Tag Archives: Biological Function

New paper casts doubt on Stuart Kauffman’s self-organization theory

One of the naturalistic theories for the origin of biological information in the origin of life is Stuart Kauffman’s “self-organization” theory. The theory attempts to account for the functional sequences of information in living systems by arguing that the information emerges automatically from a sufficiently diverse pre-biotic soup.

In his book, “At Home in the Universe”, Kauffman writes:

I hope to persuade you that life is a natural property of complex chemical systems, that when the number of different kinds of molecules in a chemical soup passes a certain threshold, a self-sustaining network of reactions—an autocatalytic metabolism—will suddenly appear. Life emerged, I suggest, not simple, but complex and whole, and has remained complex and whole ever since… The secret of life, the wellspring of reproduction, is not to be found in the beauty of Watson-Crick pairing, but in the achievement of catalytic closure.

Doug Axe explains the theory a bit more: (H/T Evolution News)

When chemicals react, they produce different chemicals. So the idea here—call it Kauffman’s conjecture—was that mixtures with a sufficient number of different chemicals are bound to give rise to local compositions that continually replenish themselves through a self-catalyzed network of chemical reactions.  Those special compositions would typically differ from the original mixture, but since they make more of themselves, they should be able to ‘grow’ by establishing themselves repeatedly in local pockets.  The ability to propagate in this way, if proven, would be something like reproduction, only at the low level of chemical composition rather than at the high level of organismal form.

It was clear enough to me why Kauffman and others liked this idea.  If some kind of reproduction and inheritance could conceivably be achieved in systems that are much, much simpler than anything we think of as living, then maybe scientists were making the problem of explaining life much, much harder than it really needed to be.

But now a new peer-reviewed research paper has cast doubt on this naturalistic theory.

Axe explains:

The paper’s title is a diplomatic statement of its main conclusion: Lack of evolvability in self-sustaining autocatalytic networks constrains metabolism-first scenarios for the origin of life.  It becomes clear on reading the paper that the word constrains is here being used euphemistically. After testing the effect of fitness on the evolution of their model compositional assemblies, they report that “some slight relative increases and decreases in their replication-mutation equilibrium frequencies are detected, but the effects are so minor that it is hard to think of any evolutionary relevance.”  The problem is that the behavior of the whole system is almost completely determined by the inherent chemistry, leaving no room for selection to do anything interesting.

The citation is “Lack of evolvability in self-sustaining autocatalytic networks constraints metabolism-first scenarios for the origin of life”, Proceedings of the National Academy of Sciences USA, vol. 107, no. 4, pp. 1470-1475.

Science Daily reports the biological functions supported by Junk DNA

Here’s the Science Daily article. (H/T Evolution News)

Excerpt:

…during early development, the proteins required for cell division come from the mother. The researchers speculate that the heterochromatin of the male D. melanogaster‘s X chromosome has rapidly evolved, such that after mating, the machinery involved in DNA packaging from a D. simulans mother no longer recognizes the D. melanogaster father’s “junk” DNA, Ferree said.

Casey Luskin writes:

Basically, so-called “junk”-DNA is involved in helping to package chromosomes in the cell. If two species have different “junk” DNA, then this prevents the proteins in the egg from properly packaging the chromosomes donated by the sperm. The organism does not develop properly.

Good news for pro-ID guys like me!

How long will it take to sort a deck of cards by trial and error?

Inside the cell, things like proteins and DNA are formed by sequencing parts together in just the right way so that the sequence will have biological function. If the sequence is wrong, because some component of the sequence is the wrong piece or is in the wrong place, the sequence has no function. It’s just like writing English or computer instructions.

To calculate the probabilities, you have to use a rule called “The Product Rule”, because the order of the parts in the sequence (“permutation”) is important. For example, the odds of getting the sequence “ABC” just by choosing three random letters is 1/26 x 1/26 x 1/26 = 1/17576. Things get very unlikely quite quickly, don’t they?

So, take a look at Neil Simpson’s latest post, where he uses cards instead of letters or amino acids, but the principle is exactly the same. His calculation is a little different because the odds actually go down a little each time you choose a card. So, for the first card, it’s 1/52, but the second card is only 1/51, and so on…

Excerpt:

This is by no means a definitive argument against evolution, but I offer it to put the “time, chance and random mutation” theory in perspective.

Everyone knows that micro-evolution occurs, such as dog breeding and bacteria becoming resistant to antibiotics.  But macro-evolutionists believe that with enough time an amazingly complex single cell of unknown origin could make lots and lots of small changes, develop reproductive capacities and eventually become humans, elephants, caterpillar/butterflies, chameleons and so much more.

Let’s consider something very simple.  Imagine that you shuffle a deck of cards.  If you shuffled it one time per second, how often would all the cards go back into their original order? (Ace of spades, King of spades, etc.)  The math is simply 1/52 (the odds of the Ace of spades being on top) times 1/51 times 1/50, etc. I left out the Jokers to make it easier.

Guess how many years it takes?

Click through to see his calculations, or do them yourself! It’s easy and fun! Neil has a pretty fun discussion going on with the angry atheists who frequent his site, too.

This is everyone should learn probabilities in school, because then we can really talk about these things with our neighbor. Shalini can even do biochemistry, so she can actually explain it even better than I can!

Remember, we are looking for a specific sequence of cards – the sequence that the cards originally came in. In this example, it’s that sequence and that sequence alone that has biological function. The other sequences are just junk – they have no biological function. And most importantly, you don’t get to save any of the cards that are in the right spots because the sequence as a whole has no present function that would allow it to be “saved” for later. You have to re-select all 52 cards each time at random!

A typical protein isn’t made of 52 parts, it’s made of around 200, and there are 80 possible amino acids, not just 26! And in the case of proteins,the vast majority of the possible sequences that you can make won’t have any biological function at all! (And there are many more problems besides, such as chirality, cross reactions, and bonding type). Even if you filled the whole universe with reactants and reacted it all at Planck time, for the entire history of the universe, you still wouldn’t be likely to get even one protein!

You can read more about the origin of life in this post.