It's alive!

Here's a strange little article from the Associated Press. Why strange? Let's take a look.

The article's headline proclaims that artificial life is "likely" within three to five years. Then there's a quote from Mark Bedau, chief operating officer of a chemical firm:

"Creating protocells has the potential to shed new light on our place in the universe," Bedau said. "This will remove one of the few fundamental mysteries about creation in the universe and our role."

This is the first oddity. How does designing artificial life in a lab remove a fundamental mystery of creation? Are we supposed to assume that life originated on Earth in the same way that it originated in the petri dish? But this is clearly incorrect. The molecular biologists working on this project are consciously designing this new life. They are planning it out and putting the pieces together in a deliberate way. As fascinating as this work may be, how can it shed light on what is presumed to be an accidental, non-designed, unplanned event - namely, the origin of life on this planet?

The quote also contains a second oddity in the phrase "one of the few fundamental mysteries about creation in our universe." One of the few? It seems to me that the deeper we look, the more mysteries we find. There is not only the mystery of life's origin as a purported result of random processes. There is also the mystery of the basic laws of nature and the cosmic constants - how they were determined and why they are so curiously "fine-tuned" to produce an orderly, stable, habitable universe. There is the mystery of quantum mechanics, which seems to show that the mind impinges on physical reality in bizarre ways, and may even call into question the nature of physical reality as such. (Is it just a projection of the mind? A few physicists think so.) There is the mystery of consciousness and its relationship to the brain, the so-called "hard problem" of neurology - how do electrochemical impulses become thoughts? How does a physical system give rise to a nonphysical phenomenon like consciousness? And there is the ultimate mystery, existence itself. Why is there something rather than nothing? Why does anything exist at all? And why are our minds capable of understanding it, of formulating laws and equations that express basic cosmological relationships so elegantly?

It seems doubtful that laboratory-created life will resolve any of these mysteries.

Next we are told:

Bedau figures there are three major hurdles to creating synthetic life:

* A container, or membrane, for the cell to keep bad molecules out, allow good ones, and the ability to multiply.

* A genetic system that controls the functions of the cell, enabling it to reproduce and mutate in response to environmental changes.

* A metabolism that extracts raw materials from the environment as food and then changes it into energy.

Here is the third oddity. We were informed that artificial life is likely in the very near future, but these "three major hurdles" sound pretty formidable. In particular, how is the "genetic system" going to be put together from scratch? The DNA of even the simplest life form contains thousands of genes in highly specific patterns that are by no means fully understood.

One of the leaders in the field, Jack Szostak at Harvard Medical School, predicts that within the next six months, scientists will report evidence that the first step -- creating a cell membrane -- is "not a big problem." Scientists are using fatty acids in that effort.

To me, this is yet another oddity. From what I understand, the cell membrane is an extremely complicated affair. One molecular biologist has made the argument that the membrane, rather than the nucleus, should be considered the true brain of the cell, because it serves as a gatekeeper, selecting which molecules are admitted and which are kept out. The admitted molecules, in turn, activate specific genes in the DNA molecule, which would otherwise remain unexpressed (dormant). Fatty acids certainly play a role in all this, but the system is immensely complex.

Szostak is also optimistic about the next step -- getting nucleotides, the building blocks of DNA, to form a working genetic system.

His idea is that once the container is made, if scientists add nucleotides in the right proportions, then Darwinian evolution could simply take over.

"We aren't smart enough to design things, we just let evolution do the hard work and then we figure out what happened," Szostak said.

This is the fifth and, to me, the oddest oddity. Apparently the hope is that the nucleotides will arrange themselves into the correct genetic sequences through "Darwinian evolution." How this is supposed to happen is entirely unclear to me. Darwinian evolution involves competition among living organisms for survival. Nucleotides are not living organisms and are not competing for survival. Now, I know that some people have theorized that the equivalent of Darwinian evolution takes place at the molecular level, but even if this is true, it would not necessarily result in a meaningful genetic code. It would simply result in maximizing the numbers of the hardier molecules and minimizing the rest. There is, I would think, a vast difference between a competition that thins out the molecular herd by disposing of the less viable molecules and a competition that actually creates a genetic sequence.

Remember that DNA is, essentially, encoded information. It is a storehouse of blueprints, in effect - blueprints that tell the cell how to build new proteins, which in turn are used to repair cell damage, power cell metabolism, eliminate cell waste, etc. It will be interesting indeed to see if just "add[ing] nucleotides in the right proportions" will be enough to produce a genetic library of this kind. It is a little like dumping a large number of letters from the alphabet into a box and expecting them to form themselves into words, sentences, and paragraphs. (Actually, to duplicate the informational content of a DNA molecule, they would have to form themselves into the Encyclopaedia Brittanica.)

Of course, I'm no biochemist, and maybe in three to five years the promised artificial life forms will appear. But I would suggest that if and when the news media report this event, you very carefully check the fine print. More than fifty years ago the Miller-Urey experiment showed that the building blocks of life, amino acids, could be created in a lab. It was confidently assumed that further steps, from amino acids to proteins to cells, would follow in due course. This has not happened. As molecular biologist Robert Shapiro points out, it's a long, long way from creating amino acids to creating proteins (complex chains of amino acids) ... and a very long, long way indeed from creating proteins to creating DNA (or RNA) and life.

Shapiro writes:

My own PhD thesis advisor, Robert B. Woodward, was awarded the Nobel Prize for his brilliant syntheses of quinine, cholesterol, chlorophyll and many other substances. It mattered little if kilograms of starting material were required to produce milligrams of product. The point was the demonstration that humans could produce, however inefficiently, substances found in nature. Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA ...

The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck.

We may be only five years away from artificial life ... or we may be seeing an example of the increasingly common trend of overpromising and overhyping in the realm of genetics. Time will tell.

Comments

[Eteponge]

I just finished reading this article several minutes before I checked your blog tonight Michael, good timing.

I agree with your insights, those are the same type of thoughts that went through my head as I was reading the article.

[Satya]

Welcome to the world of ID( http://www.uncommondescent.com/)...

Maybe you should also check out Michael Behe's latest book on Amazon called
"Edge of Evolution"

The Miller-Urey experiment is a also a dubiuos evidence for orgin of life questions as the early environment questions are still specualtive and the amino acids that came out not of resonable quality ...

[Kevin]

I had also noted this story on the AP wire. Especially chilling was the quote from Bedau:

"We're talking about a technology thet could change our world in pretty fundamental ways-in fact, in ways that are IMPOSSIBLE TO PREDICT."

I used the caps to emphasize what I considered to be the most shocking element of a story which had more than a hint of hubris to it. Add to that the very real difficulties which Michael points out in his posting and you get a fearsome combination which presages the potential for disaster. Here's another heartwarming quote from the article:

"Bedau said there are legitmate worries about creating life that could 'run amok', but there are ways of addressing it, and it will be a very long time before that is a problem".

I feel better already.

[Michael Prescott]

>Welcome to the world of ID

Actually I've been interested in ID for years and have blogged about it before. (Also here and here.) I think there are obvious weaknesses in the conventional Darwinian position.

[tina brewer]

What is most alarming to me is the INCREDIBLE arrogance contained in the entire approach to life and creation. There is simply an utter and complete lack of humility and recognition of our essentially dependent/contingent place in a miraculous order. This lack of humility is a spiritual defect which is virtually guaranteed to give birth to devastating fruits from ANY new discoveries in this regard.

[Markus Hesse]

Isn't it amusing how the hardcore materialists will scoff at "faith without evidence" yet have no problem with openly expressing their faith in a very unlikely accidental sequence of events billions of years ago?

LOL, we're talking about fundamentally primitive biochemical processes that cannot be replicated by design in customized labs with our cutting-edge bio-technology yet are supposed to have happened accidentally, entirely unaided, in the hostile environment of early Earth. Very lucky indeed.

[Richard Oboczky]

This is a CEO of a company who is counting on profits from their created patented life forms. They always speculate about the benefits but they better be ready to pay billions to victims when "their" life forms cause harm.

[Alex]

Personally, I think both the Darwinists and IDers are lunatics. It's sad when a cartoonist, Scott Adams, is one of the few people who realize that both sides lack credibility. At this point, there are too many overhyped claims from both sides to get any useful information.

[Leo]

There are a lot of problems darwinists don't undertstand how proteins form, human to ape trasformation remains a mystery also does thhe origin of life as a whole. We can never prove that a butterfly does not have a inner experiences well they may have.

[James]

"Maybe you should also check out Michael Behe's latest book on Amazon called "Edge of Evolution""

Behe's argument isn't tight. While he did refute direct Darwinian evolutionary scenarios for certain biochemical systems, his "irreducible complexity" concept doesn't touch indirect Darwinian scenarios (i.e. cooption arguments). To be fair, I don't think the Darwinists have provided plausible answers to Behe's objections, but they have correctly pointed out this flaw in his argument.

[Urban Mystic Dee]

I just read this on Uncommon Descent. Here is my response from there:
Artificial life in three to ten years? This remides me of how in the ’60s it was promised that by the ’80s we would have sidewalks that move and cars that drive themselves. Here I am, still having to use my damn legs. Where are my robot cars and sidewalks? Or my robot butlers for that matter? And what ever happened to my star wars lasers? This is just yet another case of same crap different day.

And, pardon my language (if you want you can edit it out), in response to one of the previous comments, I personally find Skep-dick Scott Adams to be an arrogant douchebag, a cultist, and someone who is collossaly ignorant and uninformed. I have absolutely no respect for the man and don't trust a single thing that comes out of his liars mouth. I write about him occasionally on The Urban Mystic and have confronted him several times with evidence that he is pattently wrong and telling people who hold him in high regards things that are outright lies and he has yet to address my refutation of his cherished dogma. The challenge I put up to him can be found at the following:
http://journals.aol.com/ordinarymortal/TheUrbanMystic/entries/2007/06/04/the-skep-dick-scott-challenge-revised-edition/460

[Adam]

Hi Michael & All,

Firstly I have a lot of respect for Robert Shapiro. His 1986 book "Origins" is still the best introduction to the issues involved in the origin of life debate for the lay-person.

But to business. There's a few misunderstandings in your post above Michael, and Shapiro is an odd person to drag out in support of "direct design". Even knowing all the problems with popular abiogenesis scenarios he still doesn't think a miracle was involved or needed.

Anyway first misunderstanding is that Darwinism is about "struggle for survival" but thinking that excludes what's commonly called "differential reproductive success" - what replicates more than any other will come to dominate a population. In the case of Szostak, or Shapiro, style molecular evolution, that means whatever combination of interacting molecules is the most fecund (produces the most copies of itself.)

Secondly cell membranes of eukaryotic cells are complex, but the plasma membranes of archeal cells aren't full of gate proteins and the like which make eukaryotic cells so complex. Some fatty acid micelles (double walled 'bubbles') are sufficiently porous to allow small molecules in and keep large polymers from escaping - sufficient for encapsulating a self-replicating set of biomolecules.

Finally the amount of information stored in a set of self-replicating biomolecules may not be very much at all. But even the simplest self-replicating organisms don't have that much information as such. For many proteins a large fraction of the amino acid sequence can be changed with no change in function. Some molecular machines are ubiquitous in function throughout the biological world - cytochrome c for example - but exist in a HUGE variety.

The simplest self-replicator known is a mycoplasma with a DNA string about 900,000 base-pairs long. There's 3 bases per codon in DNA's "language" so the mycoplasma genome is 300,000 codons long. A codon is roughly 6 bits. Thus the simplest self-replicator is the equivalent of about 225 kilobytes. There's 10,000 symbols (including spaces) per page of the Encyclopedia Britannica - I counted it out of curiosity one day. Thus a mycoplasma needs just 23 pages of Britannica to encode for its 517 genes.

Taking into account the redundancy of the DNA codon code and the roughly 50%-80% redundancy of amino acid sequences themselves, that means roughly 80-50 kilobytes of information will code a self-replicating DNA-based cell. Just 5 to 8 pages of Britannica.

Still a lot to "just happen", but not the ridiculous figures thrown out routinely by IDers. And in our ignorance of proto-biochemistry we might be missing the key element that simplifies matters even further.

But weirder things might be needed. Physicist Paul Davies has speculated that backwards causation might cause the past to be at least partially determined by the future - thus biochemistry was arranged to be consistent with the existence of Life by the (future) observation that Life exists. Else there would be no observation for that "consistent history" to ever happen. This occurred not by design, as in engineering by a god, but by mathematical consistency that the Universe be observed and thus observers should exist.

The self-referential nature of that gives me a headache, but check out Davies "The Goldilocks Enigma" (called something else in the USA) for a fuller discussion. I suspect that the quantum "look ahead" effect I've discussed elsewhere might be involved in how biomolecules formed self-replicating sets so apparently easily. And it might still happen today - there's a whole barrel of mysteries as to how proteins do what they do. We might find some pretty wild quantum effects are necessary for life itself.

Hand-waving a lot, I know, but if you were a god how would you do it?

[JoeMB]

Urban Mystic wrote:

>I just read this on Uncommon Descent. Here is my response from there:
Artificial life in three to ten years? This remides me of how in the ’60s it was promised that by the ’80s we would have sidewalks that move and cars that drive themselves.

* * * * *

Was at the airport the other day, I rode the moving sidewalks all around. They've been there for several years now.

Here is one of several cars that will flood the market in the near future...

http://www.popsci.com/popsci/whatsnew/4591181d2ec4a010vgnvcm1000004eecbccdrcrd.html

The Honda Accord ADAS, written up in the May issue of PopSci, can sense its proximity to other cars and objects and steer itself to stay within lane lines. And you thought cruise control was cool.

[Ryan]

JoeMB, I demonstrated how to embed links in posts like you asked. Read my comment on Michael's recent post on flying saucers.

[Adam]

The reason cars don't fly is the same as why planes don't flap their wings. Cars aren't planes and planes aren't birds - wrong shape for the job required.

No flying car design is sufficiently stable aerodynamically. That needs wings and flying cars, as usually envisaged, don't have them. If they did then they'd be planes. And we already have those.

However that's only true under conditions of 1 Earth gravity. Under an air-dome on the Moon, or in the thick atmosphere of Titan, the required wing-surface would be similar in size to a car. A suitably shaped car with fan-propulsors would fly quite well. Personal flying packs would also be pretty effective too. In fact with the right set of wings a human's muscle strength would be sufficient for flapping-flight.

[Urban Mystic Dee]

Moving sidewalks in airports don't count just like things at trade shows or carnivals don't count. They're just a novelty item. I still have to walk down the street to pick up a newspaper and coffee.