Abiogenesis

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“Secular Democrat”

Since: Jan 15

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#1 Aug 6, 2015
I'd like to invite contribution on the topic of abiogenesis.
This can be your own interpretation of the theoretical processes involved, or a discussion piece on the latest reasearch in the field.
As always please post appropriate links to outside sources and thankyou in advance for your contributions.

“Merry Christmas”

Since: Jan 11

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#6 Aug 7, 2015
In the interest of helping to get this started, I thought I would post a brief list of papers to background the subject. I believe all of these are freely available online. Just search the article title on Google Scholar.

Abou Mrad, Ninette, Vassilissa Vinogradoff, Fabrice Duvernay, G. Danger, P. Theulé, F. Borget & T. Chiavassa. 2015. Laboratory experimental simulations: Chemical evolution of the organic matter from interstellar and cometary ice analogs. Bull. Soc. Roy. Sci. Ličge. 84: 21-32.

Arrhenius, Gustaf O., Brian C. Sales, Stephen J. Mojzsis & T. Lee. 1997. Entropy and charge in molecular evolution—the case of phosphate. J. Theor. Biol. 187(4): 503-522.

Bada, Jeffrey L. & Antonio Lazcano. 2003. Prebiotic soup--Revisiting the Miller experiment. Science. 300(5620): 745-746.

Bahadur, Krishna. 1973. Photochemical formation of self–sustaining coacervates. Proc. Indian Nat. Sci. Acad. 39B(4): 455-467.

Chen, Irene A. & Peter Walde. 2010. From self-assembled vesicles to protocells. Cold Spring Harbor Perspect Biol. 2(7): 1-13.

Davies, Paul. 2007. Are aliens among us?. Sci. Am. 297(6): 62-69.
Sci. Am. 297(06); 0062-0069 (2007)

Eigen, Manfred & Peter Schuster. 1977. The hypercycle. A principle of natural self-organization. Part A: Emergence of the hypercycle. Naturwissenschaften. 64(11): 541-565.

Eigen, Manfred & Peter Schuster. 1978. The hypercycle. A principle of natural self-organization. Part B: The abstract hypercycle. Naturwissenschaften. 65(1): 7-41.

Eigen, Manfred & Peter Schuster. 1978. The hypercycle. A principle of natural self-organization. Part C: The realistic hypercycle. Naturwissenschaften. 65(7): 341-369.

England, Jeremy L. 2013. Statistical physics of self-replication. J. Chem. Phys. 139(121923): 1-8.

Grote, Mathias. 2011. Jeewanu, or the 'particles of life'. J. Biosci. 36(4): 563-570.

Hudgins, Douglas M., Charles W. Bauschlicher, Jr. & Louis J. Allamandola. 2005. Variations in the peak position of the 6.2 μm interstellar emission feature: A tracer of N in the interstellar polycyclic aromatic hydrocarbon population. Astrophys. J. 632(1): 316-332.

Jřrgensen, Jes K., Cécile Favre, Suzanne E. Bisschop, Ewine F. van Dishoeck & Markus Schmalzl. 2012. Detection of the simplest sugar, glycolaldehyde, in a solar-type protostar with ALMA. Astrophys. J. Lett. 757(1)(arXiv:1208.5498): 1-13.

Joyce, Gerald F. 2009. Evolution in an RNA world. Cold Spring Harbor Perspect. Biol. 74: 17-23.

Kasting, James F. 1993. Earth's early atmosphere. Science. 259(5097): 922-922.

Larralde, Rosa, Michael P. Robertson & Stanley L. Miller. 1995. Rates of decomposition of ribose and other sugars: Implications for chemical evolution. PNAS USA. 92(18): 8158-8160.

Markovitch, Omer & Doron Lancet. 2012. "Excess mutual catalysis is required for effective evolvability. Artificial Life. 18(3): 243-266.

Michaelian, Karo & Norberto Santillán Padilla. 2014. DNA denaturing through UV-C photon dissipation: A possible route to Archean non-enzymatic replication. bioRxiv(009126): 1-16.

Nowak, Martin A. & Hisashi Ohtsuki. 2008. Prevolutionary dynamics and the origin of evolution. PNAS USA. 105(39): 14924-14927.

Parker, Eric T., Henderson J. Cleaves, Jason P. Dworkin, Daniel P. Glavin, Michael Callahan, Andrew Aubrey, Antonio Lazcano & Jeffrey L. Bada. 2011. Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment. PNAS USA. 108(14): 5526-5531.

Rampelotto, Pabulo Henrique. 2010. Panspermia: A promising field of research. Astrobiology Science Conference 2010. Houston, TX: Lunar and Planetary Institute. 5224: 1-2.

“Merry Christmas”

Since: Jan 11

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#7 Aug 7, 2015
Roldan, Alberto, Nathan Hollingsworth, Anna Roffey, Husn-Ubayda Islam, J.B.M. Goodall,
C.R.A. Catlow, J.A. Darr, W. Bras, G. Sankar, K.B. Holt, G. Hogartha & N.H. de Leeuw. 2015. Bio-inspired CO2 conversion by iron sulfide catalysts under sustainable conditions. Chem. Commun. 51(35): 7501-7504.

Rosing, Minik T., Dennis K. Bird, Norman H. Sleep, William Glassley & Francis Albarede. 2006. The rise of continents—An essay on the geologic consequences of photosynthesis. Palaeogeogr. Palaeoclimatol. Palaeoecol. 232(2-4): 99-113.

Segré, Daniel, Dafna Ben-Eli, David W. Deamer & Doron Lancet. 2001. The lipid world. Origins Life Evol. Biosph. 31(1-2): 119-145.

Sheldon, Robert B. 2005. Historical development of the distinction between bio- and abiogenesis. Pp. 59061I-59061I. In Optics & photonics International Society for Optics and Photonics.

Shock, Everett L. 1997. High-temperature life without photosyntesis as a model for Mars. J. Geophys. Res. 102(E10): 23687-23694.

Vasas, Vera, Chrisantha Fernando, Mauro Santos, Stuart Kauffman & Eörs Szathmáry. 2012. Evolution before genes. Biol. Direct. 7(1): 1-14.

Wächtershäuser, Günter. 1988. Before enzymes and templates: Theory of surface metabolism. Microbiol. Rev. 52(4): 452-484.

Wilde, Simon A., John W. Valley, William H. Peck & Colin M. Graham. 2001. Evidence from detrital zircons for the existence of continental crust and oceans on the Earth 4.4 Gyr ago. Nature. 409(6817): 175-178.

Zlobin, Andrei E. 2014. Symmetry infringement in mathematical metrics of hydrogen atom as illustration of ideas by V.I. Vernadsky concerning origin of life and biosphere. Abstract. Acta Naturae. Special Issue 1: 48-48.

“Merry Christmas”

Since: Jan 11

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#8 Aug 7, 2015
My initial post was not showing up, so I attempted posting a couple of times. Now I see some have come through. If multiple posts show up, I apologize in advance of that.

“Secular Democrat”

Since: Jan 15

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#9 Aug 7, 2015
DanFromSmithville wrote:
In the interest of helping to get this started, I thought I would post a brief list of papers to background the subject. I believe all of these are freely available online. Just search the article title on Google Scholar.
Abou Mrad, Ninette, Vassilissa Vinogradoff, Fabrice Duvernay, G. Danger, P. Theulé, F. Borget & T. Chiavassa. 2015. Laboratory experimental simulations: Chemical evolution of the organic matter from interstellar and cometary ice analogs. Bull. Soc. Roy. Sci. Ličge. 84: 21-32.
Arrhenius, Gustaf O., Brian C. Sales, Stephen J. Mojzsis & T. Lee. 1997. Entropy and charge in molecular evolution—the case of phosphate. J. Theor. Biol. 187(4): 503-522.
Bada, Jeffrey L. & Antonio Lazcano. 2003. Prebiotic soup--Revisiting the Miller experiment. Science. 300(5620): 745-746.
Bahadur, Krishna. 1973. Photochemical formation of self–sustaining coacervates. Proc. Indian Nat. Sci. Acad. 39B(4): 455-467.
Chen, Irene A. & Peter Walde. 2010. From self-assembled vesicles to protocells. Cold Spring Harbor Perspect Biol. 2(7): 1-13.
Davies, Paul. 2007. Are aliens among us?. Sci. Am. 297(6): 62-69.
Sci. Am. 297(06); 0062-0069 (2007)
Eigen, Manfred & Peter Schuster. 1977. The hypercycle. A principle of natural self-organization. Part A: Emergence of the hypercycle. Naturwissenschaften. 64(11): 541-565.
Eigen, Manfred & Peter Schuster. 1978. The hypercycle. A principle of natural self-organization. Part B: The abstract hypercycle. Naturwissenschaften. 65(1): 7-41.
Eigen, Manfred & Peter Schuster. 1978. The hypercycle. A principle of natural self-organization. Part C: The realistic hypercycle. Naturwissenschaften. 65(7): 341-369.
England, Jeremy L. 2013. Statistical physics of self-replication. J. Chem. Phys. 139(121923): 1-8.
Grote, Mathias. 2011. Jeewanu, or the 'particles of life'. J. Biosci. 36(4): 563-570.
Hudgins, Douglas M., Charles W. Bauschlicher, Jr. & Louis J. Allamandola. 2005. Variations in the peak position of the 6.2 μm interstellar emission feature: A tracer of N in the interstellar polycyclic aromatic hydrocarbon population. Astrophys. J. 632(1): 316-332.
Jřrgensen, Jes K., Cécile Favre, Suzanne E. Bisschop, Ewine F. van Dishoeck & Markus Schmalzl. 2012. Detection of the simplest sugar, glycolaldehyde, in a solar-type protostar with ALMA. Astrophys. J. Lett. 757(1)(arXiv:1208.5498): 1-13.
Joyce, Gerald F. 2009. Evolution in an RNA world. Cold Spring Harbor Perspect. Biol. 74: 17-23.
Kasting, James F. 1993. Earth's early atmosphere. Science. 259(5097): 922-922.
Larralde, Rosa, Michael P. Robertson & Stanley L. Miller. 1995. Rates of decomposition of ribose and other sugars: Implications for chemical evolution. PNAS USA. 92(18): 8158-8160.
Markovitch, Omer & Doron Lancet. 2012. "Excess mutual catalysis is required for effective evolvability. Artificial Life. 18(3): 243-266.
Michaelian, Karo & Norberto Santillán Padilla. 2014. DNA denaturing through UV-C photon dissipation: A possible route to Archean non-enzymatic replication. bioRxiv(009126): 1-16.
Nowak, Martin A. & Hisashi Ohtsuki. 2008. Prevolutionary dynamics and the origin of evolution. PNAS USA. 105(39): 14924-14927.
Parker, Eric T., Henderson J. Cleaves, Jason P. Dworkin, Daniel P. Glavin, Michael Callahan, Andrew Aubrey, Antonio Lazcano & Jeffrey L. Bada. 2011. Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment. PNAS USA. 108(14): 5526-5531.
Rampelotto, Pabulo Henrique. 2010. Panspermia: A promising field of research. Astrobiology Science Conference 2010. Houston, TX: Lunar and Planetary Institute. 5224: 1-2.
Thanks, I'm not limiting the debate just trying to get the thread(s) up and running good material I'm hoping some intelligent 'opposition' shows up if that's not a contradiction in terms.

“Merry Christmas”

Since: Jan 11

Location hidden

#11 Aug 7, 2015
Paul Porter1 wrote:
<quoted text>
Thanks, I'm not limiting the debate just trying to get the thread(s) up and running good material I'm hoping some intelligent 'opposition' shows up if that's not a contradiction in terms.
That's great. Glad to hear it. Even so, the papers should prove useful.

Hope others show up as well. In the meantime, I will think of things to discuss and do some reading.

“Club Fed or Camp Cupcake?”

Since: Oct 10

White-Collar Minimum-Security

#13 Aug 7, 2015
How can life emerge from nonliving matter? UNC scientists find new evidence.
http://www.csmonitor.com/Science/2015/0623/Ho...
Researchers say new findings could help answer questions about life’s chemical origins.

“Secular Democrat”

Since: Jan 15

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#14 Aug 7, 2015
Agents of Corruption wrote:
How can life emerge from nonliving matter? UNC scientists find new evidence.
http://www.csmonitor.com/Science/2015/0623/Ho...
Researchers say new findings could help answer questions about life’s chemical origins.
It's ok to post links but this paste and run process isn't contributing an opinion so if you post back it up with a comment please

“It Is What It Is”

Since: Jul 13

Alberta, Canada

#15 Aug 7, 2015
Wow! Your thread has really taken off. You and Dan should be happy together. lol
I know you will just delete this but that is what makes it fun.

“Be strong ...”

Since: Nov 10

...I whispered to my coffee

#16 Aug 8, 2015
Abiogenesis, we know I makes sense. Topix has no end of the threads dedicated to the subject with those who follow the scientific route and those who say it was done by god.

Although the descusion is spirited and often heated, for different reasons neither side knows the answer. The god side cannot provide evidence for the primary source, yet alone the event, they make no attempt to explain it other than' it just is'. The science side know fairly accurately how it occurred and are experimenting to duplicate the process, as yet without success. On the cutting edge of science predictions are being made of success within a few years. But without that success little if anything has been published.

Synthetic life has already been created by a team lead by Craig Venter (and is observed to evolve) but artificial life has not yet been created. I eagerly await the results of this branch of science. Not only will it go some way you resolving the abiogenisis debate in that it will be proven that abiogenesis can occur spontaneously under the right conditions, it will provide technological and medical breakthroughs currently beyond our imagination.

Back to my initial statement, we know it makes sense, we weren't here once, we are here now... abiogenesis?

But the argument is bigger than one planet, can life occur on other planets? The Kepler mission has found more than 1000 planets outside our solar system, about 10% of them earthlike and within the bounds of life bearing balls of rock. Did life occur on any of these planets? One of the latest discoveries Keplar 452b was only announced a couple of weeks ago.

https://www.nasa.gov/keplerbriefing0723

I eagerly await a spectogrsphic analysis, if this shows water and carbon compounds it puts the chances that life on earth is not a unique state in the universe.

“Secular Democrat”

Since: Jan 15

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#17 Aug 8, 2015
DarkBlue wrote:
Wow! Your thread has really taken off. You and Dan should be happy together. lol
I know you will just delete this but that is what makes it fun.
anyone who wants to take part is welcome and we need some fun try to get into the debate and enjoy it there won't be any bs

“Secular Democrat”

Since: Jan 15

Location hidden

#18 Aug 8, 2015
ChristineM wrote:
Abiogenesis, we know I makes sense. Topix has no end of the threads dedicated to the subject with those who follow the scientific route and those who say it was done by god.
Although the descusion is spirited and often heated, for different reasons neither side knows the answer. The god side cannot provide evidence for the primary source, yet alone the event, they make no attempt to explain it other than' it just is'. The science side know fairly accurately how it occurred and are experimenting to duplicate the process, as yet without success. On the cutting edge of science predictions are being made of success within a few years. But without that success little if anything has been published.
Synthetic life has already been created by a team lead by Craig Venter (and is observed to evolve) but artificial life has not yet been created. I eagerly await the results of this branch of science. Not only will it go some way you resolving the abiogenisis debate in that it will be proven that abiogenesis can occur spontaneously under the right conditions, it will provide technological and medical breakthroughs currently beyond our imagination.
Back to my initial statement, we know it makes sense, we weren't here once, we are here now... abiogenesis?
But the argument is bigger than one planet, can life occur on other planets? The Kepler mission has found more than 1000 planets outside our solar system, about 10% of them earthlike and within the bounds of life bearing balls of rock. Did life occur on any of these planets? One of the latest discoveries Keplar 452b was only announced a couple of weeks ago.
https://www.nasa.gov/keplerbriefing0723
I eagerly await a spectogrsphic analysis, if this shows water and carbon compounds it puts the chances that life on earth is not a unique state in the universe.
Welcome Christine, A lot of interesting points here, personally I've been extremely encouraged by the research data coming from the study of hydrothermal vents on the deep ocean floor where life is purely biochemical and isn't influenced by the sun. I'll post some details shortly.

“Secular Democrat”

Since: Jan 15

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#19 Aug 8, 2015
Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries

Deep-sea hydrothermal vent chimneys harbor a high diversity of largely unknown microorganisms. Although the phylogenetic diversity of these microorganisms has been described previously, the adaptation and metabolic potential of the microbial communities is only beginning to be revealed. A pyrosequencing approach was used to directly obtain sequences from a fosmid library constructed from a black smoker chimney 4143-1 in the Mothra hydrothermal vent field at the Juan de Fuca Ridge. A total of 308&#8201;034 reads with an average sequence length of 227&#8201;bp were generated. Comparative genomic analyses of metagenomes from a variety of environments by two-way clustering of samples and functional gene categories demonstrated that the 4143-1 metagenome clustered most closely with that from a carbonate chimney from Lost City. Both are highly enriched in genes for mismatch repair and homologous recombination, suggesting that the microbial communities have evolved extensive DNA repair systems to cope with the extreme conditions that have potential deleterious effects on the genomes. As previously reported for the Lost City microbiome, the metagenome of chimney 4143-1 exhibited a high proportion of transposases, implying that horizontal gene transfer may be a common occurrence in the deep-sea vent chimney biosphere. In addition, genes for chemotaxis and flagellar assembly were highly enriched in the chimney metagenomes, reflecting the adaptation of the organisms to the highly dynamic conditions present within the chimney walls. Reconstruction of the metabolic pathways revealed that the microbial community in the wall of chimney 4143-1 was mainly fueled by sulfur oxidation, putatively coupled to nitrate reduction to perform inorganic carbon fixation through the Calvin–Benson–Bassham cycle. On the basis of the genomic organization of the key genes of the carbon fixation and sulfur oxidation pathways contained in the large genomic fragments, both obligate and facultative autotrophs appear to be present and contribute to biomass production.
http://www.nature.com/ismej/journal/v5/n3/ful...

“Secular Democrat”

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#20 Aug 8, 2015
Riftia pachyptila &mdash; Overview
Hydrothermal Vent Worm

Riftia pachyptila is a giant tube-dwelling annelid in the family Siboglinidae. Siboglinids are important members of deep-sea chemosynthetic communities, which include hydrothermal vents, cold seeps, whale falls, and reduced sediments. As adults, these worms lack a functional digestive system and rely on microbial endosymbionts for their energetic needs.(Hilário et al. 2011)
Microbiologists believe this is an important evolutionary stage which could lead to the development of a complex digestive system as the endosymbionts are absorbed and retained leading to advanced structures such as intestinal tracts, crude stomachs etc. There is a tentaive sign of this process occurring at the larval stage.

Like other siboglinids, adult R. pachyptila lack a gut, mouth, anus, and conventional feeding ability and possesses bacterial symbionts.(Hilário et al. 2011). Adult R. pachyptila are nourished entirely by sulfur-oxidizing endosymbiotic bacteria (Coykendall et al. 2011). Although the larvae of R. pachytila are symbiont-free and possess a transient digestive system, these digestive structures are lost during development, resulting in adult animals that are nutritionally dependent on their bacterial symbionts. Thus, each generation of tubeworms must be newly colonized with appropriate symbionts.(Nussbaumer et al. 2006)

“Merry Christmas”

Since: Jan 11

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#21 Aug 8, 2015
Paul Porter1 wrote:
<quoted text>
anyone who wants to take part is welcome and we need some fun try to get into the debate and enjoy it there won't be any bs
A replay sock.

“Merry Christmas”

Since: Jan 11

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#22 Dec 14, 2015
Recently, we have been bombarded with made up terms that serve only to create confusion and act as straw man arguments against science.

One such term is abiodarwinism. It results from the combination of the first part of abiogenesis and Darwinism (meaning evolution, but using Darwin's name to imply a sort of religious view). If you look at the word even casually, you will see that it does not have anything to do with science. The initial implication is that the word means that evolution is dependent on abiogenesis and is forcing a belief in an aspect of science that is currently hypothetical. Evolution is a concept applied to existing and past life and requires only that life exist and places no constraints for a particular origin of life. Live could have arisen through special creation, abiogenesis, seeding from outer space, extraterrestrials or any other source we could come up with and evolution would still be the process by which it diversified and shows common descent and change.

The first part of this fictional and useless term is "abio" meaning without life. The second part of the word "Darwinism" is used to imply evolution, religious worship and the idea that Darwin is some sort of prophet. Together these would mean evolution without life and that is completely the opposite of what evolution requires. Darwin was genius in his synthesis of the concept of evolution and by providing volumes of evidence to support it. But his most important contribution may be that he provided a mechanism for evolution. A natural means for evolution to act on living things. He was a scientist, a great contributor to knowledge, but he was a man. He did not form a religion. He is admired and honored for his contribution to science, human knowledge and helping to advance our understanding of the world. He is not a prophet of a religion nor is he worshipped. Efforts to support that false view are those of creationists and have so far failed, but this failure doesn't seem to stop them or prevent them from coming up with new ways to propagate this lie.
pshun2404

Cambridge, MA

#24 Jun 14, 2017
There are only 10 to the 80th power atoms in the observable universe and the odds of getting basic free floating amino acids (which all must be left handed...and in nature) to bind and form a viable protein is 10 to the 140+ power, so rationally considering this, it is not probable to assume this EVER happened let alone the excuse that it had to have happened at least once. No! It did not have to happen, it could not have happened in a universe of this size in only 13.5 billion years, and there is not a shred of evidence or proof that such an event ever occurred.

So the insistence that it did and the subsequent interpretation of evidence in an attempt to support this assumption is confirmation bias whether it is subconscious or intentional.

“Rockin The 5th Dimension”

Since: Jul 16

San Diego, Cal.

#27 Dec 6, 2017
pshun2404 wrote:
There are only 10 to the 80th power atoms in the observable universe and the odds of getting basic free floating amino acids (which all must be left handed...and in nature) to bind and form a viable protein is 10 to the 140+ power, so rationally considering this, it is not probable to assume this EVER happened let alone the excuse that it had to have happened at least once. No! It did not have to happen, it could not have happened in a universe of this size in only 13.5 billion years, and there is not a shred of evidence or proof that such an event ever occurred.

So the insistence that it did and the subsequent interpretation of evidence in an attempt to support this assumption is confirmation bias whether it is subconscious or intentional.
These old completely refuted chestnuts are the best for a good laugh.

Tell us about chariot wheels in the red sea or golden pyramids!

You even invoked confirmation bias! <giggle>

Classic..

“Club Fed or Camp Cupcake?”

Since: Oct 10

White-Collar Minimum-Security

#28 Dec 6, 2017
Does Virginia have its own ancient pyramid?
http://www.vagazette.com/opinion/va-vg-edit-l...
I have read that over the years, additional pyramids have been located in other countries, especially in Europe and China, some of which are, what I believe to be, equally as high and wide.

“Be strong ...”

Since: Nov 10

...I whispered to my coffee

#29 Dec 9, 2017
pshun2404 wrote:
There are only 10 to the 80th power atoms in the observable universe and the odds of getting basic free floating amino acids (which all must be left handed...and in nature) to bind and form a viable protein is 10 to the 140+ power, so rationally considering this, it is not probable to assume this EVER happened let alone the excuse that it had to have happened at least once. No! It did not have to happen, it could not have happened in a universe of this size in only 13.5 billion years, and there is not a shred of evidence or proof that such an event ever occurred.

So the insistence that it did and the subsequent interpretation of evidence in an attempt to support this assumption is confirmation bias whether it is subconscious or intentional.
Where you getting you figures from, big numbers ("only"... Wow, count them zeros *10*10*10...) but certainly not scientific. My guess is some creationist site pretending to have your best interest at heart while keeping you dumbed down.

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