Origin Of Life

Here, Matt Kaplan explains (Nature News, 20 February 2011), Twenty years ago the palaeontological community gasped as geoscientists revealed evidence for the oldest bacterial fossils on the planet. Now, a report in Nature Geoscience1 shows that the filament structures that were so important in the fossil descriptions are not remnants of ancient life, but instead composed of inorganic material. The finding … is not stirring feelings of jubilation. “After nearly 30 years of effort at pushing evidence for life to or beyond 3.5 billion years ago, we are reminded that the ancient record is more fraught with complications than we ever thought,” says geologist Stephen Mojzsis at the University of Colorado, Boulder. But hope springs eternal: Although the filamentous structures Read More ›

Bioethicist Gregory Kaebnick, Ph.D., has an interesting take on the recently announced synthetic cell created by a team of researchers led by J. Craig Venter at the J. Craig Venter Instititute (JVCI). In a recent article in The Scientist entitled Is the “Synthetic Cell” about Life?, Kaebnick writes:

…the technical accomplishment is not quite what the JCVI press release claimed. It’s hard to see this as a synthetic species, or a synthetic organism, or a synthetic cell; it’s a synthetic genome of Mycoplasma mycoides, which is familiar enough. David Baltimore was closer to the truth when he told the New York Times that the researchers had not created life so much as mimicked it. It might be still more accurate to say that the researchers mimicked one part and borrowed the rest.

The explanation from the Venter camp is that the genome took over the cell, and since the genome is synthetic, therefore the cell is synthetic. But this assumes a strictly top-down control structure that some biologists now question. Why not say instead that the genome and the cell managed to work out their differences and collaborate, or even that the cell adopted the genome (and its identity)? Do we know enough to say which metaphor is most accurate?

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A new measure of information has been invented – the Zettabyte = 1,000,000,000,000,000,000,000 bytes, or 10^21 bytes.
Zettabytes overtake petabytes as largest unit of digital measurement Heidi Blake, 4 May 2010, The Telegraph UK “The size of the “digital universe” will swell so rapidly this year that a new unit – the zettabyte – has been invented to measure it.”

Humanity’s total digital output currently stands at 8,000,000 petabytes – which each represent a million gigabytes – but is expected to pass 1.2 zettabytes this year. Read More ›

TED granted Jill Tartar her wish to: “empower Earthlings everywhere to become active participants in the ultimate search for cosmic company”. TED and Search for Extra Terrestrial Intelligence (SETI) has set up SETIQuest.org to:

. . . make vast amounts of SETI data available to the public for the first time. It will also publish the SETI Institute’s signal-detection algorithm as open source code, inviting brilliant coders and amateur techies to make it even better. . . . You are officially invited to join the search for extraterrestrial life. . . .With available cloud storage and processing resources, we can prov de digital signal processing experts and students with a lot of raw data … and invite them to develop new algorithms that can find other types of signals that we are now missing,”

The Challenge for ID
1) Is SETI’s methodology valid? Read More ›

RNA replications have now been discovered to be “essential” to DNA error correction systems. If they are “essential”, how could they arrive by random mutation and “selection”? On what basis does neoDarwinism predict error correction in the first place?

From Intelligent Design, methodology one expects to see evidence of design in complex biochemical systems. From engineering design, I posit a foundational ID principle to be:
“Design systems to protect their design” Read More ›

Here is her interview with David H. Koch, a Darwin-thumping multi-millionaire who has done much to front the cult to the public (“Evolution Sea Change?: David H. Koch Weighs In ,” Archaeology Today, February 17, 2009). Mazur made headlines last year when she wrote about the Altenberg 16, scientists who met in Austria to plan a way of understanding evolution that was free of tax-funded Darwin worship. Anyway, among other things, we learn:
 

Next year, the David H. Koch Hall of Human Origins opens at the Smithsonian National Museum of Natural History, where evidence of 6 million years of human evolution will be part of an interactive display that includes the Laetoli footprints and a reconstruction of Lucy. Visitors will be able to pass through a time tunnel to view early humans “floating in and out of focus,” touch models of ancient human fossils as well as watch their own faces morph into those of extinct species. The Smithsonian display follows the creation of the American Museum of Natural History’s David H. Koch Dinosaur Wing.

Rendering of proposed “Human Characteristics” display at the Smithsonian’s David H. Koch Hall of Human Origins, now in development. (Courtesy David Koch)
Richard Potts, director of the Smithsonian’s Human Origins Program, explained about the new exhibition, “David’s commitment to science and the study of human evolution will enable the Smithsonian to bring the latest discoveries in this field to the broadest audiences. The exhibition, still in the planning stages, encourages the public to explore the lengthy process of change in human characteristics over time. It also presents one of the new research themes in this field–the dramatic changes in environment that set the stage for human evolution. Although the subject can be controversial, the unearthed discoveries that bear on the question of human origins are a source of deep interest and significance for everyone to contemplate.”

David Koch is Executive Vice President of $110 billion Koch Industries (he owns 42%) and CEO of its subsidiary, Koch Chemical Technology Group. He is often described as Manhattan’s wealthiest resident, and contributes to Lincoln Center, Sloan Kettering Cancer Center, and the fertility clinic at New York-Presbyterian Hospital, to name a few. He is also is the principal private funder of PBS’s Nova series.

It gets better when she begins to challenge him: Read More ›

Steve Meyer’s SIGNATURE IN THE CELL continues to garner the praise it deserves. This from Thomas Nagel in The Times Literary Supplement: Stephen C. Meyer’s Signature in the Cell: DNA and the evidence for Intelligent Design (HarperCollins) is a detailed account of the problem of how life came into existence from lifeless matter – something that had to happen before the process of biological evolution could begin. The controversy over Intelligent Design has so far focused mainly on whether the evolution of life since its beginnings can be explained entirely by natural selection and other non-purposive causes. Meyer takes up the prior question of how the immensely complex and exquisitely functional chemical structure of DNA, which cannot be explained by Read More ›

Since in my last post a commenter put on the table thermodynamics to support evolution I decided to offer my personal answer in a specific post, although UD already dealt with this issue. As known, 2nd law of thermodynamics (SLOT, also called “entropy law”) states that in a closed system the overall energy entropy ΔS never decreases spontaneously (i.e. without an external intervention). Example: in a room (considered a closed system) a hot cup of coffee on a tabletop, loosing heat, decreases in energy entropy –ΔSc (neghentropy). Around the table the environment, absorbing heat, increases energy entropy ΔSe, in such manner that the overall energy entropy of the room ΔSr doesn’t decrease. In this example SLOT can be expressed with this formula: Read More ›

Were one to design the encoded DNA “blueprint” of life, would not one incorporate ways to preserve that “blueprint”? The Nobel prize in medicine has just been awarded for discovery of features that look amazingly like design to preserve chromosomes. See:

3 Americans win medicine Nobel for chromosome research

Three U.S. researchers were awarded the 2009 Nobel Prize in Physiology or Medicine for their work on how chromosomes are protected against degradation, the Nobel Foundation reported Monday. Read More ›

Stuart Kauffman, a big name in complexity theory, is leaving the University of Calgary for the University of Vermont . He used to be at the Santa Fe Institute.

I’m not clear on what he actually did at the University of Calgary, Canada, that attracted much attention but you can read more about him at Edge.

He wrote a book called Reinventing the Sacred, but he could have written it in Death Valley or Alaska. I am told it is the usual science-religion Templeton style book.

The press release informs me that Kauffman is ”one of the world’s most eminent scientists” and that the MacArthur foundation has officially labelled him a “genius,” stuff I could never have imagined from reading his first book, At Home in the Universe. But then I had no idea that Richard Dawkins (a guy who can’t even find his own computer code) is, by his own admission, “the most formidable intellect in public discourse” either.

Obviously, these people take the concept of humility much more seriously than most people I run into.

An interesting coincidence is that Kauffman shared the 2005 Trotter Prize at Texas A&M with our own Bill Dembski, often sighted here. Does that make Bill a genius too?

I hope not. Co-blogging with a genius, I might feel intimidated (something you sure don’t need in this business) or else start to give myself airs (“the most formidable intellect in raccoon riddance on Latimer Avenue in Toronto”). Hey, I want a more fashionable hairdresser already.

Details: Right now Read More ›

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. I can only communicate with creatures that have brains.

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

Also just up at Colliding Universes, my blog on theories about our universe: Read More ›

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 Read More ›

Semiotix – Stephen Pain The distinction between “theorising” and “belief” is extremely important because our attitude differs towards them. In a theory the reified concept of the sign does not have an ontological status but an epistemological one. While in belief, the concept has often a clear ontological one. Uexküll believed in his concept of the Bauplan in the same way as Bergson believed in the vital force. The concept of a plan is of course no different from the creationist’s concept of “intelligent design”. Any usage of the Bauplan is further complicated by its ideological usage in The Biological State, Uexküll‘s template for the German State, one that was anti-democratic and in many instances attractive to the Nazi of Read More ›

Friend Casey Luskin writes, “There He Goes Again: Ken Miller misrepresents Behe’s Arguments on the Immune System.” Well, of course he would, wouldn’t he? I’ve read Behe’s Edge of Evolution and Miller’s Finding Darwin’s God, and – to be charitable to Miller – can find no way of even ranking them in the same category. Look, let’s get this part straight: Behe fronts real science, but Miller huffs in favour of “evolution.” The former was NOT invited to the Vatican for the big Pontifical Academy of Sciences meet – even though he, as a Catholic Christian, is one of the few people who has anything worthwhile to say about the topic (I am assuming that sensible persons will discount “All Read More ›

Reading through some of Huxley’s writings caused me to pause and ask a question: After more than a century of study, trial-and-error, and free-wheeling speculation, what has history taught us about the origin of life? For an exhaustive review of this question, see Stephen Meyer’s Signature in the Cell. But the specific question was prompted by the following passage from Huxley’s Discourses Biological and Geological: Essays (1894):

But though I cannot express this conviction of mine too strongly, I must carefully guard against the supposition that I intend to suggest that no such thing as Abiogenesis  ever has taken place in the past, or ever will take place in the future. With organic chemistry, molecular physics, and physiology yet in their infancy, and every day making prodigious strides, I think it would be the height of presumption for any man to say that the conditions under which matter assumes the properties we call “vital” may not, some day, be artificially brought together. All I feel justified in affirming is, that I see no reason for believing that the feat has been performed yet.

And looking back through the prodigious vista of the past, I find no record of commencement of life, and therefore I am devoid of any means of forming a definite conclusion as to the conditions of its appearance. Belief, in the scientific sense of the word, is a serious matter, and needs strong foundations. To say, therefore, in the admitted absence of evidence, that I have any belief as to the mode in which the existing forms of life have originated, would be using words in a wrong sense. But expectation is permissible where belief is not; and if it were given me to look beyond the abyss of geologically recorded time to the still more remote period when the earth was passing through physical and chemical conditions, which it can no more see again than man can recall his infancy, I should expect to be a witness of the evolution of living protoplasm from not living matter. I should expect to see it appear under forms of great simplicity, endowed, like existing fungi, with the power of determining the formation of new protoplasm from such matters as ammonium carbonates, oxalates and tartrates, alkaline and earthy phosphates, and water, without aid of light. That is the expectation to which analogical reasoning leads me; but I beg you once more to recollect that I have no right to call my opinion anything but an act of philosophical faith (pp. 255-257).

Now more than a century later, research into the origin of life has largely proceeded on this basis. Convinced that some form of abiogenesis must be true, its primary motivation has indeed not been “scientific” but rather has proceeded as an “expectation,” an act of philosophical faith. Where, it seems reasonable to ask, has this brand of philosophical faith gotten us?
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