Showing posts with label origin of life. Show all posts
Showing posts with label origin of life. Show all posts

Monday, January 17, 2011

Origin of life: “If pigs could fly” chemistry slammed

A rabbi friend reminds me of the late Leslie Orgel, origin of life pioneer, who seems to have been well aware of the difficulties his materialist constraints created.

Responding to Shapiro's harsh criticism of the “RNA first” theory and his proposal of the “metabolism first” scenario as a more likely approach to a naturalistic origin of life:
Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own...solutions offered by supporters of geneticist or metabolist scenarios that are dependant on "if pigs could fly" hypothetical chemistry are unlikely to help."

Sunday, January 16, 2011

Origin of life: Simple cells inevitable?

A friend flags Nick Lane's "Chance or Necessity?: Bioenergetics and the Probability of Life" (Journal of Cosmology, August 2010, Vol 10, 3286-3304, suggesting that it represents a significant step in the history of origin of life research. Lane thinks bacteria would "naturally" emerge on wet, rocky planets, but that more complex life forms are a matter of chance.

Lane pin his hopes on "white smokers", that is, alkaline hydrothermal vent systems, of which he writes,
... alkaline hydrothermal vent systems should be seen as not merely the most promising setting for the origin of life, but as the only model that makes the emergence of life look like a probable and deterministic outcome of geology, geochemistry and thermodynamics (Table 1). Alkaline vents are electrochemical reactors that provide integrity, concentration, catalysis, replication and a suitable environment for selection. It is hard to imagine life not emerging in such a system, especially if one pictures the oceanic crust as host to practically contiguous vent systems, as might indeed have been the case (Russell and Arndt, 2005). One could even imagine a natural selection of vents, in which life emerges from the system with the best balance of H2, flow and catalysis, perhaps going on to infect nearby systems.
The abstract reads,
Abstract: The emergence of life is probable on any wet, rocky planet. Serpentinization gives rise to alkaline hydrothermal vents that form: (i) simple organics; (ii) catalysts that direct primordial metabolism (iii) micropores with cell-like properties; and (iv) proton gradients equivalent to the proton-motive force. Thermodynamic constraints dictate that all anaerobic chemolithotrophic cells must depend on chemiosmotic coupling, explaining the near-universal use of proton gradients today. But proton gradients also limit the evolutionary potential of prokaryotes. Only a rare and stochastic event, an endosymbiosis between prokaryotes, permitted the evolution of morphologically complex life on Earth, as only such an endosymbiosis made it possible for chemiosmotic coupling to be controlled by multiple small genome outposts across a wide area of internal membranes. This leap in bioenergetic capacity in turn enabled the expansion in cell volume and genome size characteristic of eukaryotes. The origin of life and evolution of prokaryotes is therefore deterministic and probable (necessity), while the evolution of more complex eukaryotic life is stochastic and improbable (chance). These bioenergetic principles are likely to apply throughout the universe.
I'm not sure why my friend thinks this is so significant. Didn't it used to be black smokers? But the good thing about this particular theory is that Lane spells it out clearly enough that we can know if it is not demonstrable. None of the usual mights and maybes for him.

Wednesday, January 12, 2011

Sugars for life: About face! Left turn!

A friend observes this item from Science News Daily,
ScienceDaily (Jan. 7, 2011) — Certain molecules do exist in two forms which are symmetrical mirror images of each other: they are known as chiral molecules. On Earth, the chiral molecules of life, especially amino acids and sugars, exist in only one form, either left-handed or right-handed. Why is it that life has initially chosen one form over the other? [ ... ]

…has for the first time obtained an excess of left-handed molecules (and then an excess of right-handedones) under conditions that reproduce those found in interstellar space. This result therefore supports the hypothesis that the asymmetry of biological molecules on Earth has a cosmic origin.

[ ... ]

The excess, which was over 1.3%, is comparable to that measured in primitive meteorites. The researchers thus succeeded in producing, under interstellar conditions, asymmetrical molecules of life from a mixture that did not contain chiral substances. This is the first time that a scenario that explains the origin of this asymmetry has been demonstrated using an experiment that reproduces an entirely natural synthesis.
My friend sniffs, “the production of a small (1.3%) excess of one over the other ( and then the opposite result) is a crowning achievement in a field where any success of any kind is a towering feat.”

Caution is needed. One can get 1.3% in almost any direction, at least once, before the wheels fall off.

Monday, January 3, 2011

Origin of life spoof

As we all head back to serious work ...

A friend writes, “In case you missed it here is a snippet of Doug Axe's spoof on the self-replicating ribozymes in this paper:

Biologic Institute Announces First Self-Replicating Motor Vehicle — April 1st, 2009 by Douglas Axe


Researchers at Biologic Institute have stunned the scientific community with the announcement today of a fully functioning automobile capable of replicating itself. Although simple autocatalytic versions of self-replication have previously been demonstrated, the complexity of the system described today—complete with GPS navigation, DVD player, and onboard WiFi—has taken everyone by surprise. In the minds of many, this discovery has forever altered the once fundamental distinction between life and non-life.
Reactions from the automotive industry have, understandably, been less philosophical. One executive, who wished to remain unnamed, characterized the development as “altogether unhelpful.” An assembly plant worker was less restrained: “This is unreal… I just hope they quarantine the [expletive] things before this gets out of hand.”


According to lead scientist Otto Cloner, “In the right kind of environment the process of self-replication just takes off. I still get goose bumps watching it.” The prototype self-replicator is a slightly modified version of the popular Jeep Wrangler—unmanned. When just one of these self-propelled prototypes is placed in an appropriate environment (one lacking any other self-propelled vehicles) magic happens. Or so it seems. Dr. Cloner himself takes the more modest view that “the replicative mechanism is really quite simple when properly understood”.

For more, go here.
For the Institute’s serious work, go here.

Friday, December 31, 2010

Origin of life: O he of simple faith


I was impressed by the studies made after the 1980 eruption of Mount St Helen's in Washington State, which destroyed all life for many kilometres around. Within a remarkably short time, nasty hot, evil-looking pools around the volcano were teeming with life in the form of bacteria and blue green algae. These are exactly the kinds of organisms that we know from the earliest records of life on Earth. The necessary original formula must have been one of chemistry and heat in a watery environment.


- D. V. Ager, The New Catastrophism: The Importance of the Rare Event in Geological History, Cambridge University Press: Cambridge UK, 1993, p. 149.
It really does take a lot of faith to think that the most ancient organisms could just appear in the same way that existing organisms spill into a new territory, taking advantage of the fact that the more complex organisms that usually constrain their activities, are temporarily absent.

If “chemistry and heat in a watery environment” were the solution to the origin of life, life would be popping up from nothing far more often than it does.

Hat tip: Stephen E. Jones.

Thursday, December 30, 2010

Origin of life: At least one swish of chemicals must win the lottery ...


Friend Stephen E. Jones was reading The Origin of Life by Paul Davies (2003) and came up with this nice paragraph:
Many investigators feel uneasy about stating in public that the origin of life is a mystery, even though behind closed doors they freely admit that they are baffled. There seems to be two reasons for their unease. Firstly, they feel it opens the door to religious fundamentalists and their god-of-the-gaps pseudo-explanations. Secondly, they worry that a frank admission of ignorance will undermine funding, especially for the search for life in space.


- Paul Davies, The Origin of Life, Penguin Books, London, 2003, p. xxiv
He comments,
An interpretation of this is that origin of life researchers don't tell in public that they are in a crisis, because if they did so, they would give ammunition to Intelligent Design and lose a great deal of money ...

They are die-hard materialists in both senses.
Actually, most people would probably cheer them on if they did find the origin of life, but the reason it is a mystery is their unwillingness to consider whether some features are best explained by design. They want chance to do the legwork, which is somewhat like wanting to get rich on one lottery ticket win.

Wednesday, December 29, 2010

More from the “and then rain just sort of fell” thesis on the origin of life

Stephen E. Jones  has noted,

Using information theory, astrophysicist Edward Argyle calculated the probability that a single organism arose on the early Earth by chance. Argyle concluded: “It would seem impossible for the prebiotic Earth to have generated more than about 200 bits of information, an amount that falls short of the 6 million bits in E. coli by a factor of 30,000.”


- Edward Argyle, “Chance and the Origin of Life”, Extraterrestrials – Where Are They?
Cambridge University Press, 199, p. 131.

Photo: Stromatolites, fossils of some of the earliest known life forms, US government, public domain

Friday, September 25, 2009

Lynn Margulis challenges neo-Darwinists and teaches somewhere now - but she has interesting ideas

And she was once married to Carl Sagan - "consummate egotist" gossip warning.

Here's an intriguing article about origin of life researcher Lynn Margulis in the University of Wisconsin alumni news magazine, "Evolution Revolution" by Eric Goldscheider. We learn, among many other very interesting things,
Symbiogenesis theory flies in the face of an accepted scientific dogma called neo-Darwinism, which holds that adaptations occur exclusively through random mutation, and that as genes mutate in unpredictable ways, their gradual accumulation sometimes results in useful attributes that give the organisms an advantage that eventually translates into evolutionary change.

What tipped Margulis off that new traits could arise in another way was the fact that DNA, thought to reside only in the nucleus, was found in other bodies of the same cell. This realization led to research showing not only how crucial symbiotic relationships can be to the immediate survival of organisms, but also that one of the most significant sources of innovation — indeed, even the origins of new species — occurs when, over time, symbiotic partners fuse to create new organisms.

In other words, complexity at the cell level is not the result of lethal competition from lucky mutants, but rather interactive chemistry that begins as symbiotic relationships between gene sets that together accomplish things that would otherwise have been impossible.
That sounds more plausible to me, though it all but wrecked her career.
Margulis’s observation that constituent parts of the same cell had different genetic histories was largely written off as crank science in 1964 when she started submitting her paper on the topic to academic journals. No one wanted it. After more than a dozen rejections, the Journal of Theoretical Biology published “On the Origin of Mitosing Cells” in 1967, and then something very interesting happened. Requests for reprints started pouring in, more than eight hundred in all. “Nothing like that had ever happened in the Boston University biology department,” Margulis says. Although she was a part-time adjunct professor there at the time, she won a prize for faculty publication of the year. Eventually, a full-time position that lasted twenty-two years followed.

But in spite of, or maybe because of, this modicum of recognition, the scientific establishment viewed her skeptically, if not with outright hostility. Her grant proposals weren’t funded. Margulis tells of being recruited for a distinguished professorship at Duke University, only to have it subverted at the last minute by a whispering campaign.
She ended up at the University of Massachusetts, so at least she had a job.
One thing that mars her theories, in my eye, is is statements like
“Man is the consummate egotist,” Margulis has written. “It may come as a blow to our collective ego, but we are not masters of life perched on the top rung of an evolutionary ladder.” Instead, she likes to say that “beneath our superficial differences, we are all of us walking communities of bacteria.”
. Aw c'mon! I'm always hearing from enviro-fruitcakes and anti-nuclear nutcakes who think humans will soon destroy the planet.

So walking communities of bacteria will destroy the planet? I am sure not getting involved in the squabble over the planet's fate in that case. I can only communicate with creatures that have brains.

A question related to this interesting article will shortly be posted as Contest Question 11 at Uncommon Descent.

Monday, August 24, 2009

Uncommon Descent Contest Question 9: Is accidental origin of life a doctrine that holds back science?

For a free copy of Stephen Meyer's Signature in the Cell (Harper One, 2009), help me understand the following:

Accidental origin of life is the basic thesis of origin of life researchers. Life all just somehow sort of happened one day, billions of years ago, under the right conditions - which we may be able to recreate. But there is a constant, ongoing dispute about just what those conditions were.

Here is the problem I have always had with accidental origin of life: It amounts to spontaneous generation. However, banishing the doctrine of spontaneous generation played a key role in modern medicine's success. If we assume that life forms (for medical purposes, we focus on pathogens) cannot start spontaneously, then they must have been introduced. Hence, we can develop procedures for a sterile operating room or lab.

If life can be spontaneously generated, why isn't it happening now? Conditions for life today are probably as good as they have ever been, and maybe better. For over 500 million years they have obviously been good for complex life forms, and for billions of years they have been good for simple ones.

Go here to enter.

Find out why there is an intelligent design controversy:

Friday, July 24, 2009

Origin of life: Current efforts to create life, or else find alternative life

In "Second Genesis: Life, but not as we know it," Bob Holmes (New Scientist, March 11, 2009) provides a summary of attempts to create artificial life (paywall).
We're still stuck with Life 1.0, the stuff that first quickened at least 3.5 billion years ago. There's been nothing new under the sun since then, as far as we know.

That looks likely to change. Around the world, several labs are drawing close to the threshold of a second genesis, an achievement that some would call one of the most profound scientific breakthroughs of all time.
However,
Venter's team at the J. Craig Venter Institute in Rockville, Maryland, plans to remove the genome from an existing bacterial cell and replace it with one of their own design. If successful, this will indeed result in a novel life form, but it is a far cry from the ultimate goal of a second genesis, as Venter would be the first to admit.

Other teams, however, are striving directly for that ultimate goal. The most ambitious of them do not even rely on the standard set of molecular parts, but seek to redesign a living system from first principles. If successful, they would provide an entirely new form ...
Meanwhile, others look for a shadow biosphere, an independent type of life sharing the planet with us.

My sense is that the people who use existing manufactured parts will have the best luck with their work.

Here's University of Colorado (Boulder) philosophy prof Carol Cleland'sargument in Astrobiology Magazine (12/01/06) for looking for a shadow biosphere:
The discovery of a shadow microbial biosphere would be philosophically and scientifically important. It is clear that familiar Earth life has a common origin, and hence represents a single example of life. Logically speaking, one cannot generalize on the basis of a single example. If we are to achieve a satisfactory understanding of the general nature of life, we need examples of unfamiliar forms of life.
Also, Holly Hight asks ("Does Earth harbour a shadow biosphere of alien life," Cosmos: The Science of Everything, 16 February, 2009 ):
Finding life that doesn't fit with the types we already know would be a strong indication that life developed more than one time here on Earth, increasing the chances of finding it elsewhere, said Paul Davies, an astrophysicist at Arizona State University in Tempe.

But nobody has ever seriously searched for microorganisms - or any form of life - different from the carbon-based, DNA-centred type of life about which we have long known.

If we do look, Davies said, "It's entirely feasible that we'll find a shadow biosphere," he told reporters at the annual meeting of the American Association for the Advancement of Science (AAAS) in Chicago.

"Our search for life [has been] based on our assumptions of life as we know it. Weird life and normal life could be intermingled, and filtering out the things we understand about life as we know it from the things we don't understand is tricky."
It must be hard to write science fiction these days.

Sunday, July 19, 2009

Origin of life: Quantum mechanics provided the ... ooomph!! ?

In "The Quantum Life" (Physcisworld.com, July 1, 2009), Paul Davies, astrobiologist and director of BEYOND: Center for Fundamental Concepts in Science at Arizona State University, examines the case for quantum mechanics kickstarting the origin of life (Q-life):
But why should quantum mechanics be relevant to life, beyond explaining the basic structure and interaction of molecules? One general argument is that quantum effects can serve to facilitate processes that are either slow or impossible according to classical physics. Physicists are familiar with the fact that discreteness, quantum tunnelling, superposition and entanglement produce novel and unexpected phenomena. Life has had three and a half billion years to solve problems and optimize efficiency. If quantum mechanics can enhance its performance, or open up new possibilities, it is likely that life will have discovered the fact and exploited the opportunities. Given that the basic processes of biology take place at a molecular level, harnessing quantum effects does not seem a priori implausible.
It's intriguing, the way he attributes to "life" and, elsewhere, "evolution" the attributes of a planning and thinking intelligent agent.

He almost persuades himself but
Although at least some of these examples add up to a prima facie case for quantum mechanics playing a role in biology, they all confront a serious and fundamental problem. Effects like coherence, entanglement and superposition can be maintained only if the quantum system avoids decoherence caused by interactions with its environment. In the presence of environmental noise, the delicate phase relationships that characterize quantum effects get scrambled, turning pure quantum states into mixtures and in effect marking a transition from quantum to classical behaviour. Only so long as decoherence can be kept at bay will explicitly quantum effects persist. The claims of quantum biology therefore stand or fall on the precise decoherence timescale. If a system decoheres too fast, then it will classicalize before anything of biochemical or biological interest happens.
.So we are now into the business of persuading ourselves that, based on a few studies, that would not be the normal fate of Q-life. And in the end,
How would Q-life evolve into familiar chemical life? A possible scenario is that organic molecules were commandeered by Q-life as more robust back-up information storage. A good analogy is a computer. The processor is incredibly small and fast, but delicate: switch off the computer and the data are lost. Hence computers use hard disks to back up and store the digital information. Hard disks are relatively enormous and extremely slow, but they are robust and reliable, and they retain their information under a wide range of environmental insults. Organic life could have started as the slow-but-reliable “hard-disk” of Q-life. Because of its greater versatility and toughness, it was eventually able to literally “take on a life of its own”, disconnect from its Q-life progenitor and spread to less-specialized and restrictive environments — such as Earth. Our planet accretes a continual rain of interstellar grains and cometary dust, so delivery is no problem. As to the fate of Q-life, it would unfortunately be completely destroyed by entry into the Earth’s atmosphere.
All this reminds me of a beautiful Edith Wharton short story, "Fern Seed", which I can't find on line, or worse, it might be wrecked by some clueless "ethnicity/class/gender" analysis.

The point of "Fern Seed" is that it looks as though a ghost drove a story character to suicide - but there is no actual evidence. (If you ever think of writing a ghost story, take Wharton as your guide. What make her stories work is: No one can prove anything happened, apart from catastrophic emotional impacts, and yet everyone is sure that something happened.)

Sunday, June 28, 2009

Origin of life: This time it's salt water

One of these days, I am going to make a list of all the implausible origin of life scenarios I have heard, but here is one, involving ice particles on one of Saturn's moons, Enceladus :
These salty ice grains suggest that the interior of the moon may have liquid water that is washing salty minerals out of rock into a subterranean sea.

The scientists write that the presence of alkaline salt water, along with the organic compounds and thermal energy that have been observed at the south pole, "could provide an environment well suited for the formation of life precursors."
For way more origin of life stories, go here.

Sunday, June 7, 2009

Origin of life: The misnaming of the Great Oxidation Event - which maybe never happened

British physicist David Tyler writes,
The true story of oxygen in the Earth's atmosphere has yet to be told. Most researchers have been brought up to believe the Miller-Urey model of abiogenesis, which required the Earth to have a reducing atmosphere to facilitate the spontaneous generation of life. The atmosphere was then considered to be neutral for over a billion years. The evolution of organisms capable of photosynthesis was the next important step, with rises of oxygen levels triggering the flowering of eukaryotes, the rise of the Ediacaran fauna and then the Cambrian Explosion. The first significant rise is understood to be abrupt and sufficient of a milestone in Earth history to warrant a name of its own. Richard Kerr's comments below lead us to the new research by Ohmoto and colleagues: [quote]The first living things did not require oxygen to "breathe," but early life on Earth never would have gotten much beyond pond scum without free oxygen in the atmosphere. Conventional thinking has oxygen produced by photosynthesis gaining the upper hand 2.4 billion years ago, nearly halfway into Earth history. But new laboratory results reported in tomorrow's issue of Science challenge the late arrival of this "Great Oxidation Event."

Ohmoto's hypothesis is that significant quantities of free oxygen were present in Earth's atmosphere prior to the GOE. He represents a minority position, but he continues to provide leadership in this area and a regular stream of relevant papers. One of the issues concerns patterns found in sulphur isotopes. Here is Kerr again: "Then in 2000, geochemist James Farquhar of the University of Maryland, College Park, came up with a nifty technique involving sulfur isotopes. The proportion of one isotope to another of the same element can change during a chemical reaction. Normally, the change depends on the masses of the isotopes. But Farquhar found isotopic shifts among three sulfur isotopes before 2.4 billion years ago that hadn't depended on isotope mass. As far as anyone knew, such "mass-independent fractionation" (MIF) could have happened only under solar ultraviolet radiation in an oxygen-free atmosphere - and MIF sulfur disappeared 2.4 billion years ago."

The new paper, with Farquar as one of the co-authors, proposes an alternative origin for these isotopic signatures that keep the door open for discussion of an early, oxygen-rich atmosphere. "The significance of this finding is that an abnormal isotope fractionation (of sulfur) may not be linked to the atmosphere at all," says Yumiko Watanabe, research associate [and co-author], Penn State. "The strongest evidence for an oxygen poor atmosphere 2.4 billion years ago is now brought into question."
Read more here.

Saturday, May 30, 2009

Origin of life: "Primordial soup" belief undermines traditional spirituality?

Diana Yates, Life Sciences Editor, alerts us to a study at her university, "God or science? A belief in one weakens positive feelings for the other" (12/15/08):
The researchers conducted two experiments designed to manipulate how well science or God can be used as explanations. In the first, 129 volunteers read short summaries of the Big Bang theory and the “Primordial Soup Hypothesis,” a scientific theory of the origin of life. Half then read a statement that said that the theories were strong and supported by the data. The other half read that the theories “raised more questions than they answered.”

In the second experiment, which involved 27 undergraduate students, half of the study subjects had to “list six things that you think God can explain.” The others were asked to “list six things that you think can explain or influence God.”

All the subjects were then required to quickly categorize various words as positive or negative on a computer.

“What they didn’t realize was that they were being subliminally primed immediately before each word,” Preston said. “So right before the word ‘awful’ came up on the screen, for example, there was a 15-millisecond flash of either ‘God’ or ‘science’ or a control word.”

A 15-millisecond visual cue is too brief to register in the conscious mind, but the brief word flash did have an effect. Those who had read statements emphasizing the explanatory power of science prior to the test were able to categorize positive words appearing just after the word, “science,” more quickly than those who had read statements critical of the scientific theories.

Those who were asked to use God as an ultimate explanation for various phenomena displayed a more positive association with God and a much more negative association with science than those directed to list other things that can explain God, the researchers found. Similarly, those who read the statement suggesting that the scientific theories were weak were extremely slow to identify negative words that appeared after they were primed with the word “God,” Preston said.

“It was like they didn’t want to say no to God,” she said.
Sounds like voodoo to me. And, while the Big Bang is pretty well attested, the "primordial soup" is not a hypothesis in science; it is a materialist creation story, on the level of the cosmic egg. ("Once upon a time, it all just happened, see .. ")

Friday, May 29, 2009

Origin of life: Speculation rents the "science" costume - leaves without head

In Probability's nature and nature's probability: A call to scientific integrity, information scientist Donald E. Johnson tackles, among other things, the origin of life.

Johnson takes on the aimless speculation that characterizes so much consensus science today on such issues:
... one should not be able to get away with stating "it is possible that life arose from non-life by ..." without first demonstrating that it is indeed possible (defined in the nature of probability) using known science. One could, of course, state "it may be speculated that ...," but such a statement wouldn't have the believability that its author intends to convey by the pseudo-scientific pronouncement."(p. 5)
I myself am so fed up with pseudoscientific pronouncements on the origin of life that I decided to cover all such stories here at Colliding Universes, along with speculations about the end of the universe - rather than at Post-Darwinist, where many claims, whether well-supported or not, have at least some basis in fact.

This is a great book for scientists with a background in probability who want to understand why there is a controversy over design in the universe.

Wednesday, May 20, 2009

Origin of life: The live cat vs. the dead cat

Friend Roddy Bullock writes to advise me that his new essay, titled "Life: (More Than) Some Assembly Required" is now posted at ARN's ID Report:

When it comes to creating "life" in any form, the hopeful reports keep coming, tickling the ears with the sizzle, but never showing the steak. Just last month, The Boston Globe ran the headline "Harvard Fuels Quest to Create Life From Scratch" describing the latest research of Harvard's Origins of Life Initiative. And again, if one reads beyond the attention-grabbing headline, one learns that what has actually been created is a machine that can manufacture proteins. This is, of course, quite a feat of intelligent design, but to say, as the article quotes, that "it's a step toward artificial life" because the machine can mimic a ribosome, which is the "key component of all living systems", goes too far. Hey, our dead cat is full of ribosomes. There's no need to design a machine to make proteins, and no reason to believe that if you make them you are any closer to creating real life, much less "artificial life".
About our "dead cat"? Roddy kindly writes,

Thanks to Denyse O'Leary, whose question some time ago has stuck with me: "What's the difference between a live cat and a dead cat?" I used this as the opening line in this essay that explores the "life from scratch" quest and makes a prediction for all those who believe that ID theorists make no predictions. My prediction: "Scientists will never create life from scratch, unless one or both of 'life' or 'scratch' is redefined to a meaningless ambiguity."
Well, if the researchers succeed through intelligent design, they have shown that intelligent design can reverse engineer life. That is all.

The question I raised that evening:

If we assume that current theory is correct, the life of the cat was transmitted through countless generations of previous life forms. When the cat dies, before the decay processes have begun, we have exactly the same animal - but it is no longer alive. What changed, exactly? I mean, we can say that the cat's heart stopped, obviously, so life could not continue. But what precisely cannot continue?

My question is, can life can be seen as "information in motion"? When the information flow stops, that life form is soon scavenged by others, to continue their own lives as information in motion. That view of life would better suit a design interpretation of nature than a random evolution one.
Random evolution is what happens when the cat is dead - in the strict sense that whichever scavengers are drawn to the carcass first consume it. But these other life forms continue as information in motion.

Randomness does not produce intricate information, despite dogmatic insistence by materialists of various stripes.

See also: Origin of life: Latest scenario gives RNA world a boost

Tuesday, May 19, 2009

Origin of life: Latest scenario gives RNA world a boost

In "Ribonucleotides and the revival of the "warm little pond" scenario" (ARN Reports, 05/19/09), David Tyler dissects another media meltdown over the origin of life:
According to one commentator, the newly published research provides "one of the great advances in prebiotic chemistry". The media have captured the excitement with headlines like "Chemist Shows How RNA Can Be the Starting Point for Life" (New York Times), "Molecule of life emerges from laboratory slime" (New Scientist) and "How RNA got started" (Science News). These are strong statements and they deserve closer attention. What is going on in the field of OOL research?
What indeed? Given the many scenarios offered for the origin of life, I would guess that maybe one in one hundred might provide useful information.

The biggest single problem, one that researchers gloss over and that pop science media don't reckon, is that evidence for any one theory subtracts from evidence for any other. So it is not clear that an advance in information has occurred.

An argument for RNA world is an argument against clay world or silicon world or prebiotic pizza or prebiotic soup, or whatever other flavour is on offer.

"RNA World" has been around for a while, to be sure. Tyler comments,
The researchers have synthesised both pyrimidine ribonucleotides (but not the purine ribonucleotides). As Van Noorden described it, they have "shown that it is possible to build one part of RNA from small molecules". They have not formed RNA molecules; they have not addressed the chirality problem, they have not generated any biological information and they have not made RNA do anything of biological significance, let alone become clothed with a membrane and undergo replication. Nevertheless, what they have done can be applauded as an elegant example of systems chemistry.
And as Bill Dembski notes,
Excuse me? Doing the chemical reactions in precise sequence and purifying the products at each step hardly seems like recreating realistic prebiotic conditions. In fact, it almost sounds like, dare I say it, intelligent design.
No, wait! It's not design. Those guys aren't taking any credit for it. It all just sort of happened, see?

Here's the abstract, and some links:
Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions Matthew W. Powner, Beatrice Gerland, John D. Sutherland Nature 459, 239-242 (14 May 2009) doi:10.1038/nature08013

At some stage in the origin of life, an informational polymer must have arisen by purely chemical means. According to one version of the 'RNA world' hypothesis this polymer was RNA, but attempts to provide experimental support for this have failed. In particular, although there has been some success demonstrating that 'activated' ribonucleotides can polymerize to form RNA, it is far from obvious how such ribonucleotides could have formed from their constituent parts (ribose and nucleobases). Ribose is difficult to form selectively, and the addition of nucleobases to ribose is inefficient in the case of purines and does not occur at all in the case of the canonical pyrimidines. Here we show that activated pyrimidine ribonucleotides can be formed in a short sequence that bypasses free ribose and the nucleobases, and instead proceeds through arabinose amino-oxazoline and anhydronucleoside intermediates. The starting materials for the synthesis - cyanamide, cyanoacetylene, glycolaldehyde, glyceraldehyde and inorganic phosphate - are plausible prebiotic feedstock molecules, and the conditions of the synthesis are consistent with potential early-Earth geochemical models. Although inorganic phosphate is only incorporated into the nucleotides at a late stage of the sequence, its presence from the start is essential as it controls three reactions in the earlier stages by acting as a general acid/base catalyst, a nucleophilic catalyst, a pH buffer and a chemical buffer. For prebiotic reaction sequences, our results highlight the importance of working with mixed chemical systems in which reactants for a particular reaction step can also control other steps.

See also:

Szostak, J.W., Origins of life: Systems chemistry on early Earth, Nature 459, 171-172 (14 May 2009) doi:10.1038/459171a

Van Noorden, R., RNA world easier to make, Nature News, 13 May 2009 doi:10.1038/news.2009.471

Wade, N., Chemist Shows How RNA Can Be the Starting Point for Life, New York Times, 14 May 2009.

Saturday, March 28, 2009

Extraterrestrial life? Well, maybe, but I am not putting any money on it

Apparently, Alan Boss thinks that the Kepler mission will find planets crowded with life:
I'm a bit skeptical myself, much as I would like it to be true. A vacation in another solar system would be just the thing, but ...

The thing is, Boss cannot promise more than bacteria (or - this might be wiser - archaea?), and the difficulty is (this much should be obvious): Extraterrestrialists tend to agree that bacteria (or at least archaea) could travel on asteroids.

So they might all tend to look somewhat like this. Maybe the started on Earth ...

Somewhat disappointing for a person of my "Take me to your leader" generation.

Bill Dembski blogged on this here ("Cook the primeval soup for billions of years and voila!").

Here's the YouTube:


Tuesday, March 24, 2009

Life came from dwarf planet Ceres?

Well, as Lee Pullen tells it at Space.com in "Dwarf planet may have survived early cataclysmic asteroid impacts", Joop Houtkooper from the University of Giessen argues that life could have originated on the dwarf planet Ceres:

"This idea came to me when I heard a talk about all the satellites in the solar system that consist of a large part of ice, much of which is probably still in a liquid state," says Houtkooper. "The total volume of all this water is something like 40 times greater than all the oceans on Earth."

This reminded Houtkooper of a theory about how life originated. Organisms may have first developed around hydrothermal vents, which lie at the bottom of oceans and spew hot chemicals. Many icy bodies in our solar system have rocky cores, so they may have had or still have hydrothermal vents. Houtkooper realized, "if life is not unique to the Earth and could exist elsewhere, then these icy bodies are the places where life may have originated."
If you can't place Ceres, don't worry. It's a dwarf planet (formerly thought of as an asteroid) somewhere in the asteroid belt.

This particular origin of life scenario sounds to me like publicity for the Dawn mission rather than a plausible scenario. The closest Ceres is likely to ever get to life is that Dawn flyby. But hey, it's not for me to break that guy's rice bowl. And surely not in these times.

Others have been more outspoken. Friend Rob Sheldon observes:

There are so many counter-factuals here, I hardly know where to begin.

1. Let's begin with "hydrogen peroxide" life. The theory starts with hydrogen peroxide being an antifreeze, and suggests that life built upon it could survive the cold. But then so is fuming sulfuric acid. This is hardly a place to start. And is contrary to all experience that says hydrogen peroxide is a potent oxidant and anti-biotic. I mean it destroys hydro-carbons extremely efficiently. The man who invented this theory, and amazingly got his paper published, was invited to the Astrobiology conference, where he was unable to answer any specific questions on his hypothesis. It is just another junk science PR.

2. Ceres is cold. There wont be any liquid water outside the orbit of Mars, simply because Mars average temperature is -60C. Ceres is colder by a factor 4.

3. Ceres has no atmosphere. So why would liquid water stay liquid? It would all boil off.

4. Ceres has no gravity to speak of. What would have ever held the atmosphere in place at any time in the past?

5. Ceres is made of stone, matching the stony meteorites observed on earth. Why would it have any water on it ever?

6. Ceres has no magnetic field. What is to keep the solar wind from removing any putative atmosphere it might never have had, just as solar wind denuded Mars?

7. Why would a cold, dry, stony, asteroid with no magnetic field be a better place for life to start than a wet, atmospheric, warm place like Earth?

He could go on, but it is only an e-mail, not a paper.

Another friend notes,

I think he is claiming the water is under an icy crust, like at Europa.

The rocky core might contain short-lived radionuclides that would heat the rock and produce hydrothermal vents. At least that is what planetologists surmise may be happening at Europa.

The whole hypothesis started when Houtkooper decided Earth was a dangerous place to live during the Late Heavy Bombardment (another one of their mythical tales of yore). Ceres would have been a smaller target for the life-prohibiting impacts.

These considerations don't make the hypothesis any less crazy.

I guess we would all like to believe that there is life on planets other than Earth. What we don't have is the evidence.

The skinny on Ceres, according to Solarviews,

With a diameter of about 975x909 km, Ceres is by far the largest and most massive (9.5 x1020 kg) body in the asteroid belt, and contains approximately a third of the mass (0.2 x1021 kg) of all the asteroids in the solar system. However, it is not the largest solar system object besides the Sun, planets, and their moons. Larger bodies have been found in the Kuiper belt including Pluto, 50000 Quaoar, 90482 Orcus, 90377 Sedna, and Eris. Recent observations have revealed that Ceres is nearly spherical in shape, unlike the irregular shapes of smaller bodies with less gravity. Having sufficient mass for self-gravity to overcome rigid body forces is one of the requirements for classification as a planet or dwarf planet.

[ ... ]

Ceres has a very primitive surface and like a young planet, contains water-bearing minerals, and possibly a very weak atmosphere and frost. Infrared observations show that the surface is warm with a possible maximum temperature of 235 K (-38°C). Ceres ranges in its visual brightness magnitude from +6.9 to +9.. At its brightest point it is just barely too dim to be seen with the naked eye.

[ ... ]

More will be know about Ceres when the Dawn spacecraft visits the dwarf planet in 2015. The Dawn mission is set for launch in September 2007. It will explore asteroid 4 Vesta in 2011 before arriving at Ceres.

Here's Ian O'Neill's view at Universe Today:

Although it is unknown whether or not Ceres has liquid water oceans, Joop Houtkooper believes that if it does, basic life forms may be thriving around hydrothermal vents in the hypothetical Ceres oceans. However, it is not clear how these proposed oceans can stay in a liquid state, as it seems unlikely there is significant tectonic activity (as it has very little mass to sustain a long-term molten core) and it is not orbiting a tidally disruptive body (like the icy moon Europa around Jupiter - extreme tidal forces maintain sub-surface oceans in a warm state). However, the idea remains as Ceres has a lower escape velocity than any other planetary body, meaning that microbes (hitch-hiking on fragments of Ceres) could have been kicked into space with more regularity than other planets, such as Mars.
He sees it as evidence for Panspermia (life was seeded from distant galaxies, in some versions by space aliens).

See also: Origin of life: Researchers claim life could have existed 4.4 billion years ago, before Earth cooled (and look at all the other scenarios there - only a small portion of the ones I have been collecting over the years).

(Note: The image shows Earth, the Moon and little Ceres.)

Friday, March 20, 2009

Origin of life: Researchers claim life could have existed 4.4 billion years ago, before Earth cooled.

Just when claims for Akilia, as evidence of life at 3.82 billion years ago have not held up, some researchers are even more ambitious.

As reported in New Scientist, Oleg Abramov and Steve Mojzsis of the University of Colorado in Boulder suggest that life could have existed on earth as early as 4.4 billion years ago:
... hardy life-forms could have survived if they were buried underground.
They were using a computer model and they assumed that these primeval life forms were extremophiles (simple, extremely hardy life forms).
... heat from the impacts would not have penetrated very deeply into the underlying solid crust. The layer heated to the sterilisation point, about 110 ̊C, would be only about 300 metres thick. High-temperature 'extremophile' microbes, like those in the hot springs of Yellowstone National Park, would have survived at greater depths, down to their limit of about 4 km.
Mojzsis argues that the Late Heavy Bombardment of Earth by asteroids "pruned, rather than frustrated, life."
That conclusion is reasonable, says Kevin Zahnle of NASA's Ames Research Center in California.
It certainly is, if you are looking for an argument that God created the first life on Earth. I wonder if either he or New Scientist have thought this one out ....

Abramov and Mojzsis will present their research to the Lunar and Planetary Science Conference in Texas on March 23. Here's the .pdf.

In fairness, I must warn you that I consider New Scientist the National Enquirer of popular science magazines, and I am also wary of computer models in these situations. So I would just wait and see.

See also: Podcast: Chemist Charles Garner on chemical evolution; Why the Huygens probe - sadly - probably won't tell us much; Mars red but not dead?; NASA says, could be life on Mars, could be rocks; Origin of life: What can the Saturnian moon Titan tell us?; Origin of life: Alien origin taken seriously? Ghost of Francis Crick smiles wanly; Origin of life: A meatier theory? Or just another theory?; Origin of life: There must be life out there vs. there can't be life out there; Origin of life: Oldest Earth rocks may show signs of life, in which case ... ; Origin of life: Positive evidence of intelligent design?; Origin of life: But is being greedy enough?; Origin of life: Ah, that "just so happens" intermediate series of chemical steps; Why should the search for Darwin's "warm little puddle" be publicly funded?

(Note: The photo shows an extremophile, a simple, heat-loving organism.)