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|                  by = [[User:Luke Brandt|luke]] 00:26, 20 March 2007 (CDT)
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=== [[Life]] ===
=== [[Life]] ===
<blockquote>An early question that needs to be confronted, indeed a question that in the last analysis requires definition, is: What is life? Most biologists would agree that self-replication, genetic continuity, is a fundamental trait of the life process. Systems that generally would be deemed nonbiological can exhibit a sort of self-replication, however. Examples would be the growth of a crystal lattice or a propagating clay structure. Crystals and clays propagate, unquestionably, but life they are not. There is no locus of genetic continuity, no organism. Such systems do not evolve, do not change in genetic ways to meet new challenges. Consequently, the definition of life should include the capacity for evolution as well as self-replication. Indeed, the mechanism of evolution---natural selection---is a consequence of the necessarily competing drives for self-replication that are manifest in all organisms. The definition based on those processes, then, would be that life is any self-replicating, evolving system (Norman R Pace 2001).<ref>http://www.pnas.org/cgi/content/full/98/3/805 The universal nature of biochemistry</ref></blockquote>
<blockquote>An early question that needs to be confronted, indeed a question that in the last analysis requires definition, is: What is life? Most biologists would agree that self-replication, genetic continuity, is a fundamental trait of the life process. Systems that generally would be deemed nonbiological can exhibit a sort of self-replication, however. Examples would be the growth of a crystal lattice or a propagating clay structure. Crystals and clays propagate, unquestionably, but life they are not. There is no locus of genetic continuity, no organism. Such systems do not evolve, do not change in genetic ways to meet new challenges. Consequently, the definition of life should include the capacity for evolution as well as self-replication. Indeed, the mechanism of evolution---natural selection---is a consequence of the necessarily competing drives for self-replication that are manifest in all organisms. The definition based on those processes, then, would be that life is any self-replicating, evolving system (Norman R Pace 2001).<ref>http://www.pnas.org/cgi/content/full/98/3/805 The universal nature of biochemistry</ref></blockquote>


really wonderful. [[User:Nancy Sculerati MD|Nancy Sculerati MD]] 01:49, 5 February 2007 (CST)
really wonderful. [[User:Nancy Sculerati MD|Nancy Sculerati MD]] 01:49, 5 February 2007 (CST)
== Darwin considered community origin ==
The last line of Darwin's ''on the Origin of Species'' (1st edition) reads:
<blockquote>There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.</blockquote>
'"..originally breathed into a few forms or one..."
--[[User:Anthony.Sebastian|Anthony.Sebastian]] [[User talk:Anthony.Sebastian|(Talk)]] 21:10, 12 April 2007 (CDT)
==Brief literature search ==
http://www.fasebj.org/cgi/content/full/19/9/1051
http://www.crbmb.com/cgi/content/abstract/39/2/99?ijkey=fdaad7f1da6d3417f460197f518770bef03ba8db&keytype2=tf_ipsecsha
1:  Turian G.
Origin of life. II. From prebiotic replicators to protocells.
Arch Sci Compte Rendu Seances Soc. 1999 Aug;52(2):101-9. Review.
PMID 14677551 [PubMed - indexed for MEDLINE]
2:  Szathmary E.
The origin of replicators and reproducers.
Philos Trans R Soc Lond B Biol Sci. 2006 Oct 29;361(1474):1761-76.
PMID: 17008217 [PubMed - indexed for MEDLINE]
3:  Szathmary E, Maynard Smith J.
From replicators to reproducers: the first major transitions leading to life.
J Theor Biol. 1997 Aug 21;187(4):555-71.
PMID 9299299 [PubMed - indexed for MEDLINE]
4:  Ikehara K.
Possible steps to the emergence of life: the [GADV]-protein world hypothesis.
Chem Rec. 2005;5(2):107-18. Review.
PMID 15828060 [PubMed - indexed for MEDLINE]
5:  Andras P, Andras C.
The origins of life -- the 'protein interaction world' hypothesis: protein
interactions were the first form of self-reproducing life and nucleic acids
evolved later as memory molecules.
Med Hypotheses. 2005;64(4):678-88.
PMID 15694682 [PubMed - indexed for MEDLINE]
6:  Carny O, Gazit E.
A model for the role of short self-assembled peptides in the very early stages
of the origin of life.
FASEB J. 2005 Jul;19(9):1051-5.
PMID 15985527 [PubMed - indexed for MEDLINE]
7:  Miller SL, Bada JL.
Submarine hot springs and the origin of life.
Nature. 1988 Aug 18;334(6183):609-11.
PMID 11536607 [PubMed - indexed for MEDLINE]
8:  Hoehler TM.
Biogeochemistry of dihydrogen (H2).
Met Ions Biol Syst. 2005;43:9-48. Review.
PMID 16370113 [PubMed - indexed for MEDLINE]
9:  Conrad R.
Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4,
OCS, N2O, and NO).
Microbiol Rev. 1996 Dec;60(4):609-40. Review.
PMID 8987358 [PubMed - indexed for MEDLINE]
10:  Hoehler TM, Bebout BM, Des Marais DJ.
The role of microbial mats in the production of reduced gases on the early
Earth.
Nature. 2001 Jul 19;412(6844):324-7.
PMID 11460161 [PubMed - indexed for MEDLINE]
11:  Cavalier-Smith T.
Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the
origins of the genetic code, the first cells, and photosynthesis.
J Mol Evol. 2001 Oct-Nov;53(4-5):555-95.
PMID 11675615 [PubMed - indexed for MEDLINE]
12:  Rosas A, Ferreira CP, Fontanari JF.
Evolution of protein synthesis in a lattice model of replicators.
Phys Rev Lett. 2002 Oct 28;89(18):188101. Epub 2002 Oct 10.
PMID 12398639 [PubMed - indexed for MEDLINE]
13:  Blomberg C.
On the appearance of function and organisation in the origin of life.
J Theor Biol. 1997 Aug 21;187(4):541-54.
PMID 9299298 [PubMed - indexed for MEDLINE]
14:  Szathmary E.
The evolution of replicators.
Philos Trans R Soc Lond B Biol Sci. 2000 Nov 29;355(1403):1669-76.
PMID 11127914 [PubMed - indexed for MEDLINE]
15:  Davis BK.
Molecular evolution before the origin of species.
Prog Biophys Mol Biol. 2002 May-Jul;79(1-3):77-133. Review.
PMID 12225777 [PubMed - indexed for MEDLINE]
16:  Shapiro R.
A replicator was not involved in the origin of life.
IUBMB Life. 2000 Mar;49(3):173-6.
PMID 10868906 [PubMed - indexed for MEDLINE]
17:  Koonin EV, Senkevich TG, Dolja VV.
The ancient Virus World and evolution of cells.
Biol Direct. 2006 Sep 19;1:29.
PMID 16984643 [PubMed - in process]
18:  Gibson TJ, Lamond AI.
Metabolic complexity in the RNA world and implications for the origin of
protein synthesis.
J Mol Evol. 1990 Jan;30(1):7-15.
PMID 1690303 [PubMed - indexed for MEDLINE]
19:  Szabo P, Scheuring I, Czaran T, Szathmary E.
In silico simulations reveal that replicators with limited dispersal evolve
towards higher efficiency and fidelity.
Nature. 2002 Nov 21;420(6913):340-3.
PMID 12447445 [PubMed - indexed for MEDLINE]
20:  Alberti S.
The origin of the genetic code and protein synthesis.
J Mol Evol. 1997 Oct;45(4):352-8.
PMID 9321414 [PubMed - indexed for MEDLINE]
21:  Rosas A, Fontanari JF.
Spatial dynamics and the evolution of enzyme production.
Orig Life Evol Biosph. 2003 Oct;33(4-5):357-74. Review.
PMID 14604182 [PubMed - indexed for MEDLINE]
22:  de Duve C.
A research proposal on the origin of life.
Orig Life Evol Biosph. 2003 Dec;33(6):559-74.
PMID 14601926 [PubMed - indexed for MEDLINE]
23:  Hoenigsberg H.
Evolution without speciation but with selection: LUCA, the Last Universal
Common Ancestor in Gilbert's RNA world.
Genet Mol Res. 2003 Dec 30;2(4):366-75.
PMID 15011140 [PubMed - indexed for MEDLINE]
24:  Davies P.
The origin of life. II: How did it begin?
Sci Prog. 2001;84(Pt 1):17-29.
PMID 11382135 [PubMed - indexed for MEDLINE]
25:  Beland P, Allen TF.
The origin and evolution of the genetic code.
J Theor Biol. 1994 Oct 21;170(4):359-65.
PMID 7996862 [PubMed - indexed for MEDLINE]
26:  Scheuring I, Szathmary E.
Survival of replicators with parabolic growth tendency and exponential decay.
J Theor Biol. 2001 Sep 7;212(1):99-105.
PMID 11527448 [PubMed - indexed for MEDLINE]
27:  Ikehara K.
Origins of gene, genetic code, protein and life: comprehensive view of life
systems from a GNC-SNS primitive genetic code hypothesis.
J Biosci. 2002 Mar;27(2):165-86. Review.
PMID 11937687 [PubMed - indexed for MEDLINE]
28:  Edwards MR.
Metabolite channeling in the origin of life.
J Theor Biol. 1996 Apr 21;179(4):313-22.
PMID: 8763352 [PubMed - indexed for MEDLINE]
'''
29:  Koch AL, Silver S.'''
The first cell.
Adv Microb Physiol. 2005;50:227-59.
PMID 16221582 [PubMed - indexed for MEDLINE]
The First Cell arose in the previously pre-biotic world with the coming together
of several entities that gave a single vesicle the unique chance to carry out
three essential and quite different life processes. These were: (a) to copy
informational macromolecules, (b) to carry out specific catalytic functions, and
(c) to couple energy from the environment into usable chemical forms. These
would foster subsequent cellular evolution and metabolism. Each of these three
essential processes probably originated and was lost many times prior to The
First Cell, but only when these three occurred together was life jump-started
and Darwinian evolution of organisms began. The replication of informational
molecules that made only occasional mistakes allowed evolution to form all the
basic components of cellular life. Ribozymes, the first informational molecules,
were also catalytic. Energy coupling required the formation of a closed lipid
surface to generate and maintain an ion-motive gradient. The closed vesicle
partitioned components and avoided dilution within the primordial sea. Closed
membranes were essential for the first self-reproducing cell to arise and for
its descendants to disperse. Subsequent cellular development after the origin of
The First Cell led to the beginnings of intermediary metabolism and membrane
transport processes. This long process, subject to strong evolutionary
selection, developed the cellular biology that is now shared by all extant
organisms.
30:  Krakauer DC, Sasaki A.
Noisy clues to the origin of life.
Proc Biol Sci. 2002 Dec 7;269(1508):2423-8. Review.
PMID: 12495484 [PubMed - indexed for MEDLINE]
31:  Nashimoto M.
The RNA/protein symmetry hypothesis: experimental support for reverse
translation of primitive proteins.
J Theor Biol. 2001 Mar 21;209(2):181-7.
PMID 11401460 [PubMed - indexed for MEDLINE]
[[User:David Tribe|David Tribe]] 00:12, 13 April 2007 (CDT)

Latest revision as of 10:57, 26 September 2007

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 Definition:  The birth of cells marked the passage from pre-biotic chemistry to partitioned units resembling modern cells. [d] [e]
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Life

An early question that needs to be confronted, indeed a question that in the last analysis requires definition, is: What is life? Most biologists would agree that self-replication, genetic continuity, is a fundamental trait of the life process. Systems that generally would be deemed nonbiological can exhibit a sort of self-replication, however. Examples would be the growth of a crystal lattice or a propagating clay structure. Crystals and clays propagate, unquestionably, but life they are not. There is no locus of genetic continuity, no organism. Such systems do not evolve, do not change in genetic ways to meet new challenges. Consequently, the definition of life should include the capacity for evolution as well as self-replication. Indeed, the mechanism of evolution---natural selection---is a consequence of the necessarily competing drives for self-replication that are manifest in all organisms. The definition based on those processes, then, would be that life is any self-replicating, evolving system (Norman R Pace 2001).[1]

really wonderful. Nancy Sculerati MD 01:49, 5 February 2007 (CST)

Darwin considered community origin

The last line of Darwin's on the Origin of Species (1st edition) reads:

There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

'"..originally breathed into a few forms or one..."

--Anthony.Sebastian (Talk) 21:10, 12 April 2007 (CDT)


Brief literature search

http://www.fasebj.org/cgi/content/full/19/9/1051

http://www.crbmb.com/cgi/content/abstract/39/2/99?ijkey=fdaad7f1da6d3417f460197f518770bef03ba8db&keytype2=tf_ipsecsha


1: Turian G. 

Origin of life. II. From prebiotic replicators to protocells.

Arch Sci Compte Rendu Seances Soc. 1999 Aug;52(2):101-9. Review. PMID 14677551 [PubMed - indexed for MEDLINE]

2: Szathmary E. 

The origin of replicators and reproducers.

Philos Trans R Soc Lond B Biol Sci. 2006 Oct 29;361(1474):1761-76. PMID: 17008217 [PubMed - indexed for MEDLINE]

3: Szathmary E, Maynard Smith J. 

From replicators to reproducers: the first major transitions leading to life.

J Theor Biol. 1997 Aug 21;187(4):555-71. PMID 9299299 [PubMed - indexed for MEDLINE]

4: Ikehara K. 

Possible steps to the emergence of life: the [GADV]-protein world hypothesis.

Chem Rec. 2005;5(2):107-18. Review. PMID 15828060 [PubMed - indexed for MEDLINE]

5: Andras P, Andras C. 

The origins of life -- the 'protein interaction world' hypothesis: protein

interactions were the first form of self-reproducing life and nucleic acids evolved later as memory molecules. Med Hypotheses. 2005;64(4):678-88. PMID 15694682 [PubMed - indexed for MEDLINE]

6: Carny O, Gazit E. 

A model for the role of short self-assembled peptides in the very early stages

of the origin of life. FASEB J. 2005 Jul;19(9):1051-5. PMID 15985527 [PubMed - indexed for MEDLINE]

7: Miller SL, Bada JL. 

Submarine hot springs and the origin of life.

Nature. 1988 Aug 18;334(6183):609-11. PMID 11536607 [PubMed - indexed for MEDLINE]

8: Hoehler TM. 

Biogeochemistry of dihydrogen (H2).

Met Ions Biol Syst. 2005;43:9-48. Review. PMID 16370113 [PubMed - indexed for MEDLINE]

9: Conrad R. 

Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4,

OCS, N2O, and NO). Microbiol Rev. 1996 Dec;60(4):609-40. Review. PMID 8987358 [PubMed - indexed for MEDLINE]

10: Hoehler TM, Bebout BM, Des Marais DJ. 

The role of microbial mats in the production of reduced gases on the early

Earth. Nature. 2001 Jul 19;412(6844):324-7. PMID 11460161 [PubMed - indexed for MEDLINE]

11: Cavalier-Smith T. 

Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the

origins of the genetic code, the first cells, and photosynthesis. J Mol Evol. 2001 Oct-Nov;53(4-5):555-95. PMID 11675615 [PubMed - indexed for MEDLINE]

12: Rosas A, Ferreira CP, Fontanari JF. 

Evolution of protein synthesis in a lattice model of replicators.

Phys Rev Lett. 2002 Oct 28;89(18):188101. Epub 2002 Oct 10. PMID 12398639 [PubMed - indexed for MEDLINE]

13: Blomberg C. 

On the appearance of function and organisation in the origin of life.

J Theor Biol. 1997 Aug 21;187(4):541-54. PMID 9299298 [PubMed - indexed for MEDLINE]

14: Szathmary E. 

The evolution of replicators.

Philos Trans R Soc Lond B Biol Sci. 2000 Nov 29;355(1403):1669-76. PMID 11127914 [PubMed - indexed for MEDLINE]

15: Davis BK. 

Molecular evolution before the origin of species.

Prog Biophys Mol Biol. 2002 May-Jul;79(1-3):77-133. Review. PMID 12225777 [PubMed - indexed for MEDLINE]

16: Shapiro R. 

A replicator was not involved in the origin of life.

IUBMB Life. 2000 Mar;49(3):173-6. PMID 10868906 [PubMed - indexed for MEDLINE]

17: Koonin EV, Senkevich TG, Dolja VV. 

The ancient Virus World and evolution of cells.

Biol Direct. 2006 Sep 19;1:29. PMID 16984643 [PubMed - in process]

18: Gibson TJ, Lamond AI. 

Metabolic complexity in the RNA world and implications for the origin of

protein synthesis. J Mol Evol. 1990 Jan;30(1):7-15. PMID 1690303 [PubMed - indexed for MEDLINE]

19: Szabo P, Scheuring I, Czaran T, Szathmary E. 

In silico simulations reveal that replicators with limited dispersal evolve

towards higher efficiency and fidelity. Nature. 2002 Nov 21;420(6913):340-3. PMID 12447445 [PubMed - indexed for MEDLINE]

20: Alberti S. 

The origin of the genetic code and protein synthesis.

J Mol Evol. 1997 Oct;45(4):352-8. PMID 9321414 [PubMed - indexed for MEDLINE]

21: Rosas A, Fontanari JF. 

Spatial dynamics and the evolution of enzyme production.

Orig Life Evol Biosph. 2003 Oct;33(4-5):357-74. Review. PMID 14604182 [PubMed - indexed for MEDLINE]

22: de Duve C. 

A research proposal on the origin of life.

Orig Life Evol Biosph. 2003 Dec;33(6):559-74. PMID 14601926 [PubMed - indexed for MEDLINE]

23: Hoenigsberg H. 

Evolution without speciation but with selection: LUCA, the Last Universal

Common Ancestor in Gilbert's RNA world. Genet Mol Res. 2003 Dec 30;2(4):366-75. PMID 15011140 [PubMed - indexed for MEDLINE]

24: Davies P. 

The origin of life. II: How did it begin?

Sci Prog. 2001;84(Pt 1):17-29. PMID 11382135 [PubMed - indexed for MEDLINE]

25: Beland P, Allen TF. 

The origin and evolution of the genetic code.

J Theor Biol. 1994 Oct 21;170(4):359-65. PMID 7996862 [PubMed - indexed for MEDLINE]

26: Scheuring I, Szathmary E. 

Survival of replicators with parabolic growth tendency and exponential decay.

J Theor Biol. 2001 Sep 7;212(1):99-105. PMID 11527448 [PubMed - indexed for MEDLINE]

27: Ikehara K. 

Origins of gene, genetic code, protein and life: comprehensive view of life

systems from a GNC-SNS primitive genetic code hypothesis. J Biosci. 2002 Mar;27(2):165-86. Review. PMID 11937687 [PubMed - indexed for MEDLINE]

28: Edwards MR. 

Metabolite channeling in the origin of life.

J Theor Biol. 1996 Apr 21;179(4):313-22. PMID: 8763352 [PubMed - indexed for MEDLINE]


29: Koch AL, Silver S. The first cell. Adv Microb Physiol. 2005;50:227-59. PMID 16221582 [PubMed - indexed for MEDLINE]

The First Cell arose in the previously pre-biotic world with the coming together of several entities that gave a single vesicle the unique chance to carry out three essential and quite different life processes. These were: (a) to copy informational macromolecules, (b) to carry out specific catalytic functions, and (c) to couple energy from the environment into usable chemical forms. These would foster subsequent cellular evolution and metabolism. Each of these three essential processes probably originated and was lost many times prior to The First Cell, but only when these three occurred together was life jump-started and Darwinian evolution of organisms began. The replication of informational molecules that made only occasional mistakes allowed evolution to form all the basic components of cellular life. Ribozymes, the first informational molecules, were also catalytic. Energy coupling required the formation of a closed lipid surface to generate and maintain an ion-motive gradient. The closed vesicle partitioned components and avoided dilution within the primordial sea. Closed membranes were essential for the first self-reproducing cell to arise and for its descendants to disperse. Subsequent cellular development after the origin of The First Cell led to the beginnings of intermediary metabolism and membrane transport processes. This long process, subject to strong evolutionary selection, developed the cellular biology that is now shared by all extant organisms.


30: Krakauer DC, Sasaki A. 

Noisy clues to the origin of life.

Proc Biol Sci. 2002 Dec 7;269(1508):2423-8. Review. PMID: 12495484 [PubMed - indexed for MEDLINE]

31: Nashimoto M. 

The RNA/protein symmetry hypothesis: experimental support for reverse

translation of primitive proteins. J Theor Biol. 2001 Mar 21;209(2):181-7. PMID 11401460 [PubMed - indexed for MEDLINE]

David Tribe 00:12, 13 April 2007 (CDT)

  1. ↑ http://www.pnas.org/cgi/content/full/98/3/805 The universal nature of biochemistry
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