Can We Solve the Mystery of the Origin of Life by Creating Life in the Lab?

Francis Crick said in 1981, “Every time I write a paper on the origins of life I swear I will never write another one, because there is too much speculation running after too few facts, though I must confess that in spite of this, the subject is so fascinating that I never seem to stick to my resolve.”1 He isn’t alone. With unmistakable dejection, Christian de Duve listed a number of OOL theories — pyrophosphate world, iron-sulfur world, thioester world — adding, “opinions are divided on what has been accomplished by all this activity. While much has been learned, it is clear that we are still nowhere near explaining the origin of life.”2 James Shapiro said bluntly in 2010 that origin of life theories are “still on the fringes of serious scientific discussion.”

Science-Fictions-square.gifOne group is charting a genuinely new path. Nobelist Jack Szostak seeks to construct an origin-of-life grade cell: “You want something that can grow and divide and, most importantly, exhibit Darwinian evolution. The way that we study that is by trying to make it happen in the lab.” He thinks he has succeeded with the cell membrane but “genetic material is the harder problem; the chemistry is just more complicated.” And well-known origin-of-life researcher Gerald Joyce thinks that “alien” (i.e., alternative) life forms will more likely be constructed in a laboratory than found in space. Richard Dawkins is optimistic about such efforts: “I watch from the sidelines with engaged curiosity, and I shall not be surprised if within the next few years, chemists report that they have successfully midwifed a new origin of life in the laboratory.”

The lab may be the best bet. Science writer John Horgan assesses the current programs unsparingly (but doubtless correctly): “This is by far the weakest strut of the chassis of modern biology. The origin of life is a science writer’s dream. It abounds with exotic scientists and exotic theories, which are never entirely abandoned or accepted, but merely go in and out of fashion.” We are forever on the verge of a great discovery — perhaps our hundredth such verge — but there are no dates proposed for progress evaluation. We can, however, draw some conclusions at this point:

Life’s origin on Earth may simply be impossible to determine. It was, after all, an event in time, in history, like the moment the last dinosaur died or the first human fashioned a wheel. If the origin is chance, as most models imply, it is all the more likely to be lost to follow-up.

Life produced in the lab would be a stunning feat but would not necessarily explain life’s historical origin. As evolutionary biologist Jerry Coyne told New Scientist, “Even if we can create a ‘second genesis’ in the laboratory, that won’t tell us exactly how it happened on Earth 3.8 billion years ago,” adding “There are so many different scenarios for how life got going and they all involve molecules that don’t get fossilized. It’s a clear limit.” Astrobiologists argue that life could get started a number of ways elsewhere. A successful lab experiment does not rule out other scenarios, on Earth or anywhere else.

Researchers who design their experiment so that life “just happens” a certain way in the lab are not ruling out design. A gaming commission designs a lottery to assign winning tickets randomly, using a computer algorithm. But the algorithm was designed to assign the numbers randomly. For example, a math genius might then game the algorithm by detecting the design and arranging his ticket purchases to greatly improve his odds. But, if so, he is substituting design for design, not design for chance. Indeed, one Toronto, Canada, statistician did something like that, demonstrating to the gaming commission a flaw in the algorithm for assigning the numbers, such that a design could be detected (and the game was changed as a result).

In short, setting ethical concerns aside for the moment, creating life from scratch in the lab is the only strategy that could, in principle, yield results that are subject to normal science investigation (controlled conditions in the present day). But it would not demonstrate either that life came into existence by that method or that it came into existence without design. Quite the opposite; we would now have a method of creating life by design — but still no known methods that do not include design.

Could we at least apply what we learn from designing life ourselves to the lost events of deep time? Maybe. But the most reliable methods for producing life in the lab might require the most intervention or feature the conditions we think least likely on early Earth. On the other hand, we could at least test panspermia models. Best results stemming from Mars or asteroid simulations would support panspermia far more strongly than lack of success with Earth-based models (really, panspermia is then just an argument from desperation).

And — some may think this benefit alone worth all the trouble, risk, and expense — we could ignore dozens of sketchy model-of-the-month scenarios based on contested claims about Earth’s history. Either a model creates life or it isn’t ready for prime time. Science journals can then dispense with complex conditional tenses like “might have had,” “could have had,” and “would have had” when writing about the creation of life.

In short, the lab approach offers an all-science-and-no-religion way out of the present quagmire, with the likelihood of at least some useful answers. Why not just generally adopt it, or at least work toward it? One problem is that it doesn’t support claims about the vast powers of randomness or the brute laws of nature. And no solution that dismisses both can be regarded as “science” today. So origin-of-life projects continue to head off in dozens of directions to nowhere instead.

But they at least remain free of any taint of design.

 

Article from Evolutionnews

References:

(1) Francis Crick, Life Itself (1981), p. 153.

(2) Christian de Duve, “Mysteries of Life”, in Bruce L. Gordon and William A. Dembski, The Nature of Nature: Examining the Role of Naturalism in Science (Wilmington, DE: ISI Books,
2011), p. 349.

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#id, #origin-of-life, #panspermia, #science

Where is the center of the universe?

N.W.nlund

Read the part about where in the beginning the universe was a single point. Mind boggling! If gravity is theoretical, what avenues of space-time have we overlooked that could suggest a constant metric exists in the universe of omnipresence? This may sound absurd but I think neutrinos are the blood or veins of the universe since they can pass through anything and have small mass.

What are quarks and is that somehow the frequency part in Tesla’s classic “energy, frequency and vibration” statement about the cosmos? Sentient beings, not plants and trees all must live and die together. Was there a separate Big Bang for sentience or the ephemeral that we couldn’t have seen or heard? Maybe this took place after the Big Bang, or before it. Maybe this is a good time for parts of science to replace the faith based reasoning for those that want new explanations.. I…

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A Precise Bound On The Higgs Boson Width

At 125 GeV of mass, the Higgs boson is a very heavy particle; yet its natural width is predicted to be of just 4.15 MeV in the standard model, a value much smaller than that of particles of similar mass. The top quark, for instance, has a width of 1.5 GeV; and the Z boson has a width of 2.5 GeV: three orders of magnitude larger.

Natural width -the width of the resonance shape peaking at the rest mass of the particle- is a fundamental attribute of elementary particles, and arguably an even more important one than the mass itself. In fact the width determines the lifetime of the particle: particles that live longer have a smaller width because they have more time to “settle” to their nominal rest mass. In the case of the Higgs, if we found out that its width is substantially larger than what the standard model predicts, we would immediately know that there are possible decay modes of which we know nothing about yet: it would be a clear indication of new physics. The presence of extra ways for the particle to decay in fact ensures that the lifetime will be shorter, and the width larger.

4.15 MeV are a really small number as compared to the experimental resolution in the particle mass which we may achieve with the CMS or ATLAS experiment. Hence there is no chance to measure that parameter directly: any Higgs mass distribution experimentally determined at the LHC will have a observed width waaaay larger than the natural one. However, we can measure the Higgs natural width indirectly by looking at very off-shell Higgs bosons.

It has in fact been noted by several theorists that the peculiar production processes yielding Higgs bosons at the LHC modify significantly the observable Higgs boson lineshape. In other words, what we can detect at the LHC in a histogram of the Higgs mass is the convolution of the Lorenzian shape – a peak with a width equal to the natural width of the Higgs, centered at the Higgs mass – with the production cross section, which receives enhancements at high mass due to the large coupling of the Higgs boson with the heavy top quark. The result is that instead of quickly dying out, the expected signal mass distribution has a significant tail at very high masses.

It looks strange to think that a 125 GeV Higgs boson may yield a significant signal at masses of 300 GeV and more, but that is exactly what happens. What is most interesting, however, is that the strength of the signal there is strongly dependent on the natural Higgs width. Check out for instance the picture below, which shows the reconstructed mass of ZZ pairs by CMS. A Higgs boson with a width of 25 times the SM prediction (i.e. just a bit more than 100 MeV or so) would produce a very significant enhancement!


Above, the four-lepton mass distribution of CMS data collected in 2012 8-TeV pp collisions is compared to ZZ background (blue) and SM prediction (in beige), and with a Higgs with a natural width 25 times the SM prediction (dashed histogram).

By studying both the 4-lepton final state of ZZ events and the two charged leptons + 2 neutrino final state, CMS has managed to determine an upper limit on the Higgs width at 4.2 times the standard model value, at 95% confidence level. That is already cutting into several models that could predict much larger widths by hypothesizing the existence of unknown decays. Note that results are extracted for two cases: under the assumption that the global production rate is what the SM predicts, and under no assumption on the rate. A larger global production would enhance the tails, but production rates much larger than the SM prediction are however excluded by looking at the 125 GeV peak. The x4.2 times limit is extracted under no rate assumption.

 

From Science 2.0

#higgs-boson, #natural-width, #science

The most beautiful animal you’ve never seen

The small creature I’d found was a Sapphirina copepod, or as I like to call it, a sea sapphire. Copepods are the rice of the sea, tiny shrimp-like animals at the base of the ocean food chain. And like rice, they are generally not known for their charisma. Sea sapphires are an exception. Though they are often small, a few millimeters, they are stunningly beautiful. Like their namesake gem, different species of sea sapphire shine in different hues, from bright gold to deep blue. Africa isn’t the only place they can be found. I’ve since seen them off the coasts of Rhode Island and California. When they’re abundant near the water’s surface the sea shimmers like diamonds falling from the sky.  Japanese fisherman of old had a name for this kind of water, “tama-mizu”, jeweled water.

The reason for their shimmering beauty is both complex and mysterious, relating to their unique social behavior and strange crystalline skin.

Sapphirina2

Photo by scientist, wildlife photographer and filmmaker Stefan Siebert.

A key clue: this sparkle is only seen in males. Males live free in the water column, but females make their home in the crystal palaces of a strange, barrel-shaped jellies called salps. And though they’re not flashy, these parasitic princesses have huge eyes relative to males. Perhaps female sea sapphires look out upon an endless expanse of ocean sparkling with blue and gold, searching for the a particularly luminous shine. Or it could be that males use their shimmer to compete with one another, like jousting knights in shining armor, while the females watch on. About the social life of sea sapphires, we know very little. But how do they shine in the first place?

 

Plates

Left: A single layer of hexagonal plates in the sea sapphire’s skin, as viewed from above, Right: Layers of plates as viewed from the side [1]

The secret to the sea sapphire’s shine is in microscopic layers of crystal plates inside their cells. In the case of blue sea sapphires, these crystal layers are separated by only about four ten thousandths of a millimeter; about the same distance as a wavelength of blue light. When blue light bounces off these crystal layers, it is perfectly preserved and reflected. But for other colors of light, these small differences in distance interfere, causing the colors to cancel out. So while white light is composed of all colors, only blue light is reflected back. This type of coloration is known as structural coloration, and though resembling a gem in hue, a sea sapphire’s color has more in common with an oil sheen than a pigmented jewel. Combine this nifty trick with the sea sapphire’s impressively transparent body, and you have an animal as radiant as a star in one moment, and invisible in the next.

 

I was lucky to find one, but sometimes they are found in astonishing numbers. My friend and colleague Erik Thuesen once told me about his work on an ROV, as the submersible was coming to the surface, “it passed through this amazingly sparkling layer of iridescent Sapphrina”.  A rare sight to see; not, perhaps, due to the rarity of these ocean gems, but the rarity at which we enter their world. Even as you read this, wherever you are and whatever you’re doing, they’re out there right now. Quietly shining in their own private universe of stars.

 

 Work Cited and additional reading

[1] J. Chae, S. Nishida (1994). Integumental ultrastructure and color patterns in the iridescent copepods of the family Sapphirinidae (Copepoda: Poecilostomatoida). Marine Biology, Volume 119, Issue 2, pp 205-210 

Yuval Baar, Joseph Rosen, Nadav Shashar (2014). Circular Polarization of Transmitted Light by Sapphirinidae Copepods. PloS ONE. DOI: 10.1371/journal.pone.0086131

#art, #science

Maybe if We Throw Enough Models at the Origin of Life…

… some of them will stick? This month’s issue of The Scientist offers a look at “some of the most current origin-of-life science, from new research on how RNA may have been assembled from precursor molecules to what we now know about our last universal common ancestor.” That ancestor, we are assured, is “not [Darwin’s] ‘primordial form,’ but rather a sophisticated cellular organism that, if alive today, would probably be difficult to distinguish from other extant bacteria or archaea.”

Science-Fictions-square.gifSo one and a half centuries of research have not yet turned up a single entity that, like Thomas Huxley’s hoped-for Bathybius haeckelii, is on its way to becoming life? Hardly for lack of trying! Here is a whirlwind tour of the waterfront:

Arsenic world: In December 2010, NASA researchers reported that they had taught microbes to metabolize arsenic instead of phosphorus, demonstrating that life could arise from unexpected chemicals, perhaps elsewhere in the galaxy. (Some researchers have suggested chlorine life instead.) Most researchers were unconvinced. In 2011, Science published eight articles questioning NASA’s study in a single edition and arsenic-based life featured as one of The Scientist‘s top ten scandals of 2011.

Clay world: Some theorists argue that clay (or clay hydrogels) can select for molecules that can self-organize. The Scriptural associations of clay were a gift to science writers; the details did not impress researchers. Information theorist Hubert Yockey pointed out that clay crystal structures just repeat the same information indefinitely. By contrast, life’s minimum information density is somewhere around the level of DNA. OOL theorist Leslie Orgel (1927-2007) said it wouldn’t work for RNA either: If clay had the structural irregularities needed to enable RNA to emerge, it probably wouldn’t reproduce it accurately.

Lagoons on the early Earth: Stanley Miller (1930-2007) of the textbooks’ Miller-Urey experiment believed that the conditions on early Earth’s beaches could foster pre-life reactions because chemicals would concentrate more there than out at sea. But Robert Shapiro, proponent of the “metabolism first” model, complained that “a large lagoon would have to be evaporated to the size of a puddle, without loss of its contents, to achieve that concentration. This process is not thought to occur today.” He added, with an apparent touch of impatience,

The drying lagoon claim is not unique. In a similar spirit, other prebiotic chemists have invoked freezing glacial lakes, mountainside freshwater ponds, flowing streams, beaches, dry deserts, volcanic aquifers and the entire global ocean (frozen or warm as needed) to support their requirement that the “nucleotide soup” necessary for RNA synthesis would somehow have come into existence on the early Earth.

Metabolism first: Robert Shapiro (1935-2011) questioned Leslie Orgel’s RNA world because of “the extreme improbability” that such a long, complex molecule as RNA would spontaneously arise and initiate life. His doubts earned him the title, Dr. No. Aspiring to somehow become Dr. Yes, he offered a model that life began via small molecules with a simple metabolism and progressed from there, hence “metabolism first.” He hoped, among other things, to vindicate the idea that “There’s nothing freaky about life; it’s a normal consequence of the laws of the universe.”

 

Researcher Eric Smith, a physicist at the Santa Fe Institute, offers a more recent model of early metabolism: “It seems likely that the earliest cells were rickety assemblies whose parts were constantly malfunctioning and breaking down. … How can any metabolism be sustained with such shaky support? The key is concurrent and constant redundancy.” Or “millions of years of a poor replicator”, as a summary article in Science put it, leaving unclear how hits could have mattered in those days but misses didn’t.

“RNA first” proponent Leslie Orgel responded irritably to Shapiro’s metabolism first model, “solutions … dependent on ‘if pigs could fly’ hypothetical chemistry are unlikely to help.” Near the end of his life, Orgel had perhaps forgotten that he himself once co-authored a paper with Francis Crick speculating that extraterrestrials might have started life.

Numerous less publicized models wallop through the science press, on the hope, perhaps, of a lucky strike: For example, not-obviously-promising substances such as hydrogenammoniahydrogen cyanideformaldehyde, or peptides, possibly kick started life. Maybe metals acted as catalysts. Or mica sheets. Otherwise, cold temperatures or ice helped life get started, despite the fact that cold reduces chemical reaction speed. Or a high salt environment. Or hot springs. No surprise that science writer Colin Barras observes that origin of life is “a highly polarised field of research.” Most fields have only two poles, not twenty.

One model is noteworthy for the fact that it is the closest that origin of life theorists have come so far to an ancient pagan creation myth. Yet it was published in a popular science magazine (New Scientist):

Once upon a time, 3 billion years ago, there lived a single organism called LUCA. It was enormous: a mega-organism like none seen since, it filled the planet’s oceans before splitting into three and giving birth to the ancestors of all living things on Earth today. … LUCA was the result of early life’s fight to survive, attempts at which turned the ocean into a global genetic swap shop for hundreds of millions of years. Cells struggling to survive on their own exchanged useful parts with each other without competition — effectively creating a global mega-organism.

How did it all work? “It was more important to keep the living system in place than to compete with other systems.”

 

Really? More important for whom? Who then existed for life to be more important to? The mega-organism itself? But that would imply selfhood and purpose. If selfhood and purpose were present at the origin of life, why is design a problem and not a solution?

Editor’s Note: Here are links to the whole “Science Fictions Origin of Life” series.

Photo source: TheGiantVermin/Flickr.

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Malaysia Airlines Flight MH370 – Pieces Of The Puzzle

here has been a great amount of idle speculation and misinformation about the missing flight MH370 in the media and around the web.  Much of the news story has been colored by idle speculation bordering on xenophobia regarding the stolen passports.  

That is no way to solve a puzzle.

 

The best way to solve any puzzle is to separate the available information into what is known, what is probable, what is plausible and what is mere speculation.  This may be compared to a well-known method for solving an ordinary jigsaw puzzle.  We know that there are four corners, so we identify those pieces first.  These pieces form what may be called the four anchor points of our solution.  Next we identify all of the edge pieces and place them where they appear to belong.  We now have a boundary  or frame for our solution.  Next, within that boundary we place pieces which seem to match the general color and pattern scheme of a roughly defined area.  As the puzzle nears completion we find pieces linked to each other and to the edges.  This may be regarded as an example of a chain of evidence.  The final step is, of course, to fill in the blanks.  

Many comments on MH370 around the web seem to be trying to fill in the blanks as a first step.  Some people seem even to be trying to use pieces from the wrong puzzle.

Our real life puzzle – the disappearance of flight MH370 can best be solved, if at all,  by the application of logical, scientific steps.  We first need to separate out and categorize the pieces of the puzzle.  The first category, the anchor points,  consists of what is known to a high degree of certainty.  Next we seek out what is probable and use that to define the boundaries of our solution – the edge pieces.  Next we look for what is plausible, clusters of pieces of the puzzle which seem to be part of a self-consistent pattern.  Only then should we look at what is merely theoretical – all the other bits of the jigsaw.

Some Anchor Points – what we know.

We know, to at least a reasonable degree of certainty that the first indication of a problem arose when flight MH370 reached the IGARI waypoint at FL350 (35,000 feet).  From Wikipedia –

The flight departed from Kuala Lumpur International Airport on 8 March at 00:41 local time (16:41 UTC, 7 March) and was scheduled to land at Beijing Capital International Airport at 06:30. It ascended to its assigned cruise altitude of 35,000 feet (10,600 m) and was travelling at 471 knots (542 mph; 872 km/h) when it ceased all communications and the transponder signal was lost. The aircraft’s last known position was 6°55’15?N 103°34’43?E
. This location corresponds to the navigational waypoint IGARI, at which the aircraft was due to alter its course slightly eastward.

It is reliably reported that the last voice contact – “all right, goodnight” –  was when the plane was entering Vietnamese air space.

The aviation officials said MH370’s last heard words were uttered after Malaysian air traffic controllers told the pilots that they were entering Vietnamese airspace and that air traffic controllers from Ho Chi Minh city were taking over.

Contact was lost when the plane had just reached cruise altitude at a way-point where, in the normal course of events, it would likely have altered course to the right.

As to the condition of the plane, it may be significant that the plane had suffered substantial damage to one wing in a runway incident and that this had been repaired.

We know about the stolen passports.  Too much has been made of this in the media.  On any given day there will be very many people traveling with bogus documents.  Most will be asylum seekers. If a person using bogus documents to reach a safe haven is a terrorist then so were many of those brave allied POW escapees in WW2.  The probability that MH370 was hijacked or brought down by terrorists is, in my view, exceedingly low.

Probable causes of complete loss of communication and radar contact.

Catastrophic disintegration over water creates a widespread debris field with a large number of small floating items.  No such debris has been found at or near the last confirmed location, by any air or surface search team.

Cabin depressurization not leading to catastrophic failure would not account for complete loss of communications.

One event which can incapacitate the crew and leave them unable to communicate is an unintended maneuver which creates G forces high enough to render a person unconscious but not high enough to cause the plane to disintegrate.

Plausible evidence.

Chinese satellite images may show floating wreckage.

An oil rig worker may have observed the last moments of the plane from a distance.

Some villagers from Marang may have heard the engines of the lost plane.

Those three pieces of evidence all point to a sea area not too far from the last know position of MH370.

Putting the pieces together

If – I repeat, if – the wing repair is a factor, then a major change in distribution of the forces on the wing might be the final cause of failure.  A change from climbing flight to level flight, together with a change in thrust and a change of course are certainly possibilities worthy to be considered.

There is a possibility that MH370 may have entered into a flat spin.  A flat spin would easily render the crew unconscious even more rapidly than loss of cabin pressure.

A flat spin over water would either end in a lesser impact than most other uncontrolled descent modes or disintegration could occur more slowly than usual, or at a relatively low altitude.  Either way, there would be a relatively small debris field.  The plane may even have remained broadly intact.

A flat spin entered during a turn may have a lateral component which could place the impact site tens of miles from the waypoint.

Conclusion

I do not pretend to know what happened to MH370.  All I can say is that planes have been lost before due to inadequate repairs and that, in my submission, none of the vague theories “out there” hold water.

Reference:
A very professionally written analysis of the wing repair as a possible factor in the loss of MH370 was posted on the PPRUNE forum.  It appears to have been largely ignored by the media and the bloggersphere.

The mid-span of this pylon-to-tip distance was where the 777’s RH wing was torn off. Not just damaged or dented, but TORN OFF. Did Boeing replace the entire RH wing? No it didn’t. That starboard wing was “repaired”. 

When would such a culminating inflight failure be most likely? Possibly while the aircraft was still at its heaviest and on encountering clear air turbulence at or near top of climb (or whilst accelerating to cruise Mach). Would that be its most vulnerable point? If that repair gave way, (as most inadequate or improper wing repairs eventually do), what would be the sequence of events? Remember that up until the point of failure, the gust alleviation system would have been disguising (and even moderating?) any signs of imminent failure. In my opinion any such failure in turbulence would be in a DFDR identifiable two parts – firstly the progressive failure (over a few seconds) of primary structure (wing spars and internal bracing buckling as flight loads quickly transfer to inferior sub-structure) – and then the rapid deterioration of the scenario as the secondary structure failed under the increased loadings (the secondary structure being the wing-skin -as the skin does assume much of the inflight loading). As the wing folded, the aircraft would begin to roll to the right quite rapidly (at circa 180 – (increasing to about) 360 degrees per second – around its fore-aft axis). The pilots would be out of the equation at this point – as the aircraft spiralled rapidly down. However there are reports of a garbled transmission. This is likely to have been during the first phase of failure as the pilots became aware that something was happening. However they are unlikely to have discerned that the wing was slowly folding…. or rapidly losing its structural integrity.

TheShadow

#malaysia-airlines-flight-mh370, #mh370