Comparison of Meyer 2004b to Meyer et al. 2003

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Param k = 4
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Sun Sep 26 20:33:41 GMT 2004
There are 230 lines in meyer2004_html_nonref.txt
There are 2939 lines in bio_big_bang_raw.txt
There are 13533 words in meyer2004_html_nonref.txt
There are 28080 words in bio_big_bang_raw.txt
Match 1 (1): Reference (000209 .. 000219, of 13533): Subject (020356 .. 020366, of 28080):
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 (000556 .. 000590, of 13533): Subject (008821 .. 008856, of 28080):
the situation starting in the 1970s many biologists began questioning its neo Darwinism s adequacy in explaining evolution Genetics might be adequate for explaining microevolution but microevolutionary changes in gene frequency were not seen as Synthesis is a remarkable achievement However starting in the 1970s many biologists began questioning its adequacy in explaining evolution Genetics might be adequate for explaining microevolution but microevolutionary changes in gene frequency were not seen as
Match 3 (1): Reference (000591 .. 000623, of 13533): Subject (008904 .. 008937, of 28080):
able to turn a reptile into a mammal or to convert a fish into an amphibian Microevolution looks at adaptations that concern the survival of the fittest not the arrival of the fittest able to turn a reptile into a mammal or to convert a fish into an amphibian Microevolution looks at adaptations that concern only the survival of the fittest not the arrival of the fittest
Match 4 (1): Reference (000853 .. 000862, of 13533): Subject (020356 .. 020366, of 28080):
of the origin of biological form and information during the of the origin of biological information exposes a deficiency in the
Match 5 (1): Reference (000999 .. 001010, of 13533): Subject (000571 .. 000587, of 28080):
time at least nineteen and perhaps as many as thirty five phyla time During this event at least nineteen and as many as thirty five of forty total phyla
Match 6 (1): Reference (001112 .. 001140, of 13533): Subject (001005 .. 001035, of 28080):
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 To say that the fauna of the Cambrian period appeared in a geologically sudden manner also implies the absence of clear transitional intermediates connecting the complex Cambrian animals with those simpler
Match 7 (1): Reference (001789 .. 001823, of 13533): Subject (002957 .. 002991, of 28080):
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 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
Match 8 (1): Reference (001826 .. 001897, of 13533): Subject (002993 .. 003061, of 28080):
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 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
Match 9 (1): Reference (001911 .. 001920, of 13533): Subject (003086 .. 003097, of 28080):
bases Since each of the four bases has a roughly a linear array Since each of the four bases has a roughly
Match 10 (1): Reference (001911 .. 002032, of 13533): Subject (003086 .. 003210, of 28080):
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 Just as the meaning of a sentence depends upon the specific arrangement of the letters in 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 Just as the meaning of a sentence depends upon the specific arrangement of the letters in
Match 11 (1): Reference (001911 .. 002054, of 13533): Subject (003086 .. 003235, of 28080):
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 Just 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 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 Just 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 12 (1): Reference (002057 .. 002080, of 13533): Subject (003239 .. 003262, of 28080):
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 has meant necessary to function
Match 13 (1): Reference (002162 .. 002178, of 13533): Subject (003127 .. 003144, of 28080):
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 14 (1): Reference (002407 .. 002418, of 13533): Subject (003732 .. 003752, of 28080):
Cambrian explosion represents a remarkable jump in the specified complexity or complex Cambrian explosion represents a remarkable jump in the specified information or specified complexity of the biological world FIGURE 10 Biological Complexity
Match 15 (1): Reference (002413 .. 002425, of 13533): Subject (003281 .. 003291, of 28080):
in the specified complexity or complex specified information CSI of the biological world in the specified complexity or specified information of the biological world
Match 16 (1): Reference (002430 .. 002440, of 13533): Subject (002733 .. 002747, of 28080):
years the biological realm included little more than bacteria and algae s history the biological realm included little more than unicellular bacteria and blue green algae
Match 17 (1): Reference (002496 .. 002506, of 13533): Subject (002901 .. 002911, of 28080):
and then to a much greater extent the Cambrian explosion 530 and then to a much greater extent the Cambrian explosion 530
Match 18 (1): Reference (002503 .. 002514, of 13533): Subject (003713 .. 003723, of 28080):
the Cambrian explosion 530 mya represented steep climbs up the biological complexity the Cambrian explosion represents a steep climb up the biology complexity
Match 19 (1): Reference (002591 .. 002604, of 13533): Subject (003339 .. 003353, of 28080):
Functionally more complex animals require more cell types to perform their more diverse functions Functionally more complex animal forms require more cell types to perform their more diverse functions
Match 20 (1): Reference (002613 .. 002659, of 13533): Subject (003457 .. 003504, of 28080):
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 proteins in turn require new genetic information encoded in DNA 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
Match 21 (1): Reference (002659 .. 002674, of 13533): Subject (003520 .. 003535, of 28080):
between 318 and 562 kilobase pairs of DNA to produce the proteins necessary to maintain life between 318 and 562 kilobase pairs of DNA to produce the proteins necessary to maintain life
Match 22 (1): Reference (002677 .. 002698, of 13533): Subject (003537 .. 003558, of 28080):
More complex single cells might require upward of a million base pairs Yet to build the proteins necessary to sustain a complex More complex single cells might require upward of 1 million base pairs Yet to build the proteins necessary to sustain a complex
Match 23 (1): Reference (002713 .. 002724, of 13533): Subject (003571 .. 003581, of 28080):
genome size of a modern arthropod the fruitfly Drosophila melanogaster is approximately genome size of the fly Drosophila melanogaster an arthropod is approximately
Match 24 (1): Reference (002737 .. 002756, of 13533): Subject (003608 .. 003627, of 28080):
Transitions from a single cell to colonies of cells to complex animals represent significant and in principle measurable increases in transitions from a single cell to colonies of cells to complex animals represent significant and in principle measurable increases in
Match 25 (1): Reference (002936 .. 002958, of 13533): Subject (014998 .. 015022, of 28080):
Many scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins a number of scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins
Match 26 (1): Reference (002962 .. 002980, of 13533): Subject (015026 .. 015044, of 28080):
derives from consideration of the extreme improbability and specificity of functional genes and proteins A typical gene contains over derived from consideration of the extreme improbability and specificity of functional genes and proteins A typical gene contains over
Match 27 (1): Reference (002987 .. 002997, of 13533): Subject (015052 .. 015062, of 28080):
any specific arrangement of four nucleotide bases of length n there any specific arrangement of four nucleotide bases of length n there
Match 28 (1): Reference (002999 .. 003075, of 13533): Subject (015064 .. 015143, of 28080):
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 a corresponding number of 4n possible arrangements of bases For any protein there are 20n possible arrangements of protein forming amino acids A gene of 999 bases in length represents one of 4999 possible nucleotide sequences a protein of 333 amino acids 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
Match 29 (1): Reference (003093 .. 003157, of 13533): Subject (015154 .. 015218, of 28080):
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 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
Match 30 (1): Reference (003159 .. 003224, of 13533): Subject (015220 .. 015284, of 28080):
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 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 They have questioned therefore whether an undirected search via mutation selection would have a
Match 31 (1): Reference (003159 .. 003246, of 13533): Subject (015220 .. 015300, of 28080):
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 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 They have questioned therefore 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 available
Match 32 (1): Reference (003253 .. 003274, of 13533): Subject (015303 .. 015324, of 28080):
Some have also argued that alterations in sequencing would likely result in loss of protein function before fundamentally new function could arise Some have also argued that alterations in sequencing would likely result in loss of protein function before fundamentally new function could arise
Match 33 (1): Reference (003285 .. 003349, of 13533): Subject (015330 .. 015392, of 28080):
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 genes and proteins to functional loss as the 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
Match 34 (1): Reference (003287 .. 003297, of 13533): Subject (015532 .. 015546, of 28080):
proteins are sensitive to functional loss as a result of sequence proteins are highly sensitive to functional loss as a result of alterations in the sequencing
Match 35 (1): Reference (003361 .. 003381, of 13533): Subject (015394 .. 015414, of 28080):
Mutagenesis research tests the sensitivity of proteins and by implication DNA to functional loss as a result of alterations in sequencing Mutagenesis research tests the sensitivity of proteins and by implication DNA to functional loss as a result of alterations in sequencing
Match 36 (1): Reference (003452 .. 003461, of 13533): Subject (015496 .. 015506, of 28080):
multiple as opposed to single position amino acid substitutions inevitably multiple as opposed to single amino acid substitutions generally result in
Match 37 (1): Reference (003462 .. 003529, of 13533): Subject (015505 .. 015575, of 28080):
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 result in rapid loss of protein function even when these changes occur at sites that allow variation when altered in isolation 93 Cumulatively these constraints imply that proteins are highly sensitive to functional loss as a result of alterations in the 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 38 (1): Reference (003566 .. 003578, of 13533): Subject (015583 .. 015595, of 28080):
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 39 (1): Reference (003591 .. 003777, of 13533): Subject (015603 .. 015790, of 28080):
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 natural selection acting to preserve small advantageous variations in genetic sequences and their corresponding protein products Richard Dawkins for example likens an organism to a high mountain peak 95 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 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 present a diffi culty not only for the chance origin of specified biological information that is 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
Match 40 (1): Reference (003790 .. 003862, of 13533): Subject (015799 .. 015872, of 28080):
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 Darwinists either new functional genes arise from noncoding sections in the genome or functional genes arise 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
Match 41 (1): Reference (003794 .. 003956, of 13533): Subject (015800 .. 015968, of 28080):
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 either new functional genes arise from noncoding sections in the genome or functional genes arise 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 in 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 of the
Match 42 (1): Reference (003964 .. 004022, of 13533): Subject (015963 .. 016017, of 28080):
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 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 rare functional sequences within
Match 43 (1): Reference (004025 .. 004043, of 13533): Subject (016020 .. 016038, of 28080):
of combinatorial possibilities Yet the probability of randomly assembling or finding in the previous sense a functional sequence is of combinatorial possibilities Yet the probability of randomly assembling or finding in the previous sense a functional sequence is
Match 44 (1): Reference (004054 .. 004077, of 13533): Subject (016051 .. 016078, of 28080):
suggest that the probability of attaining at random the correct sequencing for a short protein 100 amino acids long is about 1 in 1065 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 chance in 1065
Match 45 (1): Reference (004207 .. 004217, of 13533): Subject (015119 .. 015130, of 28080):
to b the whole set of possible amino acids sequences of to be rare among the set of possible amino acid sequences of
Match 46 (1): Reference (004239 .. 004248, of 13533): Subject (015115 .. 015131, of 28080):
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 47 (1): Reference (004259 .. 004318, of 13533): Subject (016099 .. 016158, of 28080):
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 has noted that Cambrian animals would have required complex proteins such as lysyl oxidase in order to support their stout body structures 98 Lysyl oxidase molecules in extant organisms comprise over 400 amino acids These molecules
Match 48 (1): Reference (004327 .. 004352, of 13533): Subject (016165 .. 016193, of 28080):
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 49 (1): Reference (004450 .. 004479, of 13533): Subject (016263 .. 016292, of 28080):
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 slow to generate the novel genes and proteins necessary to building the Cambrian animals given the duration of the explosion As Ohno has
Match 50 (1): Reference (004544 .. 004561, of 13533): Subject (016388 .. 016405, of 28080):
The selection mutation mechanism faces another probabilistic obstacle The animals that arise in the Cambrian exhibit structures that The mutation selection mechanism faces another probabilistic obstacle The animals that arise in the Cambrian exhibit structures that
Match 51 (1): Reference (004565 .. 004721, of 13533): Subject (016407 .. 016559, of 28080):
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 many new types of cells each of which would require many 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 52 (1): Reference (004729 .. 004738, of 13533): Subject (014642 .. 014649, of 28080):
the chance origin of the genetic information necessary to build the origin of the information necessary to build
Match 53 (1): Reference (004790 .. 004866, of 13533): Subject (016583 .. 016661, of 28080):
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 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 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 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 these factors suggest that the
Match 54 (1): Reference (004870 .. 004881, of 13533): Subject (014544 .. 014554, of 28080):
implausibility of any scenario for the origination of Cambrian genetic information that s previous discussion of the origin of genetic information in a
Match 55 (1): Reference (004887 .. 004949, of 13533): Subject (016684 .. 016747, of 28080):
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 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 56 (1): Reference (004951 .. 004984, of 13533): Subject (016749 .. 016783, of 28080):
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 which there is no gradually sloping backside a situation that by Dawkins s own logic is probabilistically untenable In the second scenario neo Darwinists envision novel genes and proteins arising by numerous successive mutations in
Match 57 (1): Reference (004986 .. 005019, of 13533): Subject (016785 .. 016819, of 28080):
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 preexisting genetic text that codes for proteins To adapt Dawkins s metaphor slightly this scenario envisions gradually climbing down one functional peak and then ascending another Yet mutagenesis experiments again suggest a difficulty Recent experiments
Match 58 (1): Reference (005020 .. 005048, of 13533): Subject (016827 .. 016853, of 28080):
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 show that even when exploring a region of sequence space populated by proteins of a single function most multiple position changes quickly lead to loss of function
Match 59 (1): Reference (005051 .. 005065, of 13533): Subject (016855 .. 016867, of 28080):
Yet to turn one protein into another with a completely novel structure and function requires Yet to turn one protein into another with a completely novel function requires
Match 60 (1): Reference (005132 .. 005161, of 13533): Subject (016878 .. 016908, of 28080):
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 Blanco 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 Francisco Blanco
Match 61 (1): Reference (005247 .. 005279, of 13533): Subject (017014 .. 017046, of 28080):
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 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
Match 62 (1): Reference (005300 .. 005348, of 13533): Subject (017068 .. 017118, of 28080):
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 sequences would thus 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 still less will it favor sequences that efface or destroy preexisting function Evolving genes and proteins
Match 63 (1): Reference (005350 .. 005371, of 13533): Subject (017120 .. 017141, of 28080):
range through a series of nonfunctional intermediate sequences that natural selection will not favor or preserve but will in all probability eliminate range through a series of nonfunctional intermediate sequences that natural selection will not favor or preserve but will in all probability eliminate
Match 64 (1): Reference (005378 .. 005407, of 13533): Subject (017143 .. 017173, of 28080):
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 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 already seen such a process
Match 65 (1): Reference (005413 .. 005543, of 13533): Subject (017183 .. 017317, of 28080):
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 even granting a cosmic time scale 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 to prevent deleterious or lethal consequences to the organism and to allow for the possibility of further evolution Yet the complexity and functional speci ficity of proteins imply that both these conditions will be extremely diffi cult to meet Therefore the neo Darwinian mechanism appears inadequate to generate the new information present in the novel genes and proteins that arise with the Cambrian animals
Match 66 (1): Reference (005560 .. 005595, of 13533): Subject (017335 .. 017370, of 28080):
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 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
Match 67 (1): Reference (005597 .. 005615, of 13533): Subject (017443 .. 017461, of 28080):
understanding of how body plans are built during ontogeny In the process it has also uncovered a profound difficulty understanding of how body plans are built during ontogeny In the process it has also uncovered a profound difficulty
Match 68 (1): Reference (005621 .. 005655, of 13533): Subject (017472 .. 017510, of 28080):
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 changes in the form of organisms requires attention to timing Mutations in genetic material 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
Match 69 (1): Reference (005662 .. 005681, of 13533): Subject (017520 .. 017539, of 28080):
Thus events expressed early in the development of organisms have the only realistic chance of producing large scale macroevolutionary change Thus events expressed early in the development of organisms have the only realistic chance of producing large scale macroevolutionary change
Match 70 (1): Reference (005702 .. 005718, of 13533): Subject (017555 .. 017571, of 28080):
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 71 (1): Reference (005723 .. 005754, of 13533): Subject (017588 .. 017620, of 28080):
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 For example when early acting body plan molecules or morphogens such as bicoid which helps set up the anterior posterior head to tail axis in the fly Drosophila are perturbed development shuts down
Match 72 (1): Reference (005766 .. 005837, of 13533): Subject (017622 .. 017693, of 28080):
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 For this reason 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 so tightly integrated spatially and temporally that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream For this reason
Match 73 (1): Reference (005874 .. 005887, of 13533): Subject (017856 .. 017871, of 28080):
This problem has led to what McDonald 1983 has called a great Darwinian paradox This problem has led to what geneticist John F McDonald has called a great Darwinian paradox
Match 74 (1): Reference (005914 .. 005924, of 13533): Subject (017895 .. 017905, of 28080):
major changes the very stuff of macroevolution apparently do not vary major changes the very stuff of macroevolution apparently do not vary
Match 75 (1): Reference (005934 .. 005948, of 13533): Subject (017990 .. 018004, of 28080):
doesn t need namely viable genetic mutations in DNA expressed late in development do occur doesn t need namely viable genetic mutations in DNA expressed late in development do occur
Match 76 (1): Reference (005993 .. 006006, of 13533): Subject (018031 .. 018041, of 28080):
that the kind of variations required by neo Darwinism namely favorable body plan mutations that the kind of variations required by neo Darwinism favorable mutations
Match 77 (1): Reference (006008 .. 006034, of 13533): Subject (018049 .. 018078, of 28080):
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 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 suggesting that mutations in
Match 78 (1): Reference (006043 .. 006062, of 13533): Subject (018075 .. 018095, of 28080):
suggesting that mutations in DNA alone cannot account for the morphological changes required to build a new body plan DNA suggesting that mutations in DNA alone cannot account for the morphological changes required to build a new body plan 112 DNA
Match 79 (1): Reference (006043 .. 006084, of 13533): Subject (018075 .. 018114, of 28080):
suggesting that mutations in DNA alone cannot account for the morphological changes required to build a new body plan DNA helps direct protein synthesis 7 It also helps to regulate the timing and expression of the synthesis of various proteins within cells suggesting that mutations in DNA alone cannot account for the morphological changes required to build a new body plan 112 DNA directs protein synthesis It also helps regulate the timing and expression of the synthesis of various proteins within cells
Match 80 (1): Reference (006086 .. 006104, of 13533): Subject (018116 .. 018134, of 28080):
DNA alone does not determine how individual proteins assemble themselves into larger systems of proteins still less does it DNA alone does not determine how individual proteins assemble themselves into larger systems of proteins still less does it
Match 81 (1): Reference (006106 .. 006118, of 13533): Subject (018136 .. 018148, of 28080):
determine how cell types tissue types and organs arrange themselves into body plans determine how cell types tissue types and organs arrange themselves into body plans
Match 82 (1): Reference (006124 .. 006140, of 13533): Subject (018150 .. 018164, of 28080):
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 83 (1): Reference (006149 .. 006161, of 13533): Subject (018165 .. 018181, of 28080):
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 84 (1): Reference (006163 .. 006202, of 13533): Subject (018183 .. 018224, of 28080):
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 distribute the essential proteins used during development to their correct location in the cell 114 Of course microtubules themselves are made of many protein subunits Nevertheless
Match 85 (1): Reference (006216 .. 006226, of 13533): Subject (018223 .. 018237, of 28080):
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 86 (1): Reference (006232 .. 006254, of 13533): Subject (018240 .. 018264, of 28080):
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 87 (1): Reference (006319 .. 006386, of 13533): Subject (018301 .. 018368, of 28080):
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 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 88 (1): Reference (006388 .. 006475, of 13533): Subject (018370 .. 018455, of 28080):
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 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 organs Yet clearly the properties of individual proteins or indeed the lower level parts in the hierarchy generally do not determine the organization of the higher level structures and organizational patterns
Match 89 (1): Reference (006479 .. 006523, of 13533): Subject (018457 .. 018501, of 28080):
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 It follows therefore that the genetic information that codes for proteins does not determine these higherlevel 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
Match 90 (1): Reference (006479 .. 006573, of 13533): Subject (018457 .. 018549, of 28080):
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 It follows therefore that the genetic information that codes for proteins does not determine these higherlevel 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 the 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 that DNA alone does not determine
Match 91 (1): Reference (006576 .. 006632, of 13533): Subject (018551 .. 018607, of 28080):
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 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
Match 92 (1): Reference (007139 .. 007157, of 13533): Subject (018617 .. 018636, of 28080):
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 evolutionary model for explaining the origin of novel biological form in an
Match 93 (1): Reference (007175 .. 007317, of 13533): Subject (018650 .. 018787, of 28080):
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 with 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 to account for the emergence of 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 illustrates how this might work with 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 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 connected buttons and strings reaches a critical threshold new modes of organization can arise in the system for free that is
Match 94 (1): Reference (007330 .. 007352, of 13533): Subject (018905 .. 018927, of 28080):
Another model that Kauffman develops is a system of interconnected lights Each light can flash in a variety of states on off twinkling Another model that Kauffman develops is a system of interconnected lights Each light can flash in a variety of states on off twinkling
Match 95 (1): Reference (007354 .. 007429, of 13533): Subject (018931 .. 019010, of 28080):
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 there is more than one possible state for each light and many lights there are a vast number of possible states that the system as a whole can adopt Further in his system rules determine how past states will in fluence future states Kauffman asserts that as a result of these rules the system will soon if properly tuned produce a kind of order in which a few basic patterns of light activity recur with greater than random frequency
Match 96 (1): Reference (007431 .. 007454, of 13533): Subject (019014 .. 019037, of 28080):
these actual patterns of light activity represent a small portion of the total number of possible states in which the system can reside Kauffman these actual patterns of light activity represent a small portion of the total number of possible states in which the system can reside Kauffman
Match 97 (1): Reference (007458 .. 007534, of 13533): Subject (019039 .. 019114, of 28080):
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 that self organizational laws might similarly find 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 s 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
Match 98 (1): Reference (007536 .. 007567, of 13533): Subject (019116 .. 019149, of 28080):
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 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 explanation in the history
Match 99 (1): Reference (007570 .. 007587, of 13533): Subject (019147 .. 019163, of 28080):
in the history of life Similarly in his light system the order that allegedly arises for for free in the history of life Similarly in his light system the order that allegedly arises for free
Match 100 (1): Reference (007588 .. 007616, of 13533): Subject (019174 .. 019201, of 28080):
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 actually arises only if the programmer of the model system tunes it in such a way as to keep it from either generating an excessively rigid order or
Match 101 (1): Reference (007628 .. 007687, of 13533): Subject (019214 .. 019272, of 28080):
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 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 preprogrammed rules may well settle into a small number of patterns within a much larger space of possibilities But
Match 102 (1): Reference (007689 .. 007749, of 13533): Subject (019274 .. 019333, of 28080):
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 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 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
Match 103 (1): Reference (007754 .. 007785, of 13533): Subject (019335 .. 019366, of 28080):
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 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
Match 104 (1): Reference (007795 .. 007807, of 13533): Subject (019375 .. 019390, of 28080):
would model a biologically relevant self organizational process at least if such a would model a biologically relevant self organizational process at least if the system produced such messages
Match 105 (1): Reference (007826 .. 007845, of 13533): Subject (019401 .. 019420, of 28080):
In any case Kauffman s systems do not produce specified complexity and thus do not offer promising models for explaining In any case Kauffman s systems do not produce specified complexity and thus do not offer promising models for explaining
Match 106 (1): Reference (007856 .. 007934, of 13533): Subject (019450 .. 019527, of 28080):
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 Even so Kauffman suggests that his self organizational models can specifi cally 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 120 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 107 (1): Reference (007940 .. 007979, of 13533): Subject (019530 .. 019568, of 28080):
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 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
Match 108 (1): Reference (007981 .. 007990, of 13533): Subject (019570 .. 019579, of 28080):
of lower taxa representing variations within those original body designs of lower taxa representing variations within those original body designs
Match 109 (1): Reference (008001 .. 008024, of 13533): Subject (019580 .. 019603, of 28080):
Further as Kauffman expects body plans appear suddenly and persist without significant modification over time But here again Kauffman begs the most important question Further as Kauffman expects body plans appear suddenly and persist without significant modification over time But here again Kauffman begs the most important question
Match 110 (1): Reference (008028 .. 008165, of 13533): Subject (019605 .. 019738, of 28080):
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 these are the only kind of mutations 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 produced the new Cambrian body plans in the first place Granted he invokes long jump mutations to explain this but he identifies no specific selforganizational 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 these are the only kind of mutations 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 to provide a selforganizational account of the new Cambrian body plans Clearly his model is not sufficient
Match 111 (1): Reference (008201 .. 008210, of 13533): Subject (021759 .. 021772, of 28080):
pattern of sudden appearance and stasis in the fossil record pattern of appearance and morphological isolation that is evident in the Cambrian fossil record
Match 112 (1): Reference (008258 .. 008281, of 13533): Subject (005296 .. 005321, of 28080):
According to punctuationalists natural selection functions more as a mechanism for selecting the fittest species rather than the most fit individual among a species According to many punctuationalists natural selection functions more as a mechanism for selecting the most fit species rather than the most fit individual among a species
Match 113 (1): Reference (008286 .. 008296, of 13533): Subject (005323 .. 005333, of 28080):
morphological change should occur in larger more discrete intervals than it morphological change should occur in larger more discrete intervals than traditional
Match 114 (1): Reference (008344 .. 008405, of 13533): Subject (005656 .. 005718, of 28080):
noted that the proposed mechanism of punctuated evolutionary change simply lacked the raw material upon which to work As Valentine and Erwin 1987 note the fossil record fails to document a large pool of species prior to the Cambrian Yet the proposed mechanism of species selection requires just such a pool of species upon which to act Thus they conclude that the note that the proposed mechanism of punctuated evolutionary change simply would have lacked the raw material upon which to work As Valentine and Erwin note the fossil record fails to document a large pool of species prior to the Cambrian Yet the proposed mechanism of species selection requires just such a pool of species upon which to act Thus they conclude that the
Match 115 (1): Reference (008344 .. 008410, of 13533): Subject (005656 .. 005724, of 28080):
noted that the proposed mechanism of punctuated evolutionary change simply lacked the raw material upon which to work As Valentine and Erwin 1987 note the fossil record fails to document a large pool of species prior to the Cambrian Yet the proposed mechanism of species selection requires just such a pool of species upon which to act Thus they conclude that the mechanism of species selection probably note that the proposed mechanism of punctuated evolutionary change simply would have lacked the raw material upon which to work As Valentine and Erwin note the fossil record fails to document a large pool of species prior to the Cambrian Yet the proposed mechanism of species selection requires just such a pool of species upon which to act Thus they conclude that the probability that species selection is a
Match 116 (1): Reference (009161 .. 009171, of 13533): Subject (020354 .. 020366, of 28080):
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 117 (1): Reference (009319 .. 009332, of 13533): Subject (000491 .. 000502, of 28080):
candidates for explaining the origination of biological form or the information necessary to produce can account for the origin of the biological information necessary to produce
Match 118 (1): Reference (009344 .. 009353, of 13533): Subject (020346 .. 020363, of 28080):
approach to the problem of the origin of form specifically a vast space of combinatorial possibilities Analysis of the problem of the origin of biological information exposes a
Match 119 (1): Reference (009997 .. 010007, of 13533): Subject (000227 .. 000239, of 28080):
design as an explanation for the origin of the biological information design hypothesis from consideration as an explanation for the origin of biological form
Match 120 (1): Reference (010001 .. 010011, of 13533): Subject (000493 .. 000503, of 28080):
for the origin of the biological information necessary to produce the for the origin of the biological information necessary to produce the
Match 121 (1): Reference (010175 .. 010187, of 13533): Subject (000037 .. 000048, of 28080):
and Lewontin 1978 have long acknowledged that organisms appear to have been designed and Richard Lewontin acknowledge that biological organisms appear to have been designed
Match 122 (1): Reference (010193 .. 010207, of 13533): Subject (000061 .. 000074, of 28080):
that what Ayala 1994 5 calls the obvious design of living things is only apparent that what Francisco Ayala calls the obvious design of living things is only apparent
Match 123 (1): Reference (010740 .. 010764, of 13533): Subject (014093 .. 014117, of 28080):
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 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
Match 124 (1): Reference (010776 .. 010801, of 13533): Subject (014119 .. 014142, of 28080):
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 Historical scientists in particular assess competing hypotheses by evaluating which hypothesis would if true provide the best explanation for some set of relevant data
Match 125 (1): Reference (010813 .. 010828, of 13533): Subject (014143 .. 014158, of 28080):
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 126 (1): Reference (010831 .. 010884, of 13533): Subject (014160 .. 014215, of 28080):
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 used this method of reasoning in defending his theory of universal common descent 85 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 the competing explanatory entities
Match 127 (1): Reference (010977 .. 010986, of 13533): Subject (000227 .. 000239, of 28080):
design as an explanation for the origin of biological form design hypothesis from consideration as an explanation for the origin of biological form
Match 128 (1): Reference (010977 .. 010988, of 13533): Subject (014620 .. 014631, of 28080):
design as an explanation for the origin of biological form and information design is sufficient as a causal explanation for the origin of information
Match 129 (1): Reference (011068 .. 011080, of 13533): Subject (019810 .. 019830, of 28080):
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 we know that intelligent human agents
Match 130 (1): Reference (011091 .. 011103, of 13533): Subject (019794 .. 019810, of 28080):
power to produce information in the form of linear sequence specific arrangements of powers sufficient to produce such increases in information either in the form of sequence specific lines of
Match 131 (1): Reference (011099 .. 011120, of 13533): Subject (019836 .. 019859, of 28080):
linear sequence specific arrangements of characters Indeed experience affirms that information of this type routinely arises from the activity of intelligent agents linear sequence specific arrangements of characters Indeed experience affirms that specified complex information of this type routinely arises from the activity of intelligent agents
Match 132 (1): Reference (011134 .. 011146, of 13533): Subject (019887 .. 019898, of 28080):
source invariably comes to a mind that of a software engineer or programmer source invariably we come to a mind to that of a programmer
Match 133 (1): Reference (011171 .. 011201, of 13533): Subject (019917 .. 019949, of 28080):
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 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 that is from a mind or personal agent
Match 134 (1): Reference (011203 .. 011217, of 13533): Subject (014501 .. 014512, of 28080):
Quastler 1964 put it the creation of new information is habitually associated with conscious activity Quastler the creation of new information is habitually associated with conscious activity
Match 135 (1): Reference (011226 .. 011237, of 13533): Subject (020510 .. 020521, of 28080):
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 136 (1): Reference (011258 .. 011344, of 13533): Subject (020524 .. 020613, of 28080):
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 proteins and systems of proteins new 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 subsystems that comprise them
Match 137 (1): Reference (011258 .. 011352, of 13533): Subject (020524 .. 020616, of 28080):
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 Yet we know based on our present experience 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 proteins and systems of proteins new 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 subsystems that comprise them Based on experience
Match 138 (1): Reference (011374 .. 011416, of 13533): Subject (020641 .. 020688, of 28080):
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 in which both individual modules and also the hierarchical arrangements of those modules exhibit complexity and functional 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 and connection within an integrated circuit
Match 139 (1): Reference (011420 .. 011434, of 13533): Subject (020686 .. 020704, of 28080):
and reflects further design Conscious and rational agents have as part of their powers of an integrated circuit reflects further design Conscious and rational human agents have as a consequence of their powers of
Match 140 (1): Reference (011471 .. 011484, of 13533): Subject (020728 .. 020747, of 28080):
we have good reason to doubt that mutation and selection self organizational processes or we have good reasons to doubt that either the mutation selection mechanism or self organizational processes can produce such information
Match 141 (1): Reference (011524 .. 011533, of 13533): Subject (000227 .. 000239, of 28080):
design as an explanation for the origin of biological form design hypothesis from consideration as an explanation for the origin of biological form
Match 142 (1): Reference (011524 .. 011535, of 13533): Subject (014620 .. 014631, of 28080):
design as an explanation for the origin of biological form and information design is sufficient as a causal explanation for the origin of information
Match 143 (1): Reference (011537 .. 011553, of 13533): Subject (019990 .. 020006, of 28080):
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 144 (1): Reference (011559 .. 011575, of 13533): Subject (020014 .. 020027, of 28080):
previous analysis we saw that natural selection lacked the ability to generate novel information precisely because it previous analysis natural selection lacked the ability to generate novel information precisely because it
Match 145 (1): Reference (011584 .. 011596, of 13533): Subject (020039 .. 020051, of 28080):
arisen Natural selection can favor new proteins and genes but only after they arisen Natural selection can favor new proteins and genes but only after they
Match 146 (1): Reference (011598 .. 011611, of 13533): Subject (020053 .. 020066, of 28080):
some function The job of generating new functional genes proteins and systems of proteins some function The job of generating new functional genes proteins and systems of proteins
Match 147 (1): Reference (011614 .. 011689, of 13533): Subject (020070 .. 020143, of 28080):
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 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 that is 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 b is
Match 148 (1): Reference (011693 .. 011747, of 13533): Subject (020142 .. 020201, of 28080):
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 b is informed by 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
Match 149 (1): Reference (011767 .. 011859, of 13533): Subject (020220 .. 020314, of 28080):
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 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 that is the target sequence not actual present function as a selection criterion 123 As David Berlinski has argued genetic algorithms need something akin to a forward looking memory in order to succeed 124 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
Match 150 (1): Reference (011864 .. 011879, of 13533): Subject (020317 .. 020328, of 28080):
design provides Rational agents can arrange both matter and symbols with distant goals in mind In design provides Agents can arrange matter with distant goals in mind In
Match 151 (1): Reference (012037 .. 012069, of 13533): Subject (020352 .. 020383, of 28080):
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 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
Match 152 (1): Reference (012037 .. 012073, of 13533): Subject (020352 .. 020387, of 28080):
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 Agents do have foresight
Match 153 (1): Reference (012037 .. 012090, of 13533): Subject (020352 .. 020404, of 28080):
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 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 Agents do have foresight Agents can also select functional goals before they exist They can devise or select material means to
Match 154 (1): Reference (012100 .. 012110, of 13533): Subject (020416 .. 020426, of 28080):
and then actualize those goals in accord with a preconceived design and then actualize those goals in accord with a preconceived design
Match 155 (1): Reference (012128 .. 012184, of 13533): Subject (020433 .. 020487, of 28080):
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 they are positing an entity The causal powers that natural selection lacks almost by definition are associated with the attributes of consciousness rationality and 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 they are positing an entity
Match 156 (1): Reference (012186 .. 012205, of 13533): Subject (020489 .. 020508, of 28080):
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 157 (1): Reference (012230 .. 012239, of 13533): Subject (020822 .. 020832, of 28080):
the most causally adequate explanation for the origin of the the best most causally adequate explanation for the origin of the
Match 158 (1): Reference (012275 .. 012284, of 13533): Subject (020354 .. 020366, of 28080):
the problem of the origination of biological form and the the problem of the origin of biological information exposes a deficiency in the
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