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Biology’s Next Revolution

Biology’s next revolution
by Nigel Goldenfeld and Carl Woese
Nature 445, 369 (25 January 2007)

For those without access to Nature click here for a copy of the article. This link added on 5/11/2007.

The emerging picture of microbes as gene-swapping collectives demands a revision of such concepts as organism, species and evolution itself.

Equally exciting is the realization that viruses have a fundamental role in the biosphere, in both immediate and long-term evolutionary senses. Recent work suggests that viruses are an important repository and memory of a community’s genetic information, contributing to the system’s evolutionary dynamics and stability. This is hinted at, for example, by prophage induction, in which viruses latent in cells can become activated by environmental influences. The ensuing destruction of the cell and viral replication is a potent mechanism for the dispersal of host and viral genes.

It is becoming clear that microorganisms have a remarkable ability to reconstruct their genomes in the face of dire environmental stresses, and that in some cases their collective interactions with viruses may be crucial to this. In such a situation, how valid is the very concept of an organism in isolation? It seems that there is a continuity of energy flux and informational transfer from the genome up through cells, community, virosphere and environment. We would go so far as to suggest that a defining characteristic of life is the strong dependency on flux from the environment — be it of energy, chemicals, metabolites or genes.

Horizontal gene transfer and community repositories of complex specified genetic information… these are things that fit really well with the front loading hypothesis. HGT and community gene libraries triggered by environmental cues are plausible mechanisms for preplanned evolution via saltation.

Read the rest of the Nature essay at the link above. I also recommend the science fiction book “Darwin’s Radio” by Greg Bear as it incorporates into the plot many of the HGT concepts discussed in the Nature article. As a matter of fact “Darwin’s Radio” was very favorably reviewed in Nature some years ago by accomplished geneticist Professor Michael A. Goldman. “Darwin’s Radio” is what rekindled my interest in ID. Bear doesn’t really support ID but he does a fair job of bringing into serious question the orthodox beliefs about gradualistic macroevolution. If orthodox beliefs are wrong one wonders what’s right and ID inevitably pops up as a possibility to any unbiased inquirer.

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15 Responses to Biology’s Next Revolution

  1. Woese previously had a great review paper called A New Biology for a New Century. Woese doesn’t explicitly say what area on the horizon matches his “new biology”, but I really think that ID fits the bill for what he is talking about.

    We cannot proceed further without clarifying and discussing what is meant by reductionism. The stakes here are high because the concept is deeply woven into the fabric of modern biology, and biology today has hit the wall of biocomplexity, reductionism’s nemesis. Thus, a topic that previously had been left for the philosophers and scientific dilettantes has suddenly become a very real and global issue for the practicing biologist. “Reductionism” is a confused and cathected issue at the moment, in large measure because biologists use the term in two senses, usually without distinguishing them. This we now have to do. We need to distinguish what can be called “empirical reductionism” from “fundamentalist reductionism.” Empirical reductionism is in essence methodological; it is simply a mode of analysis, the dissection of a biological entity or system into its constituent parts in order better to understand it. Empirical reductionism makes no assumptions about the fundamental nature, an ultimate understanding, of living things. Fundamentalist reductionism (the reductionism of 19th century classical physics), on the other hand, is in essence metaphysical. It is ipso facto a statement about the nature of the world: living systems (like all else) can be completely understood in terms of the properties of their constituent parts. This is a view that flies in the face of what classically trained biologists tended to take for granted, the notion of emergent properties. Whereas emergence seems to be required to explain numerous biological phenomena, fundamentalist reductionism flatly denies its existence: in all cases the whole is no more than the sum of its parts. Thus, biology of the 20th century was in the strange position of having to contort itself to conform to a world view (fundamentalist reductionism) that 20th century physics was simultaneously in the process of rejecting. In a metaphysical sense, molecular biology was outdated from the onset! What makes this curious period in biology’s history doubly bizarre is that a fundamentalist reductionist perspective wasn’t even needed in the first place in order to study biology on the molecular level. The simple empirical reductionist outlook would have done just fine, and technology was moving us in that direction anyway! It will be interesting to see what history has to say about the biology of the 20th century.

    I think the 20th century molecular era will come to be seen as a necessary and unavoidable transition stage in the overall course of biology: necessary because only by adopting a heavily reductionist orientation and the technology of classical physics could certain biological problems be brought to fruition and transitional because a biology viewed through the eyes of fundamentalist reductionism is an incomplete biology. Knowing the parts of isolated entities is not enough. A musical metaphor expresses it best: molecular biology could read notes in the score, but it couldn’t hear the music.

    The molecular cup is now empty. The time has come to replace the purely reductionist “eyes-down” molecular perspective with a new and genuinely holistic, “eyes-up,” view of the living world, one whose primary focus is on evolution, emergence, and biology’s innate complexity. (Note that this does not mean that the problems worked on in any new representation of biology will not be addressed by customary molecular methodology; it is just that they will no longer be defined from molecular biology’s procrustean reductionist perspective.)

  2. Woese is a truely great scientist even though he doesn’t like ID.

  3. If he doesn’t like ID, he’s not as smart as he seems. ID is pure reason.

  4. If he doesn’t like ID, he’s not as smart as he seems.

    No matter how fast the CPU bad data will cause it to give the wrong answer.

    ID is pure reason.

    No argument here.

  5. Borne, tribune7:

    I think you are unfair to Carl Woese. When Woese analyzed the ribosomal RNA sequences of different organisms years ago, at at time when that was a very cumbersome process, he came up with the radical notion that not all prokaryotes are the same. He met considerable initial skepticism when he proposed the three phylogenetic domains, but eventually he convinced his colleagues. How did he do it? With painstaking careful experimentation that eventually convinced his colleagues either directly or by getting them to do more experiments. More recently he decided to challenge his peers with the notion of lateral gene transfer as an important process in the evolution of unicellular organisms. There is nothing wrong with rattling your colleagues with fresh ideas, as long as you back them up with evidence.

    If Woese doesn’t accept ID right now, it is not because of “bad data”. He has demonstrated that he knows what good, convincing data are. I’d like to suggest that if the proponents of ID want to get their notion accepted by the general scientific community, they might want to adopt Woese as their role model. Go to the laboratory and provide empirical evidence that will convince everybody.

  6. Ofro

    Go to the laboratory and provide empirical evidence that will convince everybody.

    re macroevolution and origin of life

    Physician, heal thyself.

    The number of unconvinced is growing. Better get busier in those labs producing evidence that random mutation and natural selection is responsible for turning mud into man and bacteria into baboons.

    I’d wish you luck but that would be cruel. You’ll need more than luck to find evidence of something that never happened. You’ll need a miracle.

  7. Ofro, “Go to the laboratory and provide empirical evidence that will convince everybody.”

    The ID community is small compared to the research scientist community. However, the research sccientists are coming out with all sorts of evidence that cries for an ID interpretation. Do you remember those mice that had 100,000 highly conserved basepairs removed with no mesurable deleterious effects?

    “Go to the laboratory” is a platitude, a brush off. While laboratory work is being done, analysis of the laboratory work of others is a hundred times more fruitful.

  8. If Woese doesn’t accept ID right now, it is not because of “bad data”.

    Woese is very smart and is an proven independent thinker. I betcha he ends up accepting ID.

    And actually, in very narrow sense, there are times when it is appropriate not to consider ID, and this would include a research lab seeking a consistent cause for events in nature.

    The problems arise when:

    A. Those insist that only what can be found in a lab is real.

    B. And, exponentially more damning, false models are presented as real because better models that cannot be demonstrated in a lab may not be considered.

    C. And, even more exponentially damning, superior models that can be methodologically demonstrated are rejected due to the emotion-based wishful thinking of an establishment.

  9. Do you remember those mice that had 100,000 highly conserved basepairs removed with no mesurable deleterious effects?

    Speaking of this, I have a question – does ID predict that a purpose for these conserved basepairs will be found (i.e. they were conserved because they serve a subtle purpose), or no purpose will be found (the base pairs were “front loaded” and serve no current purpose although they may have served a purpose in the past or future)?

  10. And actually, in very narrow sense, there are times when it is appropriate not to consider ID, and this would include a research lab seeking a consistent cause for events in nature.

    I’m revising this to “those seeking explanations for events in nature that are not designed.”

    Then it is appropriate not to consider ID.

  11. Robin Cook’s Chromosome 6 as a novel contains a method by which a designer could use enzymes to move genes from genome to genome. Explains the how, but not the who.

  12. franky

    base pairs were “front loaded” and serve no current purpose although they may have served a purpose in the past or future

    Possibly.

    What I’m really looking for here is a mechanism other than natural selection which conserves genetic information. Thousands of sequences highly conserved between man and mouse scattered in a couple blocks of a million base pairs were cut out of the mouse genome and no one could find where it made even a tiny bit of difference to the mice.

    Unless some selection value for those sequences are found that highly conserved them for the 180 million years of divergence between man and mouse then you’re looking at the smoking gun. A mechanism that can preserve unexpressed genomic information for geologic time spans. No mechanism except natural selection has ever even been hypothesized (except by IDers) capable of conserving sequence data and that only when there’s some selection value in the sequence data.

  13. DaveScot,

    ”Unless some selection value for those sequences are found that highly conserved them for the 180 million years of divergence between man and mouse then you’re looking at the smoking gun.

    I wouldn’t call it a smoking gun, but such negative evidence could be looked at as an alternative to the established mechanism of natural selection. However, that would only be the bare beginning of developing an alternative hypothesis. Science demands that any alternative hypothesis eventually receives positive evidence. In your scenario, a mechanistic scheme is required that enables a mammalian genome to be copied many million times (you mention about 180 million years in the case of mouse and human), with a minimum of copying errors in these sequences. None of the DNA polymerases and error-correcting machineries known today (and they have been and still are carefully investigated because of their role in radiation and chemically-induced DNA damage and its relation to cancer) has the ability to provide this level of fidelity in copying DNA.

    So here lies the difficulty for the alternative hypothesis. As far as I can tell, searching the genomes for additional candidates involved in DNA replication has not yielded anything new in terms of protein-encoding genes, but it would have to be in there, somewhere. Could there be something in the “junk-DNA” that stabilizes/corrects these conserved sequences? Maybe that would be a field of research for ID proponents? In the meantime, the burden of proof for this alternative scenario isn’t any better, possibly a lot worse, than that for finding a condition under which the conserved genomic region gives a selection advantage.

  14. DaveScot
    What I’m really looking for here is a mechanism other than natural selection which conserves genetic information.

    OK. But I am curious – let’s assume that (1) the removed base pairs provide absolutely no advantage but (2) we find a new mechanism that makes certain areas of the genome particularly resistant to copying errors resulting in massively lower mutation rates than in other areas. Assuming that the mechanisms for protecting these certain regions of the genome are well understood, is the base-pair conservation still evidence of intelligent design?

  15. bFast: “…the research scientists are coming out with all sorts of evidence that cries for an ID interpretation. Do you remember those mice that had 100,000 highly conserved basepairs removed with no mesurable deleterious effects?”

    Back in the original post where this was discussed, “The Sound of Circular Reasoning Exploding” by DaveScot, http://www.uncommondescent.com/archives/1846 , Patrick said,

    I’d still like to see these mice tested for notable loss of instinctual behavior. Many tests were run but from what I’ve read it’s not been directly addressed.

    DaveScot addressed this, saying,

    Patrick,
    I thought about instinctual behavior before I wrote the article. I ran into three problems seemingly without resolution under the natural selection paradigm.
    1) what instincts are shared between mice and men
    2) which of those common instincts are so important to survival that they’d be ultra-conserved more than coding proteins? The suckling instinct came to mind.
    3) Why did the mice not show an adverse effects on losing instincts which must be so important? A baby mouse not able to suckle would die and the loss of the instinct would be easily noted to anyone closely observing the knockout mice.

    This stuck in my mind, and since then it’s been occurring to me just how many varied things both mice and men (and other organisms) often have to deal with. To name a few:

    - losing sight in one eye
    - losing hearing in one ear
    - severe winters
    - severe summers
    - starvation
    - drought
    - forest fires
    - the effects of being a sole survivor of a catastrophe
    - the effects of losing all of one’s offspring to predation or disease
    - etc…

    Anyone know if tests have been conducted to see if typical instinctual responses to such things are unaffected?

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