Cell morphology cannot be read out of genomic sequences alone.
Molecules into Cells: Specifying Spatial Architecture 1
2005 Dec
Spatial organization is perhaps the most conspicuous quality of cells and organisms, and also the most elusive. The dissection of life into its molecular constituents—the genes, enzymes, and lipid bilayers—necessarily starts with the destruction of spatial order. Yet we know that most complex functions, such as motility and division, depend on having the right molecules in their proper places. Architecture is what ultimately distinguishes a living cell from a soup of the chemicals of which it is composed. How cells generate, maintain, and reproduce their spatial organization is central to any understanding of the living state. 1 Organization, like other aspects of physiology and function, manifests the instructions encoded in the genes. Genes, acting individually or through elaborate regulatory networks, specify the structure of living matter and ensure its persistence; ultimately it is the genes that build cells.
If a protein deleted or altered by mutation plays a role in morphogenesis, the mutant's form or organization may well be affected. Examples from both prokaryotes and eukaryotes run into the hundreds . Such mutants are immensely valuable in dissecting morphogenetic pathways, but they do not show that cell form and organization are explicitly spelled out in the genetic instructions.
My comment: This paper was published in 2005. We know today that epigenetic mechanisms play a major role, if not a central role, in conjunction with genes, in how Cells are intracellularly organized.
Is cellular architecture explicitly spelled out by genes, and if so, how? If not, how is spatial organization passed from one generation to the next? How do molecules find the correct location in the cell space? What is the origin of large-scale order, as illustrated by the mitotic spindle or the endomembrane system of eukaryotic cells? How do multitudes of molecules reproducibly come together into cellular forms, which in turn serve as the targets of natural selection?
Targeting sequences direct proteins to the plasma membrane, nucleus, mitochondria, or lysosomes. Certain proteins and mRNAs are transported individually to particular locations in cell space, and this localization depends on having an appropriate sequence. Transport vesicles recognize specific target membranes, such as the Golgi, vacuole, or plasma membrane, with the aid of SNARE proteins. But there is much more to growth and division than manufacturing the parts. A rod-shaped cell must also elongate with constant diameter, construct an efficient apparatus to partition its chromosomes, locate its midpoint, lay down a septum, and undergo fission. In eukaryotic cells, targeted vesicle fusion requires, in addition to the SNAREs, both a delivery system and a secretory apparatus. This is all elaborate choreography. Genes specify the molecular parts, not their arrangement into a higher order.
Question: How did this targeting sequence emerge? And not only the sequence by itself but also the mechanisms of recognition of these target sequences. There has to be an information source, an encoder, a communication channel, a decoder (or receiver), and a user. The information source generates the information to be transmitted; the encoder transforms the information into a suitable message form for transmission over the communication channel; and the decoder performs the inverse operation of the encoder, or approximately so, for the user at the other end of the channel.
As Perry Marshall explains :
1. A code
2. An encoder that obeys the rules of a code
3. A message that obeys the rules of the code
4. A decoder that obeys the rules of the code
The rules of any communication system are always defined in advance by a process of deliberate choices. There must be prearranged agreement between sender and receiver, otherwise communication is impossible. By definition, a communication system cannot evolve from something simpler because evolution itself requires communication to exist first. You can’t make copies of a message without the message, and you can’t create a message without first having a language. And before that, you need intent. A code is an abstract, immaterial, nonphysical set of rules. There is no physical law that says ink on a piece of paper formed in the shape T-R-E-E should correspond to that large leafy organism in your front yard. You cannot derive the local rules of a code from the laws of physics, because hard physical laws necessarily exclude choice. On the other hand, the coder decides whether “1” means “on” or “off.” She decides whether “0” means “off” or “on.” Codes, by definition, are freely chosen. The rules of the code come before all else. These rules of any language are chosen with a goal in mind: communication, which is always driven by intent. That being said, conscious beings can evolve a simple code into a more complex code—if they can communicate in the first place. But even simple grunts and hand motions between two humans who share no language still require communication to occur. Pointing to a table and making a sound that means “table” still requires someone to recognize what your pointing finger means.
The paper continues:
For the purposes of cell biology, let me define self-organization as the emergence of supramolecular order from the interactions among numerous molecules that obey only local rules, without reference to an external template or global plan.
My comment: Does a rule not demand a ruler ?
The structure of the self-assembled complex is wholly specified by the structures of its parts and is therefore implicit in the genes that specify those parts: natural selection crafted those genes to specify parts that assemble into a functional complex.
My comment: Did you perceive the AD-HOC explanation? Natural selection? How does the author know this? He doesn't. Furthermore, there was no natural selection prior life began.
"Although the general public is disconcertingly unaware of it, it is a fact that scientists do not have even the slightest clue as to how life could have begun through an unguided naturalistic process absent the intervention of a conscious creative force.
Here are just a few well-chosen statements on the Origin of Life:
- (2016) “[There is] collective cluelessness…those who say this is well worked out, they know nothing, nothing about chemical synthesis…Those who think that scientists understand the details of life’s origin are wholly uninformed. Nobody understands…when will the scientific community confess to the world that they are clueless on life’s origin, that the emperor has no clothes?” (James Tour — Professor of Chemistry, Rice University (Synthetic chemist and among the top ten most cited chemists in the world))
- (2011) “The Origin of Life field is a failure.” (Eugene Koonin, microbiologist at the National Center for Biotechnology Information)
- (2011) “With respect to the Origin of Life, I find the more we learn about cells, the more complex they seem; they are just incredibly complex things, and to go from what we can see today and try to reason where it came from, I think is really impossible.” (Lee Hartwell, Nobel Prize in Medicine, 2001)
- (2007) “How? [did life begin] I have no idea.” (George Whitesides, Professor of Chemistry, Harvard University, Winner of the Priestley Medal in Chemistry (second only to the Nobel Prize))
- (2001) “The origin of life appears to me as incomprehensible as ever, a matter for wonder but not for explication.” (Franklin Harold, Professor Emeritus, Department of Biochemistry and Molecular Biology, Colorado State University)
- (1983) “In short, there is not a shred of objective evidence to support the hypothesis that life began in an organic soup here on earth.” (Sir Fred Hoyle, distinguished British astronomer, physicist, mathematician (without question one of the greatest scientific minds of the 20th century))
- (1981) “Since Science does not have the faintest idea how life on earth originated…it would only be honest to confess this to other scientists, to grantors, and to the public at large.” (Hubert Yockey, physicist and renowned information theorist)
As Biochemist Klaus Dose wrote: “Experimentation on the origin of life…has led to a better perception of the immensity of the problem of the origin of life on Earth rather than to its solution.” Researchers Carl Woese and Gunter Wachtershauser concur: “While we do not have a solution, we now have an inkling of the magnitude of the problem.”
Why are researchers having such difficulties discovering a naturalistic Origin of Life? Let’s let the aforementioned and atheist microbiologist Eugene Koonin answer this question: “Certainly this is not due to a lack of experimental and theoretical effort, but to the extraordinary intrinsic difficulty and complexity of the problem. A succession of exceedingly unlikely steps is essential for the Origin of Life…these make the final outcome seem almost like a miracle.”
Translation for the lay-person: Discovering how unguided naturalistic forces could assemble a living cell — a molecular machine that is more sophisticated and functionally complex than anything human technology has ever produced — is a problem of nightmarish proportions.
When one dispassionately contemplates the enormous difficulties involved in a naturalistic origin of life, it is not surprising at all that one often suggested solution is Intelligent Design or Divine Creation. In fact, any number of world class scientists themselves have brought up the issue:
“Abiogenesis [life from non-life] strikes many as virtually miraculous…you might get the impression from what I have written not only that the origin of life is virtually impossible, but that life itself is impossible…So what is the answer? Is life a miracle after all?” (Dr. Paul Davies)
“[We have no naturalistic explanation for] the origin of life, which is unknown so far…As long as the origin of life can’t be explained in natural terms, the hypothesis of an instant Divine creation of life cannot objectively be ruled out.” (Dr. Christian DeDuve, Nobel Prize-Medicine, 1974)
“There are only two possibilities as to how life arose. One is spontaneous generation arising to evolution; the other is a supernatural creative act of God. There is no third possibility.” (George Wald, Nobel Prize-Medicine, 1967)
“Although a biologist, I must confess I do not understand how life came about…I consider that life only starts at the level of a functional cell. The most primitive cells may require at least several hundred different specific biological macro-molecules. How such already quite complex structures may have come together remains a mystery to me. The possibility of the existence of a Creator, of God, represents to me a satisfactory solution to this problem.” (Dr. Werner Arber, Nobel Prize-Medicine, 1978)
“From my earliest training as a scientist I was very strongly brainwashed to believe that science cannot be consistent with any kind of deliberate creation. That notion has had to be very painfully shed. I am quite uncomfortable in the situation, the state of mind I now find myself in. But there is no logical way out of it; it is just not possible that life could have originated from a chemical accident.” (Chandra Wickramasinghe, mathematician, astronomer, astrobiologist – longtime collaborator of Sir Fred Hoyle)
“Indeed, such a theory [Intelligent Design] is so obvious that one wonders why it is not widely accepted as being self-evident. The reasons are psychological rather than scientific.” “A common sense interpretation of the facts suggests that a super intellect has monkeyed with the laws of physics, as well as with chemistry and biology, and that there are no blind forces worth speaking about in nature.” (Sir Fred Hoyle)
If a rational, truth-seeking individual is asked: “How did life begin; naturalistic, unguided forces or Divine Creation?” There are only two possible answers: (a) Divine Creation or (b) I don’t know, the jury is still out; but atheism – a denial of the existence of a Creator of life — is not possible anymore….unless, of course, as I stated in the title of this article, you are prepared to ignore science and scientists. And if so, you might just as well go and play children’s games and with children’s toys, like…..LEGO blocks."
1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1306800/
Molecules into Cells: Specifying Spatial Architecture 1
2005 Dec
Spatial organization is perhaps the most conspicuous quality of cells and organisms, and also the most elusive. The dissection of life into its molecular constituents—the genes, enzymes, and lipid bilayers—necessarily starts with the destruction of spatial order. Yet we know that most complex functions, such as motility and division, depend on having the right molecules in their proper places. Architecture is what ultimately distinguishes a living cell from a soup of the chemicals of which it is composed. How cells generate, maintain, and reproduce their spatial organization is central to any understanding of the living state. 1 Organization, like other aspects of physiology and function, manifests the instructions encoded in the genes. Genes, acting individually or through elaborate regulatory networks, specify the structure of living matter and ensure its persistence; ultimately it is the genes that build cells.
If a protein deleted or altered by mutation plays a role in morphogenesis, the mutant's form or organization may well be affected. Examples from both prokaryotes and eukaryotes run into the hundreds . Such mutants are immensely valuable in dissecting morphogenetic pathways, but they do not show that cell form and organization are explicitly spelled out in the genetic instructions.
My comment: This paper was published in 2005. We know today that epigenetic mechanisms play a major role, if not a central role, in conjunction with genes, in how Cells are intracellularly organized.
Is cellular architecture explicitly spelled out by genes, and if so, how? If not, how is spatial organization passed from one generation to the next? How do molecules find the correct location in the cell space? What is the origin of large-scale order, as illustrated by the mitotic spindle or the endomembrane system of eukaryotic cells? How do multitudes of molecules reproducibly come together into cellular forms, which in turn serve as the targets of natural selection?
Targeting sequences direct proteins to the plasma membrane, nucleus, mitochondria, or lysosomes. Certain proteins and mRNAs are transported individually to particular locations in cell space, and this localization depends on having an appropriate sequence. Transport vesicles recognize specific target membranes, such as the Golgi, vacuole, or plasma membrane, with the aid of SNARE proteins. But there is much more to growth and division than manufacturing the parts. A rod-shaped cell must also elongate with constant diameter, construct an efficient apparatus to partition its chromosomes, locate its midpoint, lay down a septum, and undergo fission. In eukaryotic cells, targeted vesicle fusion requires, in addition to the SNAREs, both a delivery system and a secretory apparatus. This is all elaborate choreography. Genes specify the molecular parts, not their arrangement into a higher order.
Question: How did this targeting sequence emerge? And not only the sequence by itself but also the mechanisms of recognition of these target sequences. There has to be an information source, an encoder, a communication channel, a decoder (or receiver), and a user. The information source generates the information to be transmitted; the encoder transforms the information into a suitable message form for transmission over the communication channel; and the decoder performs the inverse operation of the encoder, or approximately so, for the user at the other end of the channel.
As Perry Marshall explains :
1. A code
2. An encoder that obeys the rules of a code
3. A message that obeys the rules of the code
4. A decoder that obeys the rules of the code
The rules of any communication system are always defined in advance by a process of deliberate choices. There must be prearranged agreement between sender and receiver, otherwise communication is impossible. By definition, a communication system cannot evolve from something simpler because evolution itself requires communication to exist first. You can’t make copies of a message without the message, and you can’t create a message without first having a language. And before that, you need intent. A code is an abstract, immaterial, nonphysical set of rules. There is no physical law that says ink on a piece of paper formed in the shape T-R-E-E should correspond to that large leafy organism in your front yard. You cannot derive the local rules of a code from the laws of physics, because hard physical laws necessarily exclude choice. On the other hand, the coder decides whether “1” means “on” or “off.” She decides whether “0” means “off” or “on.” Codes, by definition, are freely chosen. The rules of the code come before all else. These rules of any language are chosen with a goal in mind: communication, which is always driven by intent. That being said, conscious beings can evolve a simple code into a more complex code—if they can communicate in the first place. But even simple grunts and hand motions between two humans who share no language still require communication to occur. Pointing to a table and making a sound that means “table” still requires someone to recognize what your pointing finger means.
The paper continues:
For the purposes of cell biology, let me define self-organization as the emergence of supramolecular order from the interactions among numerous molecules that obey only local rules, without reference to an external template or global plan.
My comment: Does a rule not demand a ruler ?
The structure of the self-assembled complex is wholly specified by the structures of its parts and is therefore implicit in the genes that specify those parts: natural selection crafted those genes to specify parts that assemble into a functional complex.
My comment: Did you perceive the AD-HOC explanation? Natural selection? How does the author know this? He doesn't. Furthermore, there was no natural selection prior life began.
"Although the general public is disconcertingly unaware of it, it is a fact that scientists do not have even the slightest clue as to how life could have begun through an unguided naturalistic process absent the intervention of a conscious creative force.
Here are just a few well-chosen statements on the Origin of Life:
- (2016) “[There is] collective cluelessness…those who say this is well worked out, they know nothing, nothing about chemical synthesis…Those who think that scientists understand the details of life’s origin are wholly uninformed. Nobody understands…when will the scientific community confess to the world that they are clueless on life’s origin, that the emperor has no clothes?” (James Tour — Professor of Chemistry, Rice University (Synthetic chemist and among the top ten most cited chemists in the world))
- (2011) “The Origin of Life field is a failure.” (Eugene Koonin, microbiologist at the National Center for Biotechnology Information)
- (2011) “With respect to the Origin of Life, I find the more we learn about cells, the more complex they seem; they are just incredibly complex things, and to go from what we can see today and try to reason where it came from, I think is really impossible.” (Lee Hartwell, Nobel Prize in Medicine, 2001)
- (2007) “How? [did life begin] I have no idea.” (George Whitesides, Professor of Chemistry, Harvard University, Winner of the Priestley Medal in Chemistry (second only to the Nobel Prize))
- (2001) “The origin of life appears to me as incomprehensible as ever, a matter for wonder but not for explication.” (Franklin Harold, Professor Emeritus, Department of Biochemistry and Molecular Biology, Colorado State University)
- (1983) “In short, there is not a shred of objective evidence to support the hypothesis that life began in an organic soup here on earth.” (Sir Fred Hoyle, distinguished British astronomer, physicist, mathematician (without question one of the greatest scientific minds of the 20th century))
- (1981) “Since Science does not have the faintest idea how life on earth originated…it would only be honest to confess this to other scientists, to grantors, and to the public at large.” (Hubert Yockey, physicist and renowned information theorist)
As Biochemist Klaus Dose wrote: “Experimentation on the origin of life…has led to a better perception of the immensity of the problem of the origin of life on Earth rather than to its solution.” Researchers Carl Woese and Gunter Wachtershauser concur: “While we do not have a solution, we now have an inkling of the magnitude of the problem.”
Why are researchers having such difficulties discovering a naturalistic Origin of Life? Let’s let the aforementioned and atheist microbiologist Eugene Koonin answer this question: “Certainly this is not due to a lack of experimental and theoretical effort, but to the extraordinary intrinsic difficulty and complexity of the problem. A succession of exceedingly unlikely steps is essential for the Origin of Life…these make the final outcome seem almost like a miracle.”
Translation for the lay-person: Discovering how unguided naturalistic forces could assemble a living cell — a molecular machine that is more sophisticated and functionally complex than anything human technology has ever produced — is a problem of nightmarish proportions.
When one dispassionately contemplates the enormous difficulties involved in a naturalistic origin of life, it is not surprising at all that one often suggested solution is Intelligent Design or Divine Creation. In fact, any number of world class scientists themselves have brought up the issue:
“Abiogenesis [life from non-life] strikes many as virtually miraculous…you might get the impression from what I have written not only that the origin of life is virtually impossible, but that life itself is impossible…So what is the answer? Is life a miracle after all?” (Dr. Paul Davies)
“[We have no naturalistic explanation for] the origin of life, which is unknown so far…As long as the origin of life can’t be explained in natural terms, the hypothesis of an instant Divine creation of life cannot objectively be ruled out.” (Dr. Christian DeDuve, Nobel Prize-Medicine, 1974)
“There are only two possibilities as to how life arose. One is spontaneous generation arising to evolution; the other is a supernatural creative act of God. There is no third possibility.” (George Wald, Nobel Prize-Medicine, 1967)
“Although a biologist, I must confess I do not understand how life came about…I consider that life only starts at the level of a functional cell. The most primitive cells may require at least several hundred different specific biological macro-molecules. How such already quite complex structures may have come together remains a mystery to me. The possibility of the existence of a Creator, of God, represents to me a satisfactory solution to this problem.” (Dr. Werner Arber, Nobel Prize-Medicine, 1978)
“From my earliest training as a scientist I was very strongly brainwashed to believe that science cannot be consistent with any kind of deliberate creation. That notion has had to be very painfully shed. I am quite uncomfortable in the situation, the state of mind I now find myself in. But there is no logical way out of it; it is just not possible that life could have originated from a chemical accident.” (Chandra Wickramasinghe, mathematician, astronomer, astrobiologist – longtime collaborator of Sir Fred Hoyle)
“Indeed, such a theory [Intelligent Design] is so obvious that one wonders why it is not widely accepted as being self-evident. The reasons are psychological rather than scientific.” “A common sense interpretation of the facts suggests that a super intellect has monkeyed with the laws of physics, as well as with chemistry and biology, and that there are no blind forces worth speaking about in nature.” (Sir Fred Hoyle)
If a rational, truth-seeking individual is asked: “How did life begin; naturalistic, unguided forces or Divine Creation?” There are only two possible answers: (a) Divine Creation or (b) I don’t know, the jury is still out; but atheism – a denial of the existence of a Creator of life — is not possible anymore….unless, of course, as I stated in the title of this article, you are prepared to ignore science and scientists. And if so, you might just as well go and play children’s games and with children’s toys, like…..LEGO blocks."
1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1306800/
