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Where Do Complex Organisms Come From?

Godexists

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Where Do Complex Organisms Come From?

Where Do Complex Organisms Come From?

Meyer, Darwins doubt, page 212:

According to neo-Darwinism, new information, form, and structure arise from natural selection acting on random mutations arising at a very low level within the biological hierarchy—within the genetic text. Yet both body-plan formation during embryological development and major morphological innovation during the history of life depend upon a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. If DNA isn’t wholly responsible for the way an embryo develops— for body-plan morphogenesis—then DNA sequences can mutate indefinitely and still not produce a new body plan, regardless of the amount of time and the number of mutational trials available to the evolutionary process. Genetic mutations are simply the wrong tool for the job at hand.

Even in a best-case scenario—one that ignores the immense improbability of generating new genes by mutation and selection—mutations in DNA sequence would merely produce new genetic information. But building a new body plan requires more than just genetic information. It requires both genetic and epigenetic information—information by definition that is not stored in DNA and thus cannot be generated by mutations to the DNA. It follows that the mechanism of natural selection acting on random mutations in DNA cannot by itself generate novel body plans, such as those that first arose in the Cambrian explosion.

Cell and body shape, and organism development depends on following :

Membrane targets and patterns
Cytoskeletal arrays

Centrosomes
Ion channels, and
Sugar molecules on the exterior of cells (the sugar code)

Gene regulatory networks

Various codes and the encoded epigenetic information is required:

The Genetic Code
The Splicing Codes
The Metabolic Code
The Signal Transduction Codes
The Signal Integration Codes
The Histone Code
The Tubulin Code
The Sugar Code
The Glycomic Code

" Junk DNA "

MicroRNAs--"Once Dismissed as Junk"--Confirmed To Have Important Gene Regulatory Function

In 2008 Scientific American noted that microRNAs were "once dismissed as junk" and said the following:
Tiny snippets of the genome known as microRNA were long thought to be genomic refuse because they were transcribed from so-called "junk DNA," sections of the genome that do not carry information for making proteins responsible for various cellular functions. Evidence has been building since 1993, however, that microRNA is anything but genetic bric-a-brac. Quite the contrary, scientists say that it actually plays a crucial role in switching protein-coding genes on or off and regulating the amount of protein those genes produce.
 

Jimmy D

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A few questions.....

When discussing biology why do you accept the word of someone who studied geology and history of science, over a biologist?

Where do complex organisms come from? I see no answer to the question you posed, just nitpicking.

All I can see is complaining that we haven't discovered every possible specific detail in the field of genetics, what does that do to further the case of ID?

Has Meyer done any actual research to further his 'ideas'?
 
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Godexists

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A few questions.....

When discussing biology why do you accept the word of someone who studied geology and history of science, over a biologist?

Where do complex organisms come from? I see no answer to the question you posed, just nitpicking.

All I can see is complaining that we haven't discovered every possible specific detail in the field of genetics, what does that do to further the case of ID?

Has Meyer done any actual research to further his 'ideas'?

The op are not Meyers " ideas ". They are the result of scientific studies, like following :

Integrins and ion channels in cell migration: implications for neuronal development, wound healing and metastatic spread.
Integrins and ion channels in cell migration: implications for neuronal development, wound healing and metastatic spread. - PubMed - NCBI

Morphogenetic fields in embryogenesis, regeneration, and cancer: Non-local control of complex patterning
Morphogenetic fields in embryogenesis, regeneration, and cancer: Non-local control of complex patterning

Principles of planar polarity in animal development
http://dev.biologists.org/content/138/10/1877

Morphogenetic Systems as cognitive agents
Tufts University: The Levin Lab, Department of Biology: Research

Research on the Dynamics of Information Processing in Biological Structures
Tufts University: The Levin Lab, Department of Biology: Research

Molecular pathways regulating mitotic spindle orientation in animal cells
http://dev.biologists.org/content/140/9/1843

Evolutionary bioscience as regulatory systems biology
Evolutionary bioscience as regulatory systems biology

Global Control Regions and Regulatory Landscapes in Vertebrate Development and Evolution
http://bejerano.stanford.edu/readings/public/80_Function_GCRs.pdf

CONTROL OF TRANSCRIPTION BY SEQUENCESPECIFIC DNA-BINDING PROTEINS
http://www.garlandscience.com/res/pdf/9780815341291_ch08.pdf

The transcription factor code: defining the role of a developmental transcription factor in the adult brain.
For the human brain to develop and function correctly, each of its 100 billion neurons must follow a specific and pre-programmed code of gene expression. This code is driven by key transcription factors that regulate the expression of numerous proteins, moulding the neurons identity to create its unique shape and electrical behaviour.
The transcription factor code: defining the role of a developmental transcription factor in the adult brain. at University of Otago on FindAPhD.com

Unraveling a novel transcription factor code determining the human arterial-specific endothelial cell signature
Our pioneering profiling study on freshly isolated ECs unveiled a combinatorial transcriptional code that induced an arterial fingerprint more proficiently than the current gold standard, HEY2, and this codeconveyed an in vivo arterial-like behavior upon venous ECs.
http://www.bloodjournal.org/content/122/24/3982?sso-checked=true

The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding.
The term 'transcriptional regulatory code' has been used to describe the interplay of these events in the complex control of transcription. With the maturation of methods for detecting in vivo protein-DNA interactions on a genome-wide scale, detailed maps of chromatin features and transcription factor localization over entire genomes of eukaryotic cells are enriching our understanding of the properties and nature of this transcriptional regulatory code.
http://www.ncbi.nlm.nih.gov/pubmed/16647254

The Splicing code
rigin and evolution of spliceosomal introns
http://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-7-11

The rna binding protein binding code
A compendium of RNA-binding motifs for decoding gene regulation
http://www.nature.com/nature/journal/v499/n7457/full/nature12311.html

microRNA binding code
The code within the code: microRNAs target coding regions
http://www.ncbi.nlm.nih.gov/pubmed/20372064

The Glycan or Sugar Code
Biological information transfer beyond the genetic code: the sugar code
http://www.ncbi.nlm.nih.gov/pubmed/10798195

Epigenetic Regulation by Heritable RNA
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990477/
 
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Jimmy D

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The op are not Meyers " ideas ". They are the result of scientific studies, like following :

Integrins and ion channels in cell migration: implications for neuronal development, wound healing and metastatic spread.
Integrins and ion channels in cell migration: implications for neuronal development, wound healing and metastatic spread. - PubMed - NCBI

Morphogenetic fields in embryogenesis, regeneration, and cancer: Non-local control of complex patterning
Morphogenetic fields in embryogenesis, regeneration, and cancer: Non-local control of complex patterning

Principles of planar polarity in animal development
http://dev.biologists.org/content/138/10/1877

Morphogenetic Systems as cognitive agents
Tufts University: The Levin Lab, Department of Biology: Research

Research on the Dynamics of Information Processing in Biological Structures
Tufts University: The Levin Lab, Department of Biology: Research

Molecular pathways regulating mitotic spindle orientation in animal cells
http://dev.biologists.org/content/140/9/1843

Evolutionary bioscience as regulatory systems biology
Evolutionary bioscience as regulatory systems biology

Global Control Regions and Regulatory Landscapes in Vertebrate Development and Evolution
http://bejerano.stanford.edu/readings/public/80_Function_GCRs.pdf

CONTROL OF TRANSCRIPTION BY SEQUENCESPECIFIC DNA-BINDING PROTEINS
http://www.garlandscience.com/res/pdf/9780815341291_ch08.pdf

The transcription factor code: defining the role of a developmental transcription factor in the adult brain.
For the human brain to develop and function correctly, each of its 100 billion neurons must follow a specific and pre-programmed code of gene expression. This code is driven by key transcription factors that regulate the expression of numerous proteins, moulding the neurons identity to create its unique shape and electrical behaviour.
The transcription factor code: defining the role of a developmental transcription factor in the adult brain. at University of Otago on FindAPhD.com

Unraveling a novel transcription factor code determining the human arterial-specific endothelial cell signature
Our pioneering profiling study on freshly isolated ECs unveiled a combinatorial transcriptional code that induced an arterial fingerprint more proficiently than the current gold standard, HEY2, and this codeconveyed an in vivo arterial-like behavior upon venous ECs.
Unraveling a novel transcription factor code determining the human arterial-specific endothelial cell signature | Blood Journal

The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding.
The term 'transcriptional regulatory code' has been used to describe the interplay of these events in the complex control of transcription. With the maturation of methods for detecting in vivo protein-DNA interactions on a genome-wide scale, detailed maps of chromatin features and transcription factor localization over entire genomes of eukaryotic cells are enriching our understanding of the properties and nature of this transcriptional regulatory code.
The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor bind... - PubMed - NCBI

The Splicing code
rigin and evolution of spliceosomal introns
Origin and evolution of spliceosomal introns | Biology Direct | Full Text

The rna binding protein binding code
A compendium of RNA-binding motifs for decoding gene regulation
http://www.nature.com/nature/journal/v499/n7457/full/nature12311.html

microRNA binding code
The code within the code: microRNAs target coding regions
http://www.ncbi.nlm.nih.gov/pubmed/20372064

The Glycan or Sugar Code
Biological information transfer beyond the genetic code: the sugar code
http://www.ncbi.nlm.nih.gov/pubmed/10798195

Epigenetic Regulation by Heritable RNA
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990477/

I hope you don't expect me to read all those. I did have a cursory look at the abstracts and failed to see anything supporting ID, in fact, the opposite...

For example...

http://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-7-11

The incentive to write this review was the conviction of the authors that, after 30 years of turmoil, a degree of clarity has been reached in the study of the evolution of eukaryotic gene architecture. This progress has been achieved through the combination of comparative analysis of numerous, diverse genomes of eukaryotes, probabilistic reconstructions of intron gains and losses, and the non-adaptive population genetic theory of evolution of genomic complexity. It now appears well established that evolution of eukaryotes as a whole as well as evolution of each of the eukaryotic supergroups started with intron-rich genomes with relatively weak, error-prone splice signals.


http://bejerano.stanford.edu/readings/public/80_Function_GCRs.pdf

Beside the mere mechanistic interest, both human genetics and evolutionary biology may rapidly benefit from these developments. While the concept of regulatory landscapes may help understand genetic syndromes for which no simple molecular etiology is available, it may also give us new avenues to think about the evolution of regulations, and hence the emergence of evolutionary novelties.

You've offered no evidence for ID and no alternative explanations for "where complex organisms come from". When Meyers can offer us anything other than doubts, in a book for laymen which is widely refuted by people actually working in the relevant fields, let us know.
 
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Godexists

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I did not claim these papers support ID.

But they do lead to understand that other mechanisms rather than mutations, natural selection, genetic drift etc. are responsible alone for body plans, cell shape, and organism development. In short, epigenetic factors are also to be taken into consideration.
 
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SteveB28

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I did not claim these papers support ID.

But they do lead to understand that other mechanisms rather than mutations, natural selection, genetic drift etc. are responsible alone for body plans, cell shape, and organism development. In short, epigenetic factors are also to be taken into consideration.

Gosh, I wonder what those "epigenetic factors" could possibly be......?



.
 
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Jimmy D

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I did not claim these papers support ID.

But they do lead to understand that other mechanisms rather than mutations, natural selection, genetic drift etc. are responsible alone for body plans, cell shape, and organism development. In short, epigenetic factors are also to be taken into consideration.

Reading back, you didn't, my apologies.

I think my confusion was caused by your extensive quote in the OP from Meyer's book which appears to champion ID, (although I haven't read it).
 
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sfs

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But they do lead to understand that other mechanisms rather than mutations, natural selection, genetic drift etc. are responsible alone for body plans, cell shape, and organism development. In short, epigenetic factors are also to be taken into consideration.
This argument (which I realize isn't yours) makes no sense at all.

Yes, "epigenetic factors"(*) control an organism's development; they are largely responsible for what it will grow into. Yes, epigenetic factors are not themselves made of DNA. They are things like transcription factors -- proteins that bind to DNA -- and microRNA and proteins that attach chemical groups to pieces of DNA. But the epigenetic factors are themselves entirely the product, ultimately, of what's coded in the DNA. A transcription factor is coded for by a piece of DNA, and it binds to a particular DNA motif, for example. So changes to epigenetic factors, and therefore development, occur because of changes to the underlying DNA. In other words, they change by the processes of mutation, natural selection, drift, etc.

(*) In quotes because most of development is controlled by things that are sometimes called epigenetic, but that aren't by a strict definition of the term. Transcription factors are not epigenetic, in the strict sense.
 
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Ophiolite

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Breaking News: Incompletely informed bystanders were astounded to learn that science is not rooted to an unchanging worldview, but continually refines and develops its theories. This is especially evident in the Theory of Evolution, which has itself evolved in powerful ways since its birth, tended by Wallace and Darwin. As further details of the process are uncovered and validated, the dramatic insight of Darwin and Wallace is seen to be even more breathtaking.
 
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Justatruthseeker

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Come on people, we all understand no new genetic code has ever been created, it is simply copies of what already exists. It might be in a different order but no new DNA has ver been produced in any experiment EVER.

You are fooling yourselves if you believe otherwise. The idea of simple to complex is unsupported by any data whatsoever.
 
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sfs

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Come on people, we all understand no new genetic code has ever been created, it is simply copies of what already exists. It might be in a different order but no new DNA has ver been produced in any experiment EVER.
Quite true. In exactly the same way, no new English sentences have ever been written. It's just the same old letters copied over and over in different orders. Wake up, sheeple -- how can you not see this?
 
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Armoured

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I hope you don't expect me to read all those. I did have a cursory look at the abstracts and failed to see anything supporting ID, in fact, the opposite...

For example...

Origin and evolution of spliceosomal introns | Biology Direct | Full Text

The incentive to write this review was the conviction of the authors that, after 30 years of turmoil, a degree of clarity has been reached in the study of the evolution of eukaryotic gene architecture. This progress has been achieved through the combination of comparative analysis of numerous, diverse genomes of eukaryotes, probabilistic reconstructions of intron gains and losses, and the non-adaptive population genetic theory of evolution of genomic complexity. It now appears well established that evolution of eukaryotes as a whole as well as evolution of each of the eukaryotic supergroups started with intron-rich genomes with relatively weak, error-prone splice signals.


http://bejerano.stanford.edu/readings/public/80_Function_GCRs.pdf

Beside the mere mechanistic interest, both human genetics and evolutionary biology may rapidly benefit from these developments. While the concept of regulatory landscapes may help understand genetic syndromes for which no simple molecular etiology is available, it may also give us new avenues to think about the evolution of regulations, and hence the emergence of evolutionary novelties.

You've offered no evidence for ID and no alternative explanations for "where complex organisms come from". When Meyers can offer us anything other than doubts, in a book for laymen which is widely refuted by people actually working in the relevant fields, let us know.
It was a Gish Gallop, you're not meant to read the links, you're meant to be super impressed by the sheer number of citations and instantly sign up for Creation Museum timeshares
 
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FrumiousBandersnatch

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Come on people, we all understand no new genetic code has ever been created, it is simply copies of what already exists. It might be in a different order but no new DNA has ver been produced in any experiment EVER.
Reminds me of the late great Eric Morcambe, when Andre Previn criticized him for playing "all the wrong notes" in Greig's Piano Concerto - he grabbed Previn by the lapels and said, "I'm playing all the right notes—but not necessarily in the right order..."

But sfs said it best in #14.

Having said that, there's been a fair amount of work on exchanging the normal DNA nucleic acids with synthetic ones (Same bases, different sugars). This makes a completely new form of DNA, which they call XNA.

So it's a question of 'what's in a name?' to paraphrase Shakespeare, "That which we call DNA. By any other name would have different bases."
 
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SteveB28

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A more interesting question for 'Godexists' might be, 'Have you ever been a pregnant woman?'

Indeed. It must be an absolute mystery to these people as to how a single simple cell can develop into a complex organism in less than a year...!


.
 
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Godexists

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This argument (which I realize isn't yours) makes no sense at all.

Yes, "epigenetic factors"(*) control an organism's development; they are largely responsible for what it will grow into. Yes, epigenetic factors are not themselves made of DNA. They are things like transcription factors -- proteins that bind to DNA -- and microRNA and proteins that attach chemical groups to pieces of DNA. But the epigenetic factors are themselves entirely the product, ultimately, of what's coded in the DNA. A transcription factor is coded for by a piece of DNA, and it binds to a particular DNA motif, for example. So changes to epigenetic factors, and therefore development, occur because of changes to the underlying DNA. In other words, they change by the processes of mutation, natural selection, drift, etc.

(*) In quotes because most of development is controlled by things that are sometimes called epigenetic, but that aren't by a strict definition of the term. Transcription factors are not epigenetic, in the strict sense.

i suggest you keep reading my links.... it answers your point.

Developmental biologists, in particular, are now discovering more and more ways that crucial information for building body plans is imparted by the form and structure of embryonic cells, including information from both the unfertilized and fertilized egg.Biologists now refer to these sources of information as “epigenetic.”10 Spemann and Mangold’s experiment is only one of many to suggest that something beyond DNA may be influencing the development of animal body plans.

the three-dimensional structure or spatial architecture of embryonic cells plays important roles in determining body-plan formation during embryogenesis. Developmental biologists have identified several sources of epigenetic information in these cells.

neither the tubulin subunits, nor the genes that produce them, account for the differences in the shape of the microtubule arrays that distinguish different kinds of embryos and developmental pathways.

preexisting membrane targets, already positioned on the inside surface of the egg cell, determine where these molecules will attach and how they will function. These membrane targets provide crucial information—spatial coordinates—for embryological development.

Experiments have shown that electromagnetic fields have “morphogenetic” effects—in other words, effects that influence the form of a developing organism.

the precisely arranged sugar molecules on the surface of cells clearly represent another source of information independent of that stored in DNA base sequences.
 
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sfs

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Developmental biologists, in particular, are now discovering more and more ways that crucial information for building body plans is imparted by the form and structure of embryonic cells, including information from both the unfertilized and fertilized egg.Biologists now refer to these sources of information as “epigenetic.”
The bolded sentence is true, but does not affect my point: all of these sources of information ultimately come from the DNA. What goes into the egg is determined by DNA. The final sentence is simply wrong: that's not what "epigenetic" means.
 
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