Saturday, December 22, 2018

Primordial Chicken Soup.

Where do we come from? How did we get here? So asks almost every child. And thinking adult. Customers in the Tavern offer answers, and few, if any, seem to satisfy the critics. Especially the atheistic ones.  Offer the most compelling - (well, to me )- that my Supplier made us, and a chorus arises from beyond the hedges. No. It has to be 'nature' they shout.

We come from the Primordial Soup !

Hah ! Even the most uncritical have a problem with that. Where did the soup come from : and is it chicken soup or egg soup?

So the question still stands. What is the Origin of Life?

Some folk think that Life is and was always 'Inevitable' simply by the workings of blind chance.

Hmmmm. Inevitable in a Universe of physical and chemical 'Laws', that is, where randomness seems to be a feature.

But is it so? Is it that simple.?

A fine fellow, Phillip C, showed up to give us a run down on the state of the scientific and mathematical arts in this pursuit of the facts......

He opened with a statement of closure from James Tour – a mate of his'n and one of the top ten leading chemists in the world:
We have no idea how the molecules that compose living systems could have been devised such that they would work in concert to fulfill biology’s functions. 
We have no idea how the basic set of molecules, carbohydrates, nucleic acids, lipids, and proteins, were made and how they could have coupled into the proper sequences, and then transformed into the ordered assemblies until there was the construction of a complex biological system, and eventually to that first cell.
Nobody has any idea how this was done when using our commonly understood mechanisms of chemical science. Those that say they understand are generally wholly uninformed regarding chemical synthesis. Those that say “Oh, this is well worked out,” they know nothing, nothing about chemical synthesis – Nothing!
Further cluelessness – From a synthetic chemical perspective, neither I nor any of my colleagues can fathom a prebiotic molecular route to construction of a complex system. We cannot figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids, and proteins. Chemists are collectively bewildered. Hence I say that no chemist understands prebiotic synthesis of the requisite building blocks let alone their assembly into a complex system.
That’s how clueless we are. I’ve asked all of my colleagues – National Academy members, Nobel Prize winners -I sit with them in offices; nobody understands this. So if your professors say it’s all worked out, your teachers say it’s all worked out, they don’t know what they’re talking about. It is not worked out. You cannot just refer this to somebody else; they don’t know what they’re talking about.”
The Origin of Life: An Inside Story - March 2016 Lecture with James Tour .
Let a more presentable chap than I do the presenting. 

If you want to go to Dr Tour then please do. It is a tad longer though.

Now, I have to admit to limitations. I serve a fine-topped ale and old Knights know a sharp sword edge from a dull one but physics and chemistry and deep maths are not really my forte. Not even my thurte. So I sat back and listened to some explanations.

Mathematical Basis for Probability Calculations Used in (the vid above) Origin
Putting the probabilities together means adding the exponents. The probability of getting a properly folded chain of one-handed amino acids, joined by peptide bonds, is one chance in 10^74+45+45, or one in 10^164 (Meyer, p. 212). This means that, on average, you would need to construct 10^164 chains of amino acids 150 units long to expect to find one that is useful.
You can follow that up here....  

The other bits below are also referenced in the YT notes for the video so go there too.
Minimal Complexity Relegates Life Origin Models To Fanciful Speculation - Nov. 2009 
Excerpt: Based on the structural requirements of enzyme activity Axe emphatically argued against a global-ascent model of the function landscape in which incremental improvements of an arbitrary starting sequence "lead to a globally optimal final sequence with reasonably high probability". For a protein made from scratch in a prebiotic soup, the odds of finding such globally optimal solutions are infinitesimally small- somewhere between 1 in 10exp140 and 1 in 10exp164 for a 150 amino acid long sequence if we factor in the probabilities of forming peptide bonds and of incorporating only left handed amino acids. 
Today, origin of life research continues under the assumptions of materialism. Researchers believe that if they can explain the formation of a building block or a possible energy source, they are making progress toward solving one of the most baffling mysteries of science. The major factor they consistently fail to address is the source of the information that is the hallmark of life. It’s not enough to get the building blocks of a cell any more than it is to get iron ore for a skyscraper. The building blocks need to be assembled and arranged in a purposeful way. That’s the sequencing problem for RNA, DNA and proteins.
Since protein machines do most of the work in living cells (both modern and primordial), their existence merits explanation.
As discussed in Origin, proteins are constructed from precisely sequenced chains of amino acids. Most proteins in the simplest life forms (Achaea) range from 156 to 283 amino acids in length.a Some shorter proteins exist (more accurately called “polypeptides”), but most of them have simpler roles in the cell, acting as signaling molecules or cofactors. Some proteins contain many hundreds or thousands of amino acids. We chose a smaller-than-average protein of 150 amino acids to illustrate the difficulty of sequencing any protein by chance—including those required in the first living cell.
The estimated probability for a 150-amino-acid protein comes from the work of Douglas Axe and Stephen Meyer. Axe published a paper in 2004 that calculated the fraction of useful proteins in random chains of amino acids. A “useful” protein must be able to fold into a stable structure to perform any function. Compared to the huge number of random chains that would not fold, the number of proteins with this ability is miniscule.
After carefully measuring the tolerance to change in particular enzymes, Axe estimated that only one in 1074 chains of 150 amino acids would fold and be functional. This implies that you would have to search through 1074 chains of that length to find a single useful protein. So we start by looking for one protein (any chain of 150 amino acids) that could be useful in a primitive cell by spontaneously folding into a stable shape.
The Case Against a Darwinian Origin of Protein Folds - Douglas Axe - 2010 
Excerpt Pg. 11: "Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin."
Hey, look, I take the view that God made us.

It sounds so simplistic, doesn't it?

My Supplier makes the Rules. He is quite able to do the probable, the improbable, the totally impossible.

He, and only He, created the Universe..... and Life.

Argue against it amongst yourselves ( as mankind has done interminably) while I pull a few pints for you. 

Give me a hoy if you come along with a better answer.

Oh, by the way, He chose to enjoy some of the 'life' bizzo He created too. Its the anniversary of His Birthday in a few days.

Believe it.


Wednesday, December 19, 2018

Lost Civilisations? Atlantis Staring Us in the Eye.

One day our civilisation may be a myth, like Atlantis. The remains may be as difficult and exciting to uncover as Roman Britain is today. Just as individuals with dementia may not even be aware of their demise, or the average Roman going about his day with visigoths and sundry barbarians in his midst, so we may be living through Western Civilisation disappearing before our eyes and many people remaining largely unaware of the impending doom. Will there be anything to show we were here?

The past few weeks have seen Europe in high fever with its vital organs being eaten away by corruption, viruses, bacteria in high places fighting Yellow Vests in the streets, and many a pock-marked black face staring down as a plague attacks the healthy. Frankly the old Tavern Keeper has been laid low for a while too, but amid the grumbles this week came some quite odd news. 

Some folk think that The End is Nigh. Western civilisation is being flooded with very unchristian hordes and my Supplier observes from on high. Just whether He will permit another world-wide destruction like the last time He sent a Flood, who knows? I am close to one of His messengers who has not whispered anything like that in my ear when he delivers the Good Ale. Little remains of what was before.

Greenies, of course, have been threatening a flood for a few decades now. The rising sea levels, they wish upon us, would swamp and destroy quite a bit of our civilisation. They want us to sink beneath the waves and become a myth. I don't know of greenies being around back in Atlantis' day and no slow rise was predicted back then as far as we are told. It was supposed to have happened overnight. There yesterday: gone the next day. Our greeny-wished flood is a tad slower. Glacial in fact.

I was hobbling around the bars  a week or two back when I came across the first hints. Graham Hancock is a British writer and journalist who specialises in theories involving ancient civilisations, stone monuments, megaliths and the like, and was settled in a quite corner speaking of the Lost City civilisation, Atlantis. He has little truk with the Wikipedia writer who barely conceals his disdain and dismissal of the notion of Atlantis altogether. 

Giving the positive a little preference, let us hear briefly from Graham before looking at the 'general' version.

His position is clear. As it that of the Wiki miserable who said: Atlantis (Ancient Greek:"island of Atlas") is a fictional island mentioned within an allegory on the hubris of nations in Plato's works Timaeus and Critias, where it represents the antagonist naval power that besieges "Ancient Athens", the pseudo-historic embodiment of Plato's ideal state in The Republic. In the story, Athens repels the Atlantean attack unlike any other nation of the known world, supposedly giving testament to the superiority of Plato's concept of a state. The story concludes with Atlantis falling out of favor with the deities and submerging into the Atlantic Ocean.

Despite its minor importance in Plato's work, the Atlantis story has had a considerable impact on literature. The allegorical aspect of Atlantis was taken up in utopian works of several Renaissance writers, such as Francis Bacon's New Atlantis and Thomas More's Utopia. On the other hand, nineteenth-century amateur scholars misinterpreted Plato's narrative as historical tradition, most notably in Ignatius L. Donnelly's Atlantis: The Antediluvian World. Plato's vague indications of the time of the events—more than 9,000 years before his time —and the alleged location of Atlantis—"beyond the Pillars of Hercules"—has led to much pseudoscientific speculation. 

As a consequence, Atlantis has become a byword for any and all supposed advanced prehistoric lost civilizations and continues to inspire contemporary fiction, from comic books to films.

While present-day philologists and classicists agree on the story's fictional character, there is still debate on what served as its inspiration. As for instance with the story of Gyges, Plato is known to have freely borrowed some of his allegories and metaphors from older traditions. This led a number of scholars to investigate possible inspiration of Atlantis from Egyptian records of the Thera eruption, the Sea Peoples invasion, or the Trojan War. Others have rejected this chain of tradition as implausible and insist that Plato created an entirely fictional nation as his example, drawing loose inspiration from contemporary events such as the failed Athenian invasion of Sicily in 415–413 BC or the destruction of Helike in 373 BC.

So then, into the bar comes young Jimmy. He has some 'pedigree' too.  Youthful and exuberant Jimmy is an  Independent researcher - Former Corporate Theft/Fraud Investigator - Army/Iraq war vet with an MBA, who has been around a bit.

I shall show you Jimmy in his engaging full flood. That word again !! But first his view is easily summarised.
Not only did the lost city of Atlantis actually exist, but its true location has been hiding in plain sight for thousands of years, completely unnoticed, as we’ve been looking in all the wrong places...Since everyone assumes that it must be under the ocean somewhere, such as in the depths of the Atlantic Ocean or the Mediterranean Sea, which have long been considered to be the most likely places for its existence. 
And no, I am not about to suggest that Antarctica is the hidden location of Atlantis, either. 
Because here I am going to connect the dots on the exact words that Plato used to describe Atlantis, its location, and the geographical land features that surround it, which were recorded in Plato’s dialogues, the Critias and Timaeus. And the details that Plato shared of Atlantis, which I’m about to share with you in side by side comparison, will show you that the Richat Structure located in Mauritania, Africa, also commonly referred to as the Eye of the Sahara, or the Eye of Africa…is the most likely location for the lost city of Atlantis.
So, go for it Jimmy. Tell us about it.

He gives an entertaining and plausible account, in my opinion. (My opinion is open to question, of course, as long as you pay for a round).

Now, you might be thinking that he has not given you enough to be 'convincing': so he came back a few days later with more.

The Bible does not mention Atlantis. Neither did Assurbanipal from his Assyrian perspectives and tales. He mentioned the Flood, of course, an ancient myth even for his mob, but then he was very unlikely to have even known of Atlantis, which was well out of his way. But the timing is quite important. 

Perhaps one day soon some internet billionaire will do as the 19C explorers and arhaeologists did and go dig around a bit. It would be about time.

Meanwhile I think Jimmy deserves a few days free run of the bars to drink his fill. His account is fascinating stuff. Fair took my mind off my ailments.

I shall raise a tankard to his efforts to date.