Intelligent Design, the best explanation of Origins

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Intelligent Design, the best explanation of Origins » Theory of evolution » The general guess work and ad hoc explanations of scientific papers related to key issues of origins

The general guess work and ad hoc explanations of scientific papers related to key issues of origins

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The general guess work and ad hoc explanations of scientific papers related to key issues of origins

When opponents of special creation asked about how x raised, they often make a quick web search, come up with the first search result which looks like a " serious " scientific paper, which explains how x  evolved, and post it as an answer. When asked to quote the relevant part of the paper, which convinced them evolution was the best answer, commonly they don't answer, because they did not make the effort to analyze carefully the proposed evidence. That shows nicely their confirmation bias. They determined already evolution must be true, since it fits their preconceived and wished worldview, so all they do, is to try to fit everything they find into their naturalistic worldview, without carefully looking if the evidence is compelling. Most scientific papers on evolution are perfect examples of how methodological naturalism works and obliges especially historical sciences to wear blinkers.  Since evolution is the only naturalistic possible explanation for the biodiversity on earth, evolution is supposed to be the answer right from the beginning, rather start with an agnostic standpoint, and after careful examination, permitting the evidence to lead wherever it is, and  propose evolution as the best explanation if that is the outcome that fits best. These papers start with evolution, end with evolution, and in the middle is a not rarely high concentration of guesswork, ad hoc explanations, and fairytale stories.

Early Evolution of Photosynthesis1

An understanding of the origin and evolution of photosynthesis is therefore of substantial interest,

Overwhelming evidence indicates,
most probably,
A wealth of evidence indicates,
Significant evidence indicates,
have clearly had distinct evolutionary trajectories,
There have been numerous suggestions,
The accumulated evidence suggests

The process of photosynthesis originated early in Earth’s history and has evolved to its current mechanistic diversity and phylogenetic distribution by a complex, nonlinear process.

The Origin of Mitochondria

There are currently two main, competing theories about the origin of mitochondria.
view is linked to the ideas
perhaps similar
might have
corollary assumption

Mitochondria arose once in evolution, and their origin entailed an endosymbiosis accompanied by gene transfers from the endosymbiont to the host.

Early Modern Homo sapiens

Our species of humans first began to evolve nearly 200,000 years ago

it is likely
Current data suggest
seems to be
It would seem
that attempt to explain
It is further suggested
It is argued
Its advocates claim
it is claimed
proposes that

Evolutionary origins of the nervous system

How did this remarkable and extraordinarily complex structure evolve?

brain evolution surely involved thousands of discrete, incremental steps, which occurred in the mists of deep time across hundreds of millions of years, and which we are unlikely to ever fully understand.  ( how funny. We don't ever fully understand it, but it certainly was through evolution. Nice gap argument )

a number of studies published in recent years have begun to shed some light on the evolutionary origins of the nervous system

These clues come from
all believed to be
at the earliest stages of their evolution, vertebrates – including humans – may have inherited the organization of their nervous systems from it as well.
provide clues

The evolution of whales

The evolution of whales

hippos are the closest living relatives of whales ( how do they know ? )
the first whales evolved over 50 million years ago( how do they know ? )
seemingly minor features provide critical evidence to link animals that are highly specialized for their lifestyles (such as whales) with their less extreme-looking relatives. ( how do they know ? )
looks like
probably comprised
indicating that
These animals evolved nostrils positioned further and further back along the snout.( how do they know ? )
also suggest
This may reflect
because whales evolved from walking land mammals( how do they know ? )
These ancient whales evolved over 40 million years ago. ( how do they know ? )
is evidence of

Last edited by Admin on Sat 19 May 2018 - 13:28; edited 5 times in total

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2 Earth’s Earliest Atmospheres on Tue 6 May 2014 - 0:07


Earth’s Earliest Atmospheres

However, photochemical studies showed that any methane (Lasaga et al. 1971) or ammonia (Kuhn and Atreya 1979; Kasting 1982) in the atmosphere would quickly be destroyed. Meanwhile geologically based arguments, which treat the atmosphere as outgassed from the solid Earth, were taken as strongly suggesting that Earth’s original atmosphere was composed mostly of H2O, CO2, and N2, with only small amounts of CO and H2, and essentially no CH4 or NH3 (Poole 1951; Holland 1962; Abelson 1966; Holland 1984). This composition of volcanic gases is determined by temperature and the QFM (quartz-fayalite-magnetite) mineral buffer pertinent to the modern mantle. Nor is there evidence of a time on Earth when things were clearly different. Geochemical evidence in Earth’s oldest igneous rocks indicates that the redox state of the Earth’s mantle has not changed over the past 3.8 Gyr (Delano 2001; Canil 2002). Miller-Urey-type experiments performed in the more oxidized mixtures of modern volcanic gases generate relatively little of prebiotic interest, especially when CO2 is abundant (Miller and Urey 1959; Schlessinger and Miller 1983; Stribling and Miller 1987). New work suggests that spark yields of ammonia, HCN, and amino acids in CO2-N2-water mixtures can be less disappointing if the water is allowed to become acidic (Cleaves et al. 2008). Nevertheless, the contrast between methane and ammonia on the one hand and carbon dioxide and dinitrogen on the other led many prebiotic chemists, Miller and Urey prominent among them, to regard the presence of life on Earth as providing a strong boundary condition on the nature of Earth’s early atmosphere.

The sense of poor prospects led some to abandon the atmosphere in favor of the hydrosphere. At the low temperatures and high water activities of hydrothermal systems, it is in theory possible to get non-negligable amounts of methane and ammonia at the QFM buffer (French 1966; Shock and Schulte 1990, 1998). Shock and Schulte (1990) used this approach to explain the abundances of organic molecules in asteroids (as sampled by carbonaceous meteorites) and suggested that such a model might have application to the origin of life on Earth (Shock 1990; Shock et al. 1995; Shock and Schulte 1998). The issue of a submarine (as opposed to a subaerial) origin of life became contentious (Miller and Bada 1988, 1993; Shock and Schulte 1993). Significant features of the hydrothermal hypothesis are that (1) it ties the origin of life to the process of making organic molecules, and (2) it implies that life is widespread in the Solar System, because hydrothermal systems may exist in many moons (Shock and McKinnon 1993).

Another workaround is to abandon the idea that organic molecules were generated in situ here on Earth. Instead the organic molecules would be delivered by comets and asteroids and interplanetary dust particles (IDPs, Anders 1989; Chyba and Sagan 1992; Whittet 1997). The basis of this proposal is that organic molecules are abundant in the Solar System. Many meteorites and dust grains are rich in complex organic molecules, and there is little doubt that comets are at least as rich. The chief difficulty is that, apart from special cases, only a small fraction of the more interesting and more delicate organic materials in comets and asteroids would survive impact (Clark 1988; Anders 1989; Chyba et al. 1990; Chyba and Sagan 1992; Whittet 1997; Pierazzo and Chyba 1999; Pasek and Lauretta 2008). The importance of an exogenic source of organics to the origin of life has probably been overstated. In the median case the quantities aren’t large and the biological potential of a modest cosmic windfall of IDPs is unclear, although a slow soft collision by a big organic-rich comet—possible but by construction unlikely—could have a huge unique effect (Clark 1988). An alternative lesson to be taken from abundant organics in the Solar System is that organic molecules are not hard to make, and so were probably also made here.

A third perspective to the origin of the atmosphere—that the earliest atmosphere was degassed from impacting material as it arrived rather than outgassed from the solid Earth into a primordial vacuum (Arrhenius et al. 1974; Lange et al. 1985; Tyburczy et al. 1986; Abe and Matsui 1986; Zahnle et al. 1988; Ahrens et al. 1989)—has gotten comparatively little traction. Recently three new theoretical studies (Schaefer and Fegley 2007, 2010; Hashimoto et al. 2007) show that atmospheres dominated by impact degassing would be much more reduced than atmospheres dominated by Earth’s mantle. A fourth recent study (Sugita and Schultz 2009) addresses impact degassing and impact synthesis in possible cometary matter experimentally. The latter can be regarded as parallel to the experiments performed by nature when the pieces of comet Shoemaker-Levy 9 struck Jupiter in July 1994. The SL9 impacts generated vast quantities of small molecules, especially CO, but the list of apparently synthetic products also included HCN, C2H2, C2H4, S2, CS, CS2, OCS, and CO2 (Zahnle et al. 1995; Harrington et al. 2004).

Here we address the state and properties of Earth’s primordial atmosphere. Our review is presented in three parts: the origin of the atmosphere, the Moon-forming impact, and events taking place after the Moon-forming impact. Placing the origin of the atmosphere before the Moon-forming impact is a choice that is founded on the high volatile contents of all known chondritic meteorites: To build Earth without volatiles is difficult if all known examples of possible source materials are more volatile-rich than Earth. Nonetheless we will also consider the alternative—volatile delivery after the Moon-forming impact—because it is one of the concepts in debate (cf. Albarède 2009) and because the hypothesis of transient, strongly reduced impact-degassed atmospheres applies obviously and directly to it.


Delivering all Earth’s volatiles after the Moon-forming impact is quantitatively challenging. Extreme siderophile elements—elements such as osmium and iridium that are strongly concentrated in the metallic core—are found in Earth’s mantle in the relative proportions that they are found in chondritic meteorites, but at much smaller concentrations. The extreme siderophiles imply that Earth accreted the equivalent of a 20 km thick blanket of chondritic materials after iron had stopped migrating to the core (Anders 1989). Some of this may represent material from the core of the Moon-forming impactor. In either case, osmium isotopes show that this material resembled ordinary chondrites rather than the more volatile-rich carbonaceous chondrites (Meisel et al. 2001; Drake and Righter 2002). The total volatile load delivered by 20 km of ordinary chondrites that are 0.3% water by weight (Schaefer and Fegley 2007) is equivalent to the delivery of only 200 m of water, well short of an ocean. Only the wettest vectors, e.g., comets, could deliver an ocean of water in such a small total mass.

Application of Schaefer and Fegley (2007, 2010) and Hashimoto et al. (2007) scenarios to the late volatile hypothesis is straightforward. Earth is fully formed and impact velocities are high. Hence impacts are extremely energetic and to first approximation we can expect all the volatiles (and many of the refractory elements as well) carried by the impactors to be vaporized by impact, to equilibrate chemically with the other materials of the impactor, and to enter the atmosphere. This situation was addressed by Hashimoto et al. (2007) and Schaefer and Fegley (2010) using carbonaceous chondrites as the starting material. Both find that the gases that result are rather strongly reducing despite the minerals being rather oxidized. This occurs because these meteorites are carbon rich, and the bulk of the carbon is present in reduced form (Fig. 2). Thus the impacts of the late bombardment represent a substantial stochastic source of reduced gases to the atmosphere.

Kasting (1990) used an atmospheric photochemical model with redox tracking to show that meteoritic material falling on young Earth can produce a CO-rich atmosphere. In these models the atmospheric chemistry is computed assuming a steady state redox balance between reduced sources (volcanic gases and exogenic input of reduced matter, principally meteoritic iron and iron sulfides) and hydrogen escape. The latter is presumed to take place at the physical upper limit imposed by diffusion of hydrogen through the background gases. The presumption is that escape is easy once the hydrogen reaches the thermosphere. Kasting did not predict the synthesis of CH4 or NH3 because he knew no effective photochemical pathways for converting CO to CH4 or N2 to NH3, and he assumed the geologist’s CO2-N2-H2O atmosphere as a base state. Kasting found that the incoming flux of meteoritic iron could be big enough to flip the redox state of the atmosphere from CO2≫CO to CO≫CO2, although to do so the mean impact flux had to be comparable to the upper bound inferred from the lunar impact record. On the other hand, Kasting treated the input of meteoritic iron as a continuous function, which is not a good approximation for a distribution of impacts, which tend to be dominated by the few largest objects. This means that the delivery of new iron and iron sulfide would be stochastic, with very large excursions from the mean. If the transient effect of impacts is considered, it seems very likely that each major impact would convert a photochemically sensitive atmosphere from CO2 to CO. It has also been suggested that iron grains can catalyze the conversion of CO to CH4 (Kress and McKay 2004). The central role of iron in an impact-driven atmospheric chemistry was anticipated by Urey (1952b).

A recent model suggesting that hydrogen escape may not have been as rapid as most photochemical calculations have taken it to be (Tian et al. 2005) is directly relevant to Kasting’s model. If hydrogen escape were truly inefficient, the lifetime of transient reduced atmospheres would be greatly extended, and the balance between CO and CO2 would tip strongly in favor of the former. A consequence is that the atmosphere would be CO-dominated through most of the Hadean. Tian et al.’s argument that hydrogen escape was inefficient on early Earth assumes that the upper atmosphere would be cold as on Venus, because the atmosphere is composed mostly of CO2. Their claim is controversial because their model depends on gases other than hydrogen to provide the radiative cooling, but their model does not actually include gases other than hydrogen. In particular, the key assumption that the upper atmosphere was cold is not obvious and needs to be addressed quantitatively. Visconti (1975) computed the temperature of Earth’s upper atmosphere if the lower atmosphere were anoxic. He obtained thermospheric temperatures well over 1000 K for current solar max EUV fluxes. EUV fluxes from the young Sun would have much bigger (Zahnle and Walker 1982), so that hotter thermospheres would be expected. Visconti’s calculations contrast markedly with the cold thermospheres in Tian et al.’s pure hydrogen escape models.

Carbon monoxide is probably the easiest prebiotically interesting gas to generate in the post-Moon-forming-impact Hadean atmosphere. CO is relatively easy to generate abiotically in a wide range of plausible atmospheres, and it is packed with energy (with it organisms can eat water). CO could be formed by lightning, by impact shocks, or photochemically if there is a significant source of meteoritic of volcanic reducing power. The cold dry atmosphere of an iceball Earth is especially favorable to CO (Zahnle et al. 2008). The possible origin-of-life aspects of CO and its derivatives formamide (for pyrimidine synthesis, Powner et al. 2009) and OCS (condensing agent for forming peptide bonds, Leman et al. 2004) are catching attention, especially among prebiotic chemists who are attempting to synthesize an RNA world (Ricardo et al. 2004; Powner et al. 2009). There is also evidence that CO metabolism is very ancient (Ragsdale 2004). Modern methanogens first convert CO2 to CO with one enzyme (CO dehydrogenase, or CODH), and then apparently send the CO as a gas down a sealed tube to a second enzyme complex where it is used for energy or for cell material (Ragsdale 2004). This is known as the Wood-Ljundahl pathway of carbon assimilation; it can be regarded as parallel to the more famous Calvin cycle. The enzymes are both based on NiFeS cubes, fitting well with a separate speculation that the first metabolism made use of natural iron sulfides as catalysts (Wächtershäuser 1992).

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Evolution of the heart from bacteria to man.

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Origin and Evolution of the Ribosome

The modern ribosome was largely formed at the time of the last common ancestor, LUCA. Hence its earliest origins likely lie in the RNA world. Central to its development were RNAs that spawned the modern tRNAs and a symmetrical region deep within the large ribosomal RNA, (rRNA), where the peptidyl transferase reaction occurs.

peptidyl transferase

The enzyme is a ribozyme. Two non-equivlant ribonucleoprotein subunits operate in non-concerted fashion in peptide elongation. The small subunit forms the mRNA-binding machinery and decoding center, the large subunit performs the main ribosomal catalytic function in the peptidyl-transferase center.

To understand pre-LUCA developments, it is argued that events that are coupled in time are especially useful if one can infer a likely order in which they occurred. Using such timing events, the relative age of various proteins and individual regions within the large rRNA are inferred. An examination of the properties of modern ribosomes strongly suggests that the initial peptides made by the primitive ribosomes were likely enriched for l-amino acids, but did not completely exclude d-amino acids. This has implications for the nature of peptides made by the first ribosomes. From the perspective of ribosome origins, the immediate question regarding coding is when did it arise rather than how did the assignments evolve. The modern ribosome is very dynamic with tRNAs moving in and out and the mRNA moving relative to the ribosome. These movements may have become possible as a result of the addition of a template to hold the tRNAs. That template would subsequently become the mRNA, thereby allowing the evolution of the code and making an RNA genome useful. Finally, a highly speculative timeline of major events in ribosome history is presented and possible future directions discussed.

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The paper: The Puzzle of the Krebs Citric Acid Cycle: Assembling the Pieces of Chemically Feasible Reactions, and Opportunism in the Design of Metabolic Pathways During Evolution
Writers: Enrique Mele´ndez-Hevia, Thomas G. Waddell,2 Marta Cascante , J Mol Evol (1996) 43:293-303

Of the phosphomalate pathway, which they had eliminated, they write: “…IT COULD BE ARGUED, however, that the feeder P-malate COULD HAVE PLAYED SOME ROLE in earlier metabolism; and thus it IT COULD HAVE BEEN AVAILABLE. It is, in fact, HIGHLY UNLIKELY that some ancient metabolic pathway involving such a compound has vanished without trace (although the original pathway has been lost, such an intermediate COULD HAVE BEEN to other purposes); however, it CANNOT BE STRICTLY DISCARDED and thus, although UNLIKELY, phosphomalate and the [alternative] Krebs cycle structure…MIGHT BE FOUND IN SOME paleospecies as a case of paleometabolism.”Melendez et al conclude: “The Krebs cycle has been frequently quoted as a key problem in the WHAT ALREADY EXISTS. The most novel resuevolution of living cells, hard to explain by Darwin’s natural selection: How could natural selection explain the building of a complicated structure in toto, when the intermediate stages have no obvious fitness functionality? ……….. In the Krebs cycle problem the intermediary stages were also useful, but for different purposes, and, therefore, its complete DESIGN (Design?) was a very clear case of opportunism. ………..the KREBS CYCLE WAS BUILT through the process that Jacob (1977) called ‘evolution by molecular tinkering,’ stating that EVOLUTION DOES NOT PRODUCE NOVELTIES FROM SCRATCH (Oh? Then how did the first models get there??): IT WORKS ON WHAT ALREADY EXISTS. The most novel of our analysis is seeing how, with minimal new material, evolution CREATED (I thought evolutionauts weren’t creationists?) the most important pathway of metabolism, achieving the BEST CHEMICALLY POSSIBLE DESIGN. IN THIS CASE, A CHEMICAL ENGINEER WHO WAS LOOKING FOR THE BEST DESIGN OF THE PROCESS COULD NOT HAVE FOUND A BETTER DESIGN THAN THE CYCLE WHICH WORKS IN LIVING CELLS”

(Astounding. This guy just disproved his own theory. The one he is trying to prove! Is he really a closet intelligent design scientist?)

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