Sunday, September 15, 2013

Life - what a concept!

Kaffikjelen asked:

I wonder: Why do you think evolution is such an accepted scientific theory, having been exposed to so much confirmation and peer-review? Is it all a conspiracy?

1. Steve has already responded in the combox.

2. I'd just add there's oftentimes a significant difference between what's communicated publicly about modern evolutionary theory and what's discussed among scientists as well as published in the specialist peer-reviewed journals and related literature.

a. For example, check out the references in James Shapiro's Evolution: A View from the 21st Century to read some of the specialist literature. Although even his "suggested readings for non-professionals" contains papers with misgivings about the traditional paradigm.

b. Also, here's another example, a roundtable discussion between George Church, Craig Venter, and the late Robert Shapiro (among others) over something in our cells called the ribosome (emphasis mine):

CHURCH: I'm a little more interested in the future than the past — but I don't dismiss it either. For example, on the top of Freeman [Dyson]'s wish list was ribosome archaeology. And Dimitar [Sasselov] asked, Is there a milestone that we think is significant.

The ribosome, both looking at the past and at the future, is a very significant structure — it's the most complicated thing that is present in all organisms. Craig does comparative genomics, and you find that almost the only thing that's in common across all organisms is the ribosome. And it's recognizable; it's highly conserved. So the question is, how did that thing come to be? And if I were to be an intelligent design defender, that's what I would focus on; how did the ribosome come to be?

The only way we're going to become good scientists and prove that it could come into being spontaneously is to develop a much better in vitro system where you can make smaller versions of the ribosome that still work, and make all kinds of variations on it to do really useful things but that are really wildly different, and so forth, and get real familiarity with this really complicated machine. Because it does a really great thing: it does this mutual information trick, but not from changing something kind of trivial, from DNA to RNA; that's really easy. It can change from DNA three nucleotides into one amino acid. That's really marvelous. We need to understand that better.

VENTER: And you can't have life without it.

CHURCH: Definitely. It's common to all life. We need to understand that, and the way we're going to fund it — there's not that much funding for prebiotic science, but if there's a lot of funding for understanding the ribosome in the future and in the present, inevitably it will much enable studies of it in the archaeological and ancient biology sense.

VENTER: But using these tools, it's my hope we can do something similar to what you suggest. We can extrapolate back once we have the database of Planet Earth genes to what might have been a precursor species, and then we should be able to build that in the lab and see if it was really viable, and then start to do component mixtures to see if you can spontaneously generate such things.

CHURCH: But isn't it the case that, if we take all the life forms we have so far, isn't the minimum for the ribosome about 53 proteins and 3 polynucleotides? And hasn't that kind of already reached a plateau where adding more genomes doesn't reduce that number of proteins?

VENTER: Below ribosomes, yes: you certainly can't get below that. But you have to have self-replication.

CHURCH: But that's what we need to do — otherwise they'll call it irreducible complexity. If you say you can't get below a ribosome, we're in trouble, right? We have to find a ribosome that can do its trick with less than 53 proteins.

VENTER: In the RNA world, you didn't need ribosomes.

CHURCH: But we need to construct that. Nobody has constructed a ribosome that works well without proteins.


SHAPIRO: I can only suggest that a ribosome forming spontaneously has about the same probability as an eye forming spontaneously.

CHURCH: It won't form spontaneously; we'll do it bit by bit.

SHAPIRO: Both are obviously products of long evolution of preexisting life through the process of trial and error.

CHURCH: But none of us has recreated that any.

SHAPIRO: There must have been much more primitive ways of putting together catalysts.

CHURCH: But prove it.


BTW, here's an idealized animal cell to better situate people (click to enlarge):

On the one hand, Church, Venter, and Shapiro all but agree the ribosome is irreducibly complex (although they don't want to have to use the term). They agree a ribosome can't be further broken down into smaller bits and pieces from an evolutionary perspective: we "can't get below that," i.e., a ribosome that's composed of "53 proteins and 3 polynucleotides".

But on the other hand, at least as far as I'm aware they're all atheists or agnostics, as well as neo-Darwinists, and so must have "self-replication" of one sort or another to explain the origin of life in accord with their worldview. Venter proposes the RNA world, while Shapiro (from elsewhere) would favor a metabolism first hypothesis. But Church essentially says there's no empirical proof.

In other words, they're aware there are problems explaining how the ribosome could have come into being given modern evolutionary theory, which at a minimum implicitly casts some doubt on at least some aspects of the theory, but they seem reluctant to explicitly say so.

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