How OOL science continues to be the weak link on design deniers' team.

 Game Over? Nick Lane Wants Another Inning 

David Coppedge 

The score is 36-0, but the Darwin Team isn’t ready to concede. Lehigh University biochemist Michael Behe, writing for World Magazine (see our coverage here), described how he attended a conference of scientists to hear Nobel laureate John E. Walker, the world’s expert on ATP synthase, explain how it might have evolved. To design advocates, this rotary engine is a paragon of intelligent design. Walker, who shared a Nobel Prize for elucidating the motor’s rotary mechanism, spent his whole time describing the intricacies of this molecular machine, and never offered an evolutionary explanation for it until the Q&A session. Then, he was asked directly how a mindless process could produce such a stunning piece of work. Walker stumbled, offering only a fragment of speculation that it must have arisen “Slowly, through some sort of intermediate or other.” That’s when Behe, out of earshot, muttered two simple words, “Game over.”

Game over. The losing team heads for the showers with heads bowed. The Darwin Team’s MVP had just struck out at the bottom of the ninth. Calling the game in such an obvious wipeout would have been superfluous. The crowds file out of the stands. Suddenly, eight players run onto the field! “Wait! Wait!” they cry. “Let us have a time at bat!”

The rescue team, led by Nick Lane of University College London, waves a paper over their heads. It’s hot off the press from PLOS Biology, titled, “A prebiotic basis for ATP as the universal energy currency.” Lane shouts, We have the intermediate! It’s AcP! One of the refs eyeballs the paper for a minute. Will it be worth calling the teams back onto the field for another inning? 

A Plausible Scenario? 

The gist of the hypothesis is that acetyl phosphate (AcP), a simple molecule with the formula C2H5O5P, can phosphorylate ADP into ATP in water, if ferric ion (Fe3+) is present. The team believes their lab work offers a plausible scenario for prebiotic ATP formation without the need for ATP synthase. 

ATP is universally conserved as the principal energy currency in cells, driving metabolism through phosphorylation and condensation reactions. Such deep conservation suggests that ATP arose at an early stage of biochemical evolution. Yet purine synthesis requires 6 phosphorylation steps linked to ATP hydrolysis.This autocatalytic requirement for ATP to synthesize ATP implies the need for an earlier prebiotic ATP equivalent, which could drive protometabolism before purine synthesis. Why this early phosphorylating agent was replaced, and specifically with ATP rather than other nucleoside triphosphates, remains a mystery. Here, we show that the deep conservation of ATP might reflect its prebiotic chemistry in relation to another universally conserved intermediate, acetyl phosphate (AcP), which bridges between thioester and phosphate metabolism by linking acetyl CoA to the substrate-level phosphorylation of ADP. We confirm earlier results showing that AcP can phosphorylate ADP to ATP at nearly 20% yield in water in the presence of Fe3+ions. We then show that Fe3+ and AcP are surprisingly favoured.  

Sounds Impressive. Can It Work?  

The team tells the referee about additional surprising benefits of their intermediate. Visions of the Miller spark apparatus come to mind: 

Surprisingly, our results demonstrate that maximal ATP synthesis occurred at high water activity and low ion concentrations, indicating that prebiotic ATP synthesis would be most feasible in freshwater systems.Likewise, ferrous iron can be oxidized to ferric iron by photochemical reactions or oxidants such as NO derived from volcanic emissions, meteorite impacts, or lightning strikes, which also points to terrestrial geothermal systems as a plausible environment for aqueous ATP synthesis. 

Questions & Answers 

powers a disequilibrium in the ratio of ADP to ATP, which amounts to 10 orders of magnitude from equilibrium in the cytosol of modern cells. Molecular engines such as the ATP synthase use ratchet-like mechanical mechanisms to convert environmental redox disequilibria into a highly skewed ratio of ADP to ATP.” But we cannot say how that happened.

But how could a simple prebiotic system composed mostly of monomers sustain a disequilibrium in ATP to ADP ratio that powers work? Well, “One possibility is that dynamic environments could sustain critical disequilibria across short distances such as protocell membranes.”

Didn’t you just assume the existence of a protocell with a membrane? Where did those come from? Look, we’re not trying to come up with a complete picture of how life originated. We’re just trying to explain why ATP is the universal energy currency for life as it exists today, and how it might have emerged.

Emerged… by chance, you mean? Isn’t that circular reasoning? How so? What other possibility is there?

There’s intelligence, the only cause ever observed that is capable of assembling complex parts into a functional whole. Sorry; we thought this was a scientific baseball diamond.

It is. So what is your explanation for the functional information in the simplest life? Your paper admits that “ATP links energy metabolism with genetic information.” What is the source of that genetic information? Uh, some sort of intermediate or other.

The referees convene and shout out, “GAME OVER!” 

On reading the fossil record.

 Fossil Friday: Moniopterus — Snake, Beetle, or Mollusk?

Günter BechlyEgg-shaped fossils of about two inch size have been described as Moniopterus japonicus from the Miocene of Japan. It is a perfect showcase for how paleontologists play fast and loose with the over-interpretation of poorly preserved fossils. Moniopterus was initially described as the only known example of fossil sea-snake eggs by Hatai et al. (1974). Wow, that sounds interesting, if we gloss over the little lapse that the authors accidentally placed the fossils in the bony fish family Ophichthyidae instead of the sea-snake subfamily Hydrophiinae, because both animals have the same common name in Japanese. Ooops, that’s an embarrassing mistake for professional scientists writing a technical paper, but anyway, at least they found the first sea-snake eggs, or did they?

About twenty years later, another study recognized the same material as fossilized pupal chambers of a coleopteran insect (Johnston et al. 1996). Hmmm, that’s quite a different take on the same fossils, but it gets even better. A re-examination of the holotype specimen by Haga et al. (2010) provided no evidence in support of these previous interpretations. Instead the fossils turned out to be borings of a rock-boring mytilid bivalve of the genus Lithophaga. So, a trace fossil of a mollusk had been misidentified in different phyla as snake egg and as beetle pup

That this case of blatant misidentifications is not an isolated example is shown by the case of alleged vertebrate eggs from the Cretaceous of the Gobi Desert, which turned out to be fossilized pupal chambers of beetles (Johnston et al. 1996). But on the other hand, should we trust the latter study at all, given the blunder they made with Moniopterus? Scientists are only humans and many of them see what they want to see. Fossils often leave a lot of room for wild imagination and wishful thinking. Of course, they still prove Darwinian evolution beyond a reasonable doubt! Just follow the science and don’t ask silly questions.a. 

References 

1.Hatai K, Masuda K & Noda H 1974. Marine fossils from the Moniwa Formation along the Natori river, Sendai, northeast Honshu, Japan, part 2. Problematica from the Moniwa Formation. Transactions and Proceedings of the Paleontological Society of Japan NS 95, 364–371. DOI: https://doi.org/10.14825/prpsj1951.1974.95_364.

2.Johnston PA, Eberth DA & Anderson PK 1996. Alleged vertebrate eggs from Upper Cretaceous redbeds, Gobi Desert, are fossil insect (Coleoptera) pupal chambers: Fictovichnus new ichnogenus. Canadian Journal of Earth Sciences 33(4), 511–525. DOI: https://doi.org/10.1139/e96-040.

3.Haga T, Kurihara Y, Kase T 2010. Reinterpretation of the Miocene Sea-Snake Egg Moniopterus japonicus as a Boring of Rock-Boring Bivalve Lithophaga (Mytilidae: Mollusca). Journal of Paleontology 84(5), 848–857. DOI: https://doi.org/10.1666/09-126.1.

I rant some more against reductive spiritualism.

 Psalms139:13BSB"For You formed my inmost being;a

You knit me(Objective first person singular) together in my mother’s womb." 

Can a reductive spirit soul be the fruit of sexual reproduction. Note that natural processes occurring in the impregnated womb are not merely responsible for the impersonal tent that the ghost who is the real person(the real me) ,but are JEHOVAH'S instrumentalities in bringing the soul into being. 

John3:6NIV"Flesh gives birth to flesh, but the Spirit gives birth to spirit." 

So the human cannot give birth to the superhuman. 

Matthew22:17,18NIV"17Then what was said through the prophet Jeremiah was fulfilled:

18“A voice is heard in Ramah,

weeping and great mourning,

Rachel weeping for her children

and refusing to be comforted,

because they(objective third person plural) are no more.” d" 

Death for the bible writers resulted in a reversion to one pre life state not a progression to a high post life existence. This is why they can coherently present the resurrection of the dead as a hope and not an incoherent word salad as is the case with Christendom's theologians. Thus it was not merely the impersonal fleshly coverings of these children that was dissolved their personhood came to an end. Until the one who calls things that are not(including things that once we're) as though they are(see romans 4:17) calls them to mind. 

Can we talk about this? II

 Listen: Demonizers and Dehumanizers 

Evolution News @DiscoveryCSC 

A new episode of ID the Future brings the second half of a panel discussion at the 2022 Center for Science & Culture Insider’s Briefing. This portion begins with bioethicist and Discovery Institute Senior Fellow Wesley J. Smith making a surprising argument: His own field, bioethics, is at war with true medical ethics. Specifically, its most prominent figures — hailing from elite universities in the United States and Europe — are dedicated to emptying our medical culture of traditional ethical standards that protect human rights and are guided by a commitment to inherent human dignity.

Some leading bioethicists see human beings as of no more inherent value than yeast. Smith stands athwart this anti-human trend and urges listeners to wake up and resist. Then John West, managing director of Discovery Institute’s CSC, spotlights those who demonize people who have resisted demands to be vaccinated against the COVID-19 virus, with some even calling for such people to be restricted to house arrest, or imprisoned. West also notes that many of those calling for such strong-arm tactics make no distinction between those who have and haven’t already had COVID-19, despite the fact that there is abundant scientific evidence that having had COVID-19 is a more effective form of vaccination than any vaccination shot. West decries the demonizing and bullying tactics he references, calling such behavior anti-science and anti-reason. He urges supporters of vaccinations to meet the other side not with insults but with reasoned discourse and scientific evidence. Download the podcast or listen to it here.