo Darwinists envision new genetic information arising from those sections of the genetic text that can presumably vary freely without consequence to the organism According to this scenario noncoding sections of the genome or duplicated sections of coding regions can experience a protracted period of neutral evolution during which alterations in nucleotide sequences have no discernible effect on the function of the organism Eventually however a new gene sequence will arise that can code for a novel protein At that point natural selection can favor the new gene and its functional protein product thus securing the preservation and heritability of both This scenario has the advantage of allowing the genome to vary through many generations as mutations search the space of possible base sequences The scenario has an overriding problem however the size of the combinatorial space and the extreme rarity and isolation of the
Match 36 (1): Reference (003964 .. 004022, of 13533): Subject (003045 .. 003103, of 8267):
and the extreme rarity and isolation of the functional sequences within that space of possibilities Since natural selection can do nothing to help generate new functional sequences but rather can only preserve such sequences once they have arisen chance alone random variation must do the work of information generation that is of finding the exceedingly rare functional sequences within and the extreme rarity and isolation of the functional sequences within that space of possibilities Since natural selection can do nothing to help generate new functional sequences but rather can only preserve such sequences once they have arisen chance alone random variation must do the work of information generation that is of finding the exceedingly rare functional sequences within
Match 37 (1): Reference (004026 .. 004043, of 13533): Subject (003105 .. 003124, of 8267):
combinatorial possibilities Yet the probability of randomly assembling or finding in the previous sense a functional sequence is combinatorial universe of possibilities Yet the probability of randomly assembling or finding in the previous sense a functional sequence is
Match 38 (1): Reference (004054 .. 004085, of 13533): Subject (003137 .. 003172, of 8267):
suggest that the probability of attaining at random the correct sequencing for a short protein 100 amino acids long is about 1 in 1065 Reidhaar Olson Sauer 1990 Behe 1992 65 69 s mutagenesis experiments imply that the probability of attaining at random the correct sequencing for a short protein 100 amino acids long is about 1 in 1065 Reidhaar Olson and Sauer 1990 Behe 1992 65 9
Match 39 (1): Reference (004207 .. 004217, of 13533): Subject (002183 .. 002194, of 8267):
to b the whole set of possible amino acids sequences of to be rare among the set of possible amino acid sequences of
Match 40 (1): Reference (004239 .. 004248, of 13533): Subject (002179 .. 002195, of 8267):
a functional protein among the possible amino acid sequences corresponding generally thought functional proteins to be rare among the set of possible amino acid sequences of corresponding
Match 41 (1): Reference (004259 .. 004318, of 13533): Subject (003193 .. 003252, of 8267):
Other considerations imply additional improbabilities First new Cambrian animals would require proteins much longer than 100 residues to perform many necessary specialized functions Ohno 1996 has noted that Cambrian animals would have required complex proteins such as lysyl oxidase in order to support their stout body structures Lysyl oxidase molecules in extant organisms comprise over 400 amino acids These molecules Other considerations imply additional improbabilities First new Cambrian animals would require proteins much longer than 100 residues to perform necessary specialized functions Susumu Ohno 1996 has noted that Cambrian animals would have required complex proteins such as lysyl oxidase in order to support their stout body structures Lysyl oxidase molecules in extant organisms comprise over 400 amino acids These molecules
Match 42 (1): Reference (004327 .. 004352, of 13533): Subject (003259 .. 003287, of 8267):
specified Reasonable extrapolation from mutagenesis experiments done on shorter protein molecules suggests that the probability of producing functionally sequenced proteins of this length at random is specified arrangements of matter Reasonable extrapolation from mutagenesis experiments done on shorter protein molecules suggests that the probability of producing functionally sequenced proteins of this length at random is
Match 43 (1): Reference (004450 .. 004479, of 13533): Subject (003355 .. 003385, of 8267):
Third DNA mutation rates are far too low to generate the novel genes and proteins necessary to building the Cambrian animals given the most probable duration of the explosion as Third DNA mutation rates are far too low to generate the novel genes and proteins necessary to building the Cambrian animals given the duration of the explosion As Susumo Ohno has
Match 44 (1): Reference (004543 .. 004721, of 13533): Subject (003460 .. 003636, of 8267):
4 The selection mutation mechanism faces another probabilistic obstacle The animals that arise in the Cambrian exhibit structures that would have required many new types of cells each of which would have required many novel proteins to perform their specialized functions Further new cell types require systems of proteins that must as a condition of functioning act in close coordination with one another The unit of selection in such systems ascends to the system as a whole Natural selection selects for functional advantage But new cell types require whole systems of proteins to perform their distinctive functions In such cases natural selection cannot contribute to the process of information generation until after the information necessary to build the requisite system of proteins has arisen Thus random variations must again do the work of information generation and now not simply for one protein but for many proteins arising at nearly the same time Yet the odds of this occurring by chance alone are of course far smaller than the odds of the chance origin of a single gene or protein 3475 The selection mutation mechanism faces another probabilistic obstacle The animals that arise in the Cambrian exhibit structures that would have required many new types of cells each of which would have required many types novel proteins to perform their specialized functions Further new cell types require systems of proteins that must as a condition of function act in close coordination with one another The unit of selection in such systems ascends to the system as a whole Natural selection selects for functional advantage But new cell types require whole systems of proteins to perform their distinctive functions In such cases natural selection cannot contribute to the process of information generation until after the information necessary to build the requisite system of proteins has arisen Thus random variations must again do the work of information generation and now not simply for one protein but for many proteins arising at nearly the same time Yet the odds of this occurring by chance are far smaller than the odds of the chance origin of a single gene or protein
Match 45 (1): Reference (004726 .. 004737, of 13533): Subject (000579 .. 000589, of 8267):
as to render the chance origin of the genetic information necessary to as an explanation for the origin of the information necessary to
Match 46 (1): Reference (004790 .. 004828, of 13533): Subject (003659 .. 003698, of 8267):
The neutral theory of evolution which by its own logic prevents natural selection from playing a role in generating genetic information until after the fact relies on entirely too much luck The sensitivity of proteins to functional loss the The neutral theory of evolution which by its own logic prevents natural selection from playing a role in generating genetic information until after the fact relies on entirely too much luck The sensitivity of proteins to functional loss as the
Match 47 (1): Reference (004828 .. 004883, of 13533): Subject (003705 .. 003759, of 8267):
the need for long proteins to build new cell types and animals the need for whole new systems of proteins to service new cell types the probable brevity of the Cambrian explosion relative to mutation rates all suggest the immense improbability and implausibility of any scenario for the origination of Cambrian genetic information that relies upon the need for long proteins to build new cell types and animals the need for whole new systems of proteins to service new cell types the brevity of the Cambrian explosion relative to mutation rates all suggest the immense improbability and implausibility of any scenario for the origin of Cambrian genetic information that relies upon
Match 48 (1): Reference (004886 .. 004949, of 13533): Subject (003761 .. 003825, of 8267):
alone unassisted by natural selection Yet the neutral theory requires novel genes and proteins to arise essentially by random mutation alone Adaptive advantage accrues after the generation of new functional genes and proteins Thus natural selection cannot play a role until new information bearing molecules have independently arisen Thus neutral theorists envisioned the need to scale the steep face of a Dawkins style precipice alone unassisted by natural selection Yet the neutral theory requires novel genes and proteins to arise essentially by random mutation alone Adaptive advantage accrues after the generation of new functional genes and proteins Thus natural selection cannot play a role until new information bearing molecules have independently arisen Thus the neutral theory envisions the need to scale the steep face of a Dawkins style precipice
Match 49 (1): Reference (004951 .. 005019, of 13533): Subject (003827 .. 003895, of 8267):
which there is no gradually sloping backside a situation that by Dawkins own logic is probabilistically untenable In the second scenario neo Darwinists envisioned novel genes and proteins arising by numerous successive mutations in the preexisting genetic text that codes for proteins To adapt Dawkins s metaphor this scenario envisions gradually climbing down one functional peak and then ascending another Yet mutagenesis experiments again suggest a difficulty Recent experiments which there is no gradually sloping backside a situation that by Dawkins own logic is probabilistically untenable In the second scenario neo Darwinists envision novel genes and proteins arising by numerous successive mutations in the preexisting genetic text that codes for proteins To adapt Dawkins s metaphor this scenario envisions gradually climbing down one functional peak and then ascending another Yet mutagenesis experiments again suggest a difficulty Recent experiments
Match 50 (1): Reference (005020 .. 005070, of 13533): Subject (003903 .. 003954, of 8267):
show that even when exploring a region of sequence space populated by proteins of a single fold and function most multiple position changes quickly lead to loss of function Axe 2000 Yet to turn one protein into another with a completely novel structure and function requires specified changes at many sites show that even when exploring a region of sequence space populated by proteins of a single fold and function most multiple position changes quickly lead to loss of function Axe 2000 Yet to turn one protein into another with a completely novel structure and function requires specified changes at many more sites
Match 51 (1): Reference (005094 .. 005116, of 13533): Subject (003955 .. 003978, of 8267):
Given this the probability of escaping total functional loss during a random search for the changes needed to produce a new function is Given this reality the probability of escaping total functional loss during a random search for the changes needed to produce a new function is
Match 52 (1): Reference (005118 .. 005160, of 13533): Subject (003980 .. 004020, of 8267):
small and this probability diminishes exponentially with each additional requisite change Axe 2000 Thus Axe s results imply that in all probability random searches for novel proteins through sequence space will result in functional loss long before any novel functional protein will emerge small and this probability diminishes exponentially with each additional requisite change Thus Axe s results imply that in all probability random searches for novel proteins through sequence space will result in functional loss long before any novel functional protein will emerge
Match 53 (1): Reference (005245 .. 005543, of 13533): Subject (004164 .. 004468, of 8267):
1999 741 Thus although this second neo Darwinian scenario has the advantage of starting with functional genes and proteins it also has a lethal disadvantage any process of random mutation or rearrangement in the genome would in all probability generate nonfunctional intermediate sequences before fundamentally new functional genes or proteins would arise Clearly nonfunctional intermediate sequences confer no survival advantage on their host organisms Natural selection favors only functional advantage It cannot select or favor nucleotide sequences or polypeptide chains that do not yet perform biological functions and still less will it favor sequences that efface or destroy preexisting function Evolving genes and proteins will range through a series of nonfunctional intermediate sequences that natural selection will not favor or preserve but will in all probability eliminate Blanco et al 1999 Axe 2000 When this happens selection driven evolution will cease At this point neutral evolution of the genome unhinged from selective pressure may ensue but as we have seen such a process must overcome immense probabilistic hurdles even granting cosmic time Thus whether one envisions the evolutionary process beginning with a noncoding region of the genome or a preexisting functional gene the functional specificity and complexity of proteins impose very stringent limitations on the efficacy of mutation and selection In the first case function must arise first before natural selection can act to favor a novel variation In the second case function must be continuously maintained in order to prevent deleterious or lethal consequences to the organism and to allow further evolution Yet the complexity and functional specificity of proteins implies that both these conditions will be extremely difficult to meet Therefore the neo Darwinian mechanism appears to be inadequate to generate the new information present in the novel genes and proteins that arise with the Cambrian animals 1999 741 Thus although this second neo Darwinian scenario has the advantage of starting with functional genes and proteins it also has a lethal disadvantage any process of random mutation or rearrangement in the genome would in all probability generate nonfunctional intermediate sequences before fundamentally new functional genes or proteins would arise Figure 20 1 Clearly nonfunctional intermediate sequences confer no survival advantage on their host organisms Yet natural selection favors only functional advantage It cannot select or favor nucleotide sequences or polypeptide chains that do not yet perform biological functions and still less will it favor sequences that efface or destroy preexisting function Evolving genes and proteins will almost inevitably range through a series of nonfunctional intermediate sequences that natural selection will not favor or preserve but will in all probability eliminate Blanco et al 1999 Axe 2000 When this happens selection driven evolution will cease At this point neutral evolution of the genome unhinged from selective pressure may ensue but as we have seen such a process must overcome immense probabilistic hurdles even granting cosmic time Thus whether one envisions the evolutionary process beginning with a noncoding region of the genome or a preexisting functional gene the functional specificity and complexity of proteins impose very stringent limitations on the efficacy of mutation and selection In the first case function must arise first before natural selection can act to favor a novel variation In the second case function must be continuously maintained in order to prevent deleterious or lethal consequences to the organism and to allow further evolution Yet the complexity and functional specificity of proteins implies that both these conditions will be extremely difficult to meet Therefore the neo Darwinian mechanism appears to be inadequate to generate the new information present in the novel genes and proteins that arise with the Cambrian animals
Match 54 (1): Reference (005547 .. 005693, of 13533): Subject (004472 .. 004617, of 8267):
The problems with the neo Darwinian mechanism run deeper still In order to explain the origin of the Cambrian animals one must account not only for new proteins and cell types but also for the origin of new body plans Within the past decade developmental biology has dramatically advanced our understanding of how body plans are built during ontogeny In the process it has also uncovered a profound difficulty for neo Darwinism Significant morphological change in organisms requires attention to timing Mutations in genes that are expressed late in the development of an organism will not affect the body plan Mutations expressed early in development however could conceivably produce significant morphological change Arthur 1997 21 Thus events expressed early in the development of organisms have the only realistic chance of producing large scale macroevolutionary change Thomson 1992 As John and Miklos 1988 309 explain macroevolutionary change requires The problems with the neo Darwinian mechanism run deeper still In order to explain the origin of the Cambrian animals one must account not only for new proteins and cell types but also for the origin of new body plans Within the past decade developmental biology has dramatically advanced our understanding of how body plans are built during ontogeny In the process it has also uncovered a profound difficulty for neo Darwinism Significant morphological change in organisms requires attention to timing Mutations in genes that are expressed late in the development of an organism will not affect the body plan Mutations expressed early in development however could conceivably produce significant morphological change Arthur 1997 21 Thus events expressed early in the development of organisms have the only realistic chance of producing large scale macroevolutionary change Thomson 1992 As John and Miklos explain 11 macroevolutionary change requires
Match 55 (1): Reference (005702 .. 005718, of 13533): Subject (004625 .. 004641, of 8267):
Yet recent studies in developmental biology make clear that mutations expressed early in development typically have deleterious Yet recent studies in developmental biology make clear that mutations expressed early in development typically have deleterious
Match 56 (1): Reference (005723 .. 005761, of 13533): Subject (004661 .. 004701, of 8267):
For example when early acting body plan molecules or morphogens such as bicoid which helps to set up the anterior posterior head to tail axis in Drosophila are perturbed development shuts down Nusslein Volhard Wieschaus 1980 Lawrence Struhl 1996 For example when early acting body plan molecules or morphogens such as bicoid which helps to set up the anterior posterior head to tail axis in Drosophila are perturbed development shuts down Nusslein Volhard and Wieschaus 1980 Lawrence and Struhl 1996
Match 57 (1): Reference (005766 .. 005834, of 13533): Subject (004702 .. 004773, of 8267):
The resulting embryos die Moreover there is a good reason for this If an engineer modifies the length of the piston rods in an internal combustion engine without modifying the crankshaft accordingly the engine won t start Similarly processes of development are tightly integrated spatially and temporally such that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream The resulting embryos die Moreover there is a good reason for this If an engineer modifies the length of the piston rods in an internal combustion engine without modifying the crankshaft accordingly the engine won t start Similarly processes of development are tightly integrated spatially and temporally in such a way that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream
Match 58 (1): Reference (005870 .. 005879, of 13533): Subject (004801 .. 004809, of 8267):
fingers Kauffman 1995 200 This problem has led to what fingers 1995 200 This problem has led to what
Match 59 (1): Reference (005914 .. 005924, of 13533): Subject (004844 .. 004854, of 8267):
major changes the very stuff of macroevolution apparently do not vary major changes the very stuff of macroevolution apparently do not vary
Match 60 (1): Reference (005925 .. 005956, of 13533): Subject (004912 .. 004943, of 8267):
In other words mutations of the kind that macroevolution doesn t need namely viable genetic mutations in DNA expressed late in development do occur but those that it does need namely beneficial In other words mutations of the kind that macroevolution doesn t need namely viable genetic mutations in DNA expressed late in development do occur but those that it does need namely beneficial
Match 61 (1): Reference (005925 .. 005971, of 13533): Subject (004912 .. 004953, of 8267):
In other words mutations of the kind that macroevolution doesn t need namely viable genetic mutations in DNA expressed late in development do occur but those that it does need namely beneficial body plan mutations expressed early in development apparently don t occur 6 According to Darwin In other words mutations of the kind that macroevolution doesn t need namely viable genetic mutations in DNA expressed late in development do occur but those that it does need namely beneficial Bauplan mutations expressed early in development don t occur Darwin
Match 62 (1): Reference (005996 .. 006006, of 13533): Subject (004975 .. 004989, of 8267):
of variations required by neo Darwinism namely favorable body plan mutations of development suggest that variations of the kind required by neo Darwinism favorable Bauplan mutations
Match 63 (1): Reference (006008 .. 006037, of 13533): Subject (004992 .. 005023, of 8267):
occur Developmental biology has raised another formidable problem for the mutation selection mechanism Embryological evidence has long shown that DNA does not wholly determine morphological form Goodwin 1985 Nijhout 1990 occur Developmental biology has raised another formidable problem for the mutation selection mechanism Embryological evidence has long shown that DNA does not wholly determine morphological form Goodwin 1985 Sapp 1987 Nijhout 1990
Match 64 (1): Reference (006043 .. 006061, of 13533): Subject (005024 .. 005042, of 8267):
suggesting that mutations in DNA alone cannot account for the morphological changes required to build a new body plan suggesting that mutations in DNA alone cannot account for the morphological changes required to build a new body plan
Match 65 (1): Reference (006062 .. 006084, of 13533): Subject (005047 .. 005067, of 8267):
DNA helps direct protein synthesis 7 It also helps to regulate the timing and expression of the synthesis of various proteins within cells DNA directs protein synthesis It also helps to regulate the timing and expression of the synthesis of various proteins within cells
Match 66 (1): Reference (006086 .. 006118, of 13533): Subject (005069 .. 005101, of 8267):
DNA alone does not determine how individual proteins assemble themselves into larger systems of proteins still less does it solely determine how cell types tissue types and organs arrange themselves into body plans DNA alone does not determine how individual proteins assemble themselves into larger systems of proteins still less does it solely determine how cell types tissue types and organs arrange themselves into body plans
Match 67 (1): Reference (006124 .. 006140, of 13533): Subject (005102 .. 005116, of 8267):
Instead other factors such as the three dimensional structure and organization of the cell membrane and cytoskeleton Instead other factors such as the structure and organization of the cell membrane and cytoskeleton
Match 68 (1): Reference (006149 .. 006161, of 13533): Subject (005117 .. 005133, of 8267):
play important roles in determining body plan formation during embryogenesis For example the play important roles in determining developmental pathways that determine body plan formation during embryogenesis For example the
Match 69 (1): Reference (006163 .. 006202, of 13533): Subject (005135 .. 005176, of 8267):
and location of the cytoskeleton influence the patterning of embryos Arrays of microtubules help to distribute the essential proteins used during development to their correct locations in the cell Of course microtubules themselves are made of many protein subunits Nevertheless and location of microtubules in the cytoskeleton influence the patterning of embryos Arrays of microtubules help to distribute the essential proteins used during development to their correct locations in the cell Of course microtubules themselves are made of many protein subunits Nevertheless
Match 70 (1): Reference (006216 .. 006226, of 13533): Subject (005175 .. 005189, of 8267):
subunits in the cell s microtubules are identical to one another subunits Nevertheless the protein subunits in the cell s microtubules are identical to one another
Match 71 (1): Reference (006232 .. 006254, of 13533): Subject (005192 .. 005216, of 8267):
nor the genes that produce them account for the different shape of microtubule arrays that distinguish different kinds of embryos and developmental pathways nor the genes that produce them account for the different shapes and locations of microtubule arrays that distinguish different kinds of embryos and developmental pathways
Match 72 (1): Reference (006316 .. 006386, of 13533): Subject (005255 .. 005325, of 8267):
clarify the point At a building site builders will make use of many materials lumber wires nails drywall piping and windows Yet building materials do not determine the floor plan of the house or the arrangement of houses in a neighborhood Similarly electronic circuits are composed of many components such as resistors capacitors and transistors But such lower level components do not determine their own arrangement in an integrated circuit Biological clarify the point At a building site builders will make use of many materials lumber wires nails drywall piping and windows Yet building materials do not determine the floor plan of the house or the arrangement of houses in a neighborhood Similarly electronic circuits are composed of many components such as resistors Capacitors and transistors But such lower level components do not determine their own arrangement in an integrated circuit Biological
Match 73 (1): Reference (006388 .. 006634, of 13533): Subject (005327 .. 005573, of 8267):
also depend on hierarchical arrangements of parts Genes and proteins are made from simple building blocks nucleotide bases and amino acids arranged in specific ways Cell types are made of among other things systems of specialized proteins Organs are made of specialized arrangements of cell types and tissues And body plans comprise specific arrangements of specialized organs Yet clearly the properties of individual proteins or indeed the lower level parts in the hierarchy generally do not fully determine the organization of the higher level structures and organizational patterns Harold 2001 125 It follows that the genetic information that codes for proteins does not determine these higher level structures either These considerations pose another challenge to the sufficiency of the neo Darwinian mechanism Neo Darwinism seeks to explain the origin of new information form and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy namely within the genetic text Yet major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy a level that DNA alone does not determine Yet if DNA is not wholly responsible for body plan morphogenesis then DNA sequences can mutate indefinitely without regard to realistic probabilistic limits and still not produce a new body plan Thus the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans including those that first arose in the Cambrian explosion Of course also depend on hierarchical arrangements of parts Genes and proteins are made from simple building blocks nucleotide bases and amino acids arranged in specific ways Cell types are made of among other things systems of specialized proteins Organs are made of specialized arrangements of cell types and tissues And body plans comprise specific arrangements of specialized organs Yet clearly the properties of individual proteins or indeed the lower level parts in the hierarchy generally do not determine the organization of these higher level structures and organizational patterns It follows therefore that the genetic information that codes for proteins does not determine these higher level structures either These considerations pose another challenge to the sufficiency of the neo Darwinian mechanism Neo Darwinism seeks to explain the origin of new information form and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy namely within the genetic text Yet major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy a level that DNA alone does not determine Yet if DNA is not wholly responsible for body plan morphogenesis then DNA sequences can mutate indefinitely without regard to realistic probabilistic limits and still not produce a new body plan Thus the mechanism of natural selection acting on random mutations in DNA cannot in Principle generate novel body plans including those that first arose in the Cambrian explosion SELF ORGANIZATIONAL MODELS Of course
Match 74 (1): Reference (007139 .. 007157, of 13533): Subject (005572 .. 005591, of 8267):
Of course neo Darwinism is not the only evolutionary theory for explaining the origin of novel biological form Kauffman Of course neo Darwinism is not the only naturalistic model for explaining the origin of novel biological form Stuart Kauffman
Match 75 (1): Reference (007159 .. 007173, of 13533): Subject (005595 .. 005609, of 8267):
doubts the efficacy of the mutation selection mechanism Nevertheless he has advanced a self organizational doubts the efficacy of the mutation selection mechanism Nevertheless he has advanced a self organizational
Match 76 (1): Reference (007175 .. 007240, of 13533): Subject (005611 .. 005672, of 8267):
to account for the emergence of new form and presumably the information necessary to generate it Whereas neo Darwinism attempts to explain new form as the consequence of selection acting on random mutation Kauffman suggests that selection acts not mainly on random variations but on emergent patterns of order that self organize via the laws of nature Kauffman 1995 47 92 illustrates how this might work to account for the emergence of new form and presumably the information necessary to generate it Whereas neo Darwinism attempts to explain new form as the consequence of selection acting on random mutation Kauffman suggests that selection acts not mainly on random variations but on emergent patterns of order that selforganize via the laws of nature Kauffman illustrates how this might work
Match 77 (1): Reference (007242 .. 007317, of 13533): Subject (005674 .. 005751, of 8267):
various model systems in a computer environment In one he conceives a system of buttons connected by strings Buttons represent novel genes or gene products strings represent the law like forces of interaction that obtain between gene products i e proteins Kauffman suggests that when the complexity of the system as represented by the number of buttons and strings reaches a critical threshold new modes of organization can arise in the system for free that is various model systems in a computer environment 1995 47 92 In one he conceives a system of buttons connected by strings Buttons represent novel genes or gene products strings represent the lawlike forces of interaction that obtain between gene products that is proteins Kauffman suggests that when the complexity of the system as represented by the number of buttons and strings reaches a critical threshold new modes of organization can arise in the system for free that is
Match 78 (1): Reference (007321 .. 007352, of 13533): Subject (005755 .. 005786, of 8267):
after the manner of a phase transition in chemistry Another model that Kauffman develops is a system of interconnected lights Each light can flash in a variety of states on off twinkling after the manner of a phase transition in chemistry Another model that Kauffman develops is a system of interconnected lights Each light can flash in a variety of states on off twinkling
Match 79 (1): Reference (007350 .. 007454, of 13533): Subject (005789 .. 005890, of 8267):
on off twinkling etc Since there is more than one possible state for each light and many lights there are a vast number of possible states that the system can adopt Further in his system rules determine how past states will influence future states Kauffman asserts that as a result of these rules the system will if properly tuned eventually produce a kind of order in which a few basic patterns of light activity recur with greater than random frequency Since these actual patterns of light activity represent a small portion of the total number of possible states in which the system can reside Kauffman on Since there is more than one possible state for each light and many lights there is a vast number of possible states that the system can adopt Further in his system rules determine how past states will influence future states Kauffman asserts that as a result of these rules the system will if properly tuned eventually produce a kind of order in which a few basic patterns of light activity recur with greater than random frequency Since these actual patterns of light activity represent a small portion of the total number of possible states in which the system can reside Kaufman
Match 80 (1): Reference (007458 .. 007587, of 13533): Subject (005892 .. 006020, of 8267):
that self organizational laws might similarly result in highly improbable biological outcomes perhaps even sequences of bases or amino acids within a much larger sequence space of possibilities Do these simulations of self organizational processes accurately model the origin of novel genetic information It is hard to think so First in both examples Kauffman presupposes but does not explain significant sources of preexisting information In his buttons and strings system the buttons represent proteins themselves packets of CSI and the result of preexisting genetic information Where does this information come from Kauffman 1995 doesn t say but the origin of such information is an essential part of what needs to be explained in the history of life Similarly in his light system the order that allegedly arises for for free that self organizational laws might similarly result in highly improbable biological outcomes perhaps even sequences of bases or amino acids within a much larger sequence space of possibilities Do these simulations of self organizational processes accurately model the origin of novel genetic information It is hard to think so First in both examples Kaufmann presupposes but does not explain significant sources of preexisting information In his buttons and strings system the buttons represent proteins themselves packets of CSI and the result of preexisting genetic information Where does this information come from Kauffman doesn t say but the origin of such information is an essential part of what needs to be explained in the history of life Similarly in his light system the order that allegedly arises for for free
Match 81 (1): Reference (007588 .. 007617, of 13533): Subject (006030 .. 006059, of 8267):
actually arises only if the programmer of the model system tunes it in such a way as to keep it from either a generating an excessively rigid order or b actually arises only if the programmer of the model system tunes it in such a way as to keep it from either a generating an excessively rigid order or b
Match 82 (1): Reference (007619 .. 007788, of 13533): Subject (006061 .. 006228, of 8267):
into chaos pp 86 88 Yet this necessary tuning involves an intelligent programmer selecting certain parameters and excluding others that is inputting information Second Kauffman s model systems are not constrained by functional considerations and thus are not analogous to biological systems A system of interconnected lights governed by pre programmed rules may well settle into a small number of patterns within a much larger space of possibilities But because these patterns have no function and need not meet any functional requirements they have no specificity analogous to that present in actual organisms Instead examination of Kauffman s 1995 model systems shows that they do not produce sequences or systems characterized by specified complexity but instead by large amounts of symmetrical order or internal redundancy interspersed with aperiodicity or mere complexity pp 53 89 102 Getting a law governed system to generate repetitive patterns of flashing lights even with a certain amount of variation is clearly interesting but not biologically relevant On the other hand a system of lights flashing into chaos 86 8 Yet this necessary tuning involves an intelligent programmer selecting certain parameters and excluding others that is inputting information Second Kauffman s model systems are not constrained by functional considerations and thus are not analogous to biological systems A system of interconnected lights governed by pre programmed rules may well settle into a small number of patterns within a much larger space of possibilities But because these patterns have no function and need not meet any functional requirement they have no specificity analogous to that present in actual organisms Instead examination of Kauffman s model systems shows that they produce sequences or systems characterized not by specified complexity but instead by large amounts of symmetrical order or internal redundancy interspersed with aperiodicity or mere complexity 53 89 102 Getting a law governed system to generate repetitive patterns of flashing lights even with a certain amount of variation is clearly interesting but it is not biologically relevant On the other hand a system of lights flashing
Match 83 (1): Reference (007795 .. 007807, of 13533): Subject (006233 .. 006245, of 8267):
would model a biologically relevant self organizational process at least if such a would model a biologically relevant self organizational process at least if such messages
Match 84 (1): Reference (007813 .. 007934, of 13533): Subject (006246 .. 006365, of 8267):
arose without intelligent agents previously programming the system with equivalent amounts of CSI In any case Kauffman s systems do not produce specified complexity and thus do not offer promising models for explaining the new genes and proteins that arose in the Cambrian Even so Kauffman suggests that his self organizational models can specifically elucidate aspects of the Cambrian explosion According to Kauffman 1995 199 201 new Cambrian animals emerged as the result of long jump mutations that established new body plans in a discrete rather than gradual fashion He also recognizes that mutations affecting early development are almost inevitably harmful Thus he concludes that body plans once established will not change and that any subsequent evolution must occur within an established arose without agents previously programming the system with equivalent amounts of CSI In any case Kauffman s systems do not produce specified complexity and thus they do not offer promising models for explaining the new genes and proteins that arose in the Cambrian Even so Kauffman suggests that his self organizational models can specifically elucidate aspects of the Cambrian explosion According to Kauffman new Cambrian animals emerged as the result of long jump mutations that established new body plans in a discrete rather than gradual fashion 199201 He also recognizes that mutations affecting early development are almost inevitably harmful Thus he concludes that body plans once established will not change and that any subsequent evolution must occur within an established
Match 85 (1): Reference (007940 .. 007990, of 13533): Subject (006367 .. 006416, of 8267):
And indeed the fossil record does show a curious from a neo Darwinian point of view top down pattern of appearance in which higher taxa and the body plans they represent appear first only later to be followed by the multiplication of lower taxa representing variations within those original body designs And indeed the fossil record does show a curious from a Darwinian point of view top down pattern of appearance in which higher taxa and the body plans they represent appear first only later to be followed by the multiplication of lower taxa representing variations within those original body designs
Match 86 (1): Reference (008001 .. 008090, of 13533): Subject (006417 .. 006506, of 8267):
Further as Kauffman expects body plans appear suddenly and persist without significant modification over time But here again Kauffman begs the most important question which is what produces the new Cambrian body plans in the first place Granted he invokes long jump mutations to explain this but he identifies no specific self organizational process that can produce such mutations Moreover he concedes a principle that undermines the plausibility of his own proposal Kauffman acknowledges that mutations that occur early in development are almost inevitably deleterious Yet developmental biologists know that Further as Kauffman expects body plans appear suddenly and persist without significant modification over time But here again Kauffman begs the most important question which is what produces the new Cambrian body plans in the first place Granted he invokes long jump mutations to explain this but he identifies no specific self organizational process that can produce such mutations Moreover he concedes a principle that undermines the plausibility of his own proposal Kauffman acknowledges that mutations that occur early in development are almost inevitably deleterious Yet developmental biologists know that
Match 87 (1): Reference (008098 .. 008165, of 13533): Subject (006515 .. 006581, of 8267):
that have a realistic chance of producing large scale evolutionary change i e the big jumps that Kauffman invokes Though Kauffman repudiates the neo Darwinian reliance upon random mutations in favor of self organizing order in the end he must invoke the most implausible kind of random mutation in order to provide a self organizational account of the new Cambrian body plans Clearly his model is not sufficient that have a realistic chance of producing large scale evolutionary change that is the big jumps that Kauffman invokes Though Kauffman repudiates the neo Darwinian reliance upon random mutations in favor of self organizing order in the end he must invoke the most implausible kind of random mutation in order to provide a selforganizational account of the new Cambrian body plans Clearly his model is not sufficient
Match 88 (1): Reference (009161 .. 009171, of 13533): Subject (007726 .. 007738, of 8267):
the problem of the origin of form and information since the the problem of the origin of biological information exposes a deficiency in the
Match 89 (1): Reference (009319 .. 009331, of 13533): Subject (000372 .. 000384, of 8267):
candidates for explaining the origination of biological form or the information necessary to and their combination for the origin of biological information Further in order to
Match 90 (1): Reference (009321 .. 009333, of 13533): Subject (000638 .. 000652, of 8267):
explaining the origination of biological form or the information necessary to produce it explain the origin of the novel biological form and the information necessary to produce it
Match 91 (1): Reference (010000 .. 010011, of 13533): Subject (000276 .. 000286, of 8267):
explanation for the origin of the biological information necessary to produce the explanation for the origin of the information necessary to produce the
Match 92 (1): Reference (010175 .. 010187, of 13533): Subject (006594 .. 006604, of 8267):
and Lewontin 1978 have long acknowledged that organisms appear to have been designed and Richard Lewontin acknowledge that organisms appear to have been designed
Match 93 (1): Reference (010188 .. 010207, of 13533): Subject (006628 .. 006646, of 8267):
Of course neo Darwinists assert that what Ayala 1994 5 calls the obvious design of living things is only apparent Of course living neo Darwinists assert that what Ayala calls the obvious design of living things is only apparent
Match 94 (1): Reference (010233 .. 010243, of 13533): Subject (006709 .. 006717, of 8267):
neo Darwinists affirm that mutation and selection and perhaps other similarly neo Darwinists mutation and selection and perhaps other similar
Match 95 (1): Reference (010245 .. 010269, of 13533): Subject (006722 .. 006745, of 8267):
mechanisms are fully sufficient to explain the appearance of design in biology Self organizational theorists and punctuationalists modify this claim but affirm its essential tenet mechanisms are fully sufficient to explain the appearance of design in biological systems Self organizational theorists modify this claim but affirm its essential tenet
Match 96 (1): Reference (010273 .. 010294, of 13533): Subject (006747 .. 006768, of 8267):
argue that natural selection acting on self organizing order can explain the complexity of living things again without any appeal to design argue that natural selection acting on self organizing order can explain the complexity of living things again without any appeal to design
Match 97 (1): Reference (010520 .. 010541, of 13533): Subject (006858 .. 006876, of 8267):
the presence of CSI in living organisms and the discontinuous increases of CSI that occurred during events such as the Cambrian explosion the presence of CSI in living organisms and the discontinuous increases of CSI that occurred during the Cambrian explosion
Match 98 (1): Reference (010563 .. 010573, of 13533): Subject (006799 .. 006811, of 8267):
of the genetic and other forms of CSI necessary to produce of design including the genetic and other forms of CSI necessary to produce
Match 99 (1): Reference (010589 .. 010600, of 13533): Subject (006942 .. 006953, of 8267):
information rich genes proteins cell types and body plans have resulted from information rich genes proteins cell types and body plans have resulted from
Match 100 (1): Reference (010602 .. 010616, of 13533): Subject (006955 .. 006970, of 8267):
design rather than a purposeless process that merely mimics the powers of a designing intelligence Design rather than from a purposeless process that merely mimics the powers of a designing intelligence
Match 101 (1): Reference (010740 .. 010768, of 13533): Subject (007018 .. 007046, of 8267):
and philosophy of science have shown that many scientific theories particularly in the historical sciences are formulated and justified as inferences to the best explanation Lipton 1991 32 88 and philosophy of science have shown that many scientific theories particularly in the historical sciences are formulated and justified as inferences to the best explanation Lipton 1991 32 88
Match 102 (1): Reference (010773 .. 010801, of 13533): Subject (007047 .. 007073, of 8267):
Sober 2000 44 Historical scientists in particular assess or test competing hypotheses by evaluating which hypothesis would if true provide the best explanation for some set of relevant data Sober 2000 44 Historical scientists in particular assess competing hypotheses by evaluating which hypothesis would if true provide the best explanation of some set of relevant data
Match 103 (1): Reference (010813 .. 010828, of 13533): Subject (007074 .. 007089, of 8267):
Those with greater explanatory power are typically judged to be better more probably true theories Darwin Those with greater explanatory power are typically judged to be better more probably true theories Darwin
Match 104 (1): Reference (010831 .. 010890, of 13533): Subject (007091 .. 007156, of 8267):
used this method of reasoning in defending his theory of universal common descent Moreover contemporary studies on the method of inference to the best explanation have shown that determining which among a set of competing possible explanations constitutes the best depends upon judgments about the causal adequacy or causal powers of competing explanatory entities Lipton 1991 32 88 In the used this method of reasoning in defending his theory of universal common descent Darwin 1896 437 Moreover contemporary studies on the method of inference to the best explanation have shown that determining which among a set of competing possible explanations constitutes the best one depends upon judgments about the causal adequacy or causal powers of competing explanatory entities Lipton 32 88 I have argued that the
Match 105 (1): Reference (010980 .. 010991, of 13533): Subject (002830 .. 002845, of 8267):
explanation for the origin of biological form and information This review and a difficulty not only for the chance origin of specified biological information i e for random
Match 106 (1): Reference (011068 .. 011080, of 13533): Subject (007204 .. 007221, of 8267):
of hierarchically arranged systems of parts In the first place intelligent human agents of code or hierarchically arranged systems of parts Clearly they do In the first place intelligent human agents
Match 107 (1): Reference (011091 .. 011103, of 13533): Subject (007188 .. 007204, of 8267):
power to produce information in the form of linear sequence specific arrangements of powers sufficient to produce such increases in CSI either in the form of sequence specific lines of
Match 108 (1): Reference (011099 .. 011201, of 13533): Subject (007228 .. 007330, of 8267):
linear sequence specific arrangements of characters Indeed experience affirms that information of this type routinely arises from the activity of intelligent agents A computer user who traces the information on a screen back to its source invariably comes to a mind that of a software engineer or programmer The information in a book or inscriptions ultimately derives from a writer or scribe from a mental rather than a strictly material cause Our experience based knowledge of information flow confirms that systems with large amounts of specified complexity especially codes and languages invariably originate from an intelligent source from a mind or personal agent linear sequence specific arrangements of characters Indeed experience affirms that information of this type routinely arises from the activity of intelligent agents A computer user who traces the information on a screen back to its source invariably comes to a mind that of a software engineer or programmer The information in a book or inscription ultimately derives from a writer or scribe from a mental rather than a strictly material cause Our experience based knowledge of information flow confirms that systems with large amounts of specified complexity especially codes and languages invariably originate from an intelligent source from a mind or personal agent
Match 109 (1): Reference (011207 .. 011217, of 13533): Subject (000420 .. 000430, of 8267):
the creation of new information is habitually associated with conscious activity the creation of new information is habitually associated with conscious activity
Match 110 (1): Reference (011226 .. 011237, of 13533): Subject (007882 .. 007893, of 8267):
the highly specified hierarchical arrangements of parts in animal body plans also the highly specified hierarchical arrangements of parts in animal body plans also
Match 111 (1): Reference (011258 .. 011344, of 13533): Subject (007896 .. 007982, of 8267):
At every level of the biological hierarchy organisms require specified and highly improbable arrangements of lower level constituents in order to maintain their form and function Genes require specified arrangements of nucleotide bases proteins require specified arrangements of amino acids new cell types require specified arrangements of systems of proteins body plans require specialized arrangements of cell types and organs Organisms not only contain information rich components such as proteins and genes but they comprise information rich arrangements of those components and the systems that comprise them At every level of the biological hierarchy organisms require specified and highly improbable arrangements of lower level constituents in order to maintain their form and function Genes require specified arrangements of nucleotide bases proteins require specified arrangements of amino acids new cell types require specified arrangements of systems of proteins body plans require specialized arrangements of cell types and organs Not only do organisms contain information rich components such as proteins and genes they also comprise informationrich arrangements of those components and the systems that comprise them
Match 112 (1): Reference (011320 .. 011352, of 13533): Subject (007957 .. 007985, of 8267):
only contain information rich components such as proteins and genes but they comprise information rich arrangements of those components and the systems that comprise them Yet we know based on our present experience only do organisms contain information rich components such as proteins and genes they also comprise informationrich arrangements of those components and the systems that comprise them Based on experience
Match 113 (1): Reference (011367 .. 011484, of 13533): Subject (008003 .. 008124, of 8267):
the ability to produce information rich hierarchies in which both individual modules and the arrangements of those modules exhibit complexity and specificity information so defined Individual transistors resistors and capacitors exhibit considerable complexity and specificity of design at a higher level of organization their specific arrangement within an integrated circuit represents additional information and reflects further design Conscious and rational agents have as part of their powers of purposive intelligence the capacity to design information rich parts and to organize those parts into functional information rich systems and hierarchies Further we know of no other causal entity or process that has this capacity Clearly we have good reason to doubt that mutation and selection self organizational processes or the ability to produce information rich hierarchies in which both individual modules and the arrangements of those modules exhibit complexity and specificity information so defined Individual transistors resistors and capacitors exhibit considerable complexity and specificity of design at a higher level of organization their specific arrangement within an integrated circuit represents additional information and reflects further design Conscious and rational agents have as part of their powers of purposive intelligence the capacity to design information rich parts and to organize those parts into functional information rich systems and hierarchies Further we know of no other causal entity or process that has this capacity Clearly we have good reason to doubt that either mutation and selection or selforganizational processes can produce the information
Match 114 (1): Reference (011488 .. 011497, of 13533): Subject (008121 .. 008130, of 8267):
can produce the information rich components systems and body plans can produce the information rich components systems and body plans
Match 115 (1): Reference (011527 .. 011537, of 13533): Subject (002830 .. 002843, of 8267):
explanation for the origin of biological form and information purposive agents a difficulty not only for the chance origin of specified biological information i e
Match 116 (1): Reference (011537 .. 011553, of 13533): Subject (007356 .. 007372, of 8267):
agents have just those necessary powers that natural selection lacks as a condition of its causal adequacy agents have just those necessary powers that natural selection lacks as a condition of its causal adequacy
Match 117 (1): Reference (011563 .. 011596, of 13533): Subject (007384 .. 007423, of 8267):
that natural selection lacked the ability to generate novel information precisely because it can only act after new functional CSI has arisen Natural selection can favor new proteins and genes but only after they that natural selection lacks the ability to generate novel information precisely because it can act only after the fact that is after new functional CSI has already arisen Natural selection can favor new proteins and genes but only after they
Match 118 (1): Reference (011598 .. 011865, of 13533): Subject (007425 .. 007694, of 8267):
some function The job of generating new functional genes proteins and systems of proteins therefore falls entirely to random mutations Yet without functional criteria to guide a search through the space of possible sequences random variation is probabilistically doomed What is needed is not just a source of variation i e the freedom to search a space of possibilities or a mode of selection that can operate after the fact of a successful search but instead a means of selection that a operates during a search before success and that b is guided by information about or knowledge of a functional target Demonstration of this requirement has come from an unlikely quarter genetic algorithms Genetic algorithms are programs that allegedly simulate the creative power of mutation and selection Dawkins and Kuppers for example have developed computer programs that putatively simulate the production of genetic information by mutation and natural selection Dawkins 1986 47 49 Kuppers 1987 355 369 Nevertheless as shown elsewhere Meyer 1998 127 128 2003 247 248 these programs only succeed by the illicit expedient of providing the computer with a target sequence and then treating relatively greater proximity to future function i e the target sequence not actual present function as a selection criterion As Berlinski 2000 has argued genetic algorithms need something akin to a forward looking memory in order to succeed Yet such foresighted selection has no analogue in nature In biology where differential survival depends upon maintaining function selection cannot occur before new functional sequences arise Natural selection lacks foresight What natural selection lacks intelligent selection purposive or goal directed design provides some function The job of generating new functional genes proteins and systems of proteins therefore falls to entirely random mutations Yet without functional criteria to guide a search through the space of possible sequences random variation is probabilistically doomed What is needed is not just a source of variation i e the freedom to search a space of possibilities or a mode of selection that can operate after the fact of a successful search but instead a means of selection that a operates during a search before success and that b is guided by information about or knowledge of a functional target Demonstration of this requirement has come from an unlikely quarter genetic algorithms Genetic algorithms are programs that allegedly simulate the creative power of mutation and selection Richard Dawkins and Bernd Olaf Kuppers for example have developed computer programs that putatively simulate the production of genetic information by mutation and natural selection Dawkins 1986 47 9 Kuppers 1987 355 69 Nevertheless as I have shown elsewhere Meyer 1998b 127 8 these programs succeed only by the illicit expedient of providing the computer with a target sequence and then treating relatively greater proximity to future function i e the target sequence not actual present function as a selection criterion As David Berlinski 2000 has argued genetic algorithms need something akin to a forward looking memory in order to succeed Yet such foresighted selection has no analogue in nature In biology where differential survival depends upon maintaining function selection cannot occur before new functional sequencing arises Natural selection lacks foresight What natural selection lacks intelligent selection purposive or goaldirected design provides
Match 119 (1): Reference (011598 .. 011879, of 13533): Subject (007425 .. 007704, of 8267):
some function The job of generating new functional genes proteins and systems of proteins therefore falls entirely to random mutations Yet without functional criteria to guide a search through the space of possible sequences random variation is probabilistically doomed What is needed is not just a source of variation i e the freedom to search a space of possibilities or a mode of selection that can operate after the fact of a successful search but instead a means of selection that a operates during a search before success and that b is guided by information about or knowledge of a functional target Demonstration of this requirement has come from an unlikely quarter genetic algorithms Genetic algorithms are programs that allegedly simulate the creative power of mutation and selection Dawkins and Kuppers for example have developed computer programs that putatively simulate the production of genetic information by mutation and natural selection Dawkins 1986 47 49 Kuppers 1987 355 369 Nevertheless as shown elsewhere Meyer 1998 127 128 2003 247 248 these programs only succeed by the illicit expedient of providing the computer with a target sequence and then treating relatively greater proximity to future function i e the target sequence not actual present function as a selection criterion As Berlinski 2000 has argued genetic algorithms need something akin to a forward looking memory in order to succeed Yet such foresighted selection has no analogue in nature In biology where differential survival depends upon maintaining function selection cannot occur before new functional sequences arise Natural selection lacks foresight What natural selection lacks intelligent selection purposive or goal directed design provides Rational agents can arrange both matter and symbols with distant goals in mind In some function The job of generating new functional genes proteins and systems of proteins therefore falls to entirely random mutations Yet without functional criteria to guide a search through the space of possible sequences random variation is probabilistically doomed What is needed is not just a source of variation i e the freedom to search a space of possibilities or a mode of selection that can operate after the fact of a successful search but instead a means of selection that a operates during a search before success and that b is guided by information about or knowledge of a functional target Demonstration of this requirement has come from an unlikely quarter genetic algorithms Genetic algorithms are programs that allegedly simulate the creative power of mutation and selection Richard Dawkins and Bernd Olaf Kuppers for example have developed computer programs that putatively simulate the production of genetic information by mutation and natural selection Dawkins 1986 47 9 Kuppers 1987 355 69 Nevertheless as I have shown elsewhere Meyer 1998b 127 8 these programs succeed only by the illicit expedient of providing the computer with a target sequence and then treating relatively greater proximity to future function i e the target sequence not actual present function as a selection criterion As David Berlinski 2000 has argued genetic algorithms need something akin to a forward looking memory in order to succeed Yet such foresighted selection has no analogue in nature In biology where differential survival depends upon maintaining function selection cannot occur before new functional sequencing arises Natural selection lacks foresight What natural selection lacks intelligent selection purposive or goaldirected design provides Agents can arrange matter with distant goals in mind In
Match 120 (1): Reference (012037 .. 012073, of 13533): Subject (007724 .. 007759, of 8267):
Analysis of the problem of the origin of biological information therefore exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess Intelligent agents have foresight Analysis of the problem of the origin of biological information exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess Intelligent agents have foresight
Match 121 (1): Reference (012037 .. 012110, of 13533): Subject (007724 .. 007795, of 8267):
Analysis of the problem of the origin of biological information therefore exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess Intelligent agents have foresight Such agents can select functional goals before they exist They can devise or select material means to accomplish those ends from among an array of possibilities and then actualize those goals in accord with a preconceived design Analysis of the problem of the origin of biological information exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess Intelligent agents have foresight Agents can select functional goals before they exist They can devise or select material means to accomplish those ends from among an array of possibilities and then actualize those goals in accord with a preconceived design
Match 122 (1): Reference (012037 .. 012116, of 13533): Subject (007724 .. 007802, of 8267):
Analysis of the problem of the origin of biological information therefore exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess Intelligent agents have foresight Such agents can select functional goals before they exist They can devise or select material means to accomplish those ends from among an array of possibilities and then actualize those goals in accord with a preconceived design plan or set of functional requirements Analysis of the problem of the origin of biological information exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess Intelligent agents have foresight Agents can select functional goals before they exist They can devise or select material means to accomplish those ends from among an array of possibilities and then actualize those goals in accord with a preconceived design and or independent set of functional requirements
Match 123 (1): Reference (012128 .. 012179, of 13533): Subject (007803 .. 007853, of 8267):
The causal powers that natural selection lacks almost by definition are associated with the attributes of consciousness and rationality with purposive intelligence Thus by invoking design to explain the origin of new biological information contemporary design theorists are not positing an arbitrary explanatory element unmotivated by a consideration of the evidence Instead The causal powers that natural selection lacks almost by definition are associated with the attributes of consciousness and rationality with purposive intelligence Thus by invoking Intelligent Design to explain the origin of new information design theorists are not positing an arbitrary explanatory element unmotivated by a consideration of the evidence Instead
Match 124 (1): Reference (012186 .. 012205, of 13533): Subject (007861 .. 007880, of 8267):
precisely the attributes and causal powers that the phenomenon in question requires as a condition of its production and explanation precisely the attributes and causal powers that the phenomenon in question requires as a condition of its production and explanation
Match 125 (1): Reference (012230 .. 012242, of 13533): Subject (000441 .. 000452, of 8267):
the most causally adequate explanation for the origin of the complex specified information the best most causally adequate explanation for the origin of the information
Match 126 (1): Reference (012230 .. 012248, of 13533): Subject (008186 .. 008205, of 8267):
the most causally adequate explanation for the origin of the complex specified information required to build the Cambrian animals the best most causally adequate explanation for the origin of the complex specified information required to build the Cambrian animals
Match 127 (1): Reference (012275 .. 012284, of 13533): Subject (007726 .. 007738, of 8267):
the problem of the origination of biological form and the the problem of the origin of biological information exposes a deficiency in the
Match 128 (1): Reference (012612 .. 012621, of 13533): Subject (000278 .. 000286, of 8267):
the origin of the genetic information necessary to produce these the origin of the information necessary to produce the
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