The Talk.Origins Archive Post of the Month: January 2002

Subject:    Re: A musing
Newsgroups: talk.origins
Date:       January 16, 2002
Message-ID: 3c47f5ae.7381465@news.mira.net

>"Ian Musgrave & Peta O'Donohue" <ian.musgrave_insert@adelaide.edu.au> wrote in message
>news:<Y29CPB+MQrtT2mWZSz14ytKV86Uw@4ax.com>...
>
>> >> Articles that misrepresent progress in various fields by either
>> >> incompetence or design is not "dross"?
>> >
>> >I reject that all my references fit that description, though I accept that
>> >in part they may. The good, bad and ugly of the web, compiled by a non-expert.
>>
>> Let's see, so far you have:
>> 1) A newspaper article that claims abiogenesis is a fiendishly
>> difficult problem. [Duh! This negates evidence of progress how?]
>> 2) A newspaper article that quotes two unidentified "experts" as
>> saying RNA formation would take a miracle [no attributions, counter
>> evidence from experimental work, see the Higgs boson discussion below]
>> 3) An apologetics site that quotes [probably out of context] two
>> marginal figures as modern "experts" and avoids any actual data.
>> 4) A long quote from Behe that is both false and misleading.
>>
>> 1) doesn't even support your original contention. If that's not dross
>> what is?
>
>3) could have more detail I admit,

<incredulous tone> MORE detail? </incredulous tone> It had NO detail. Look, if you really think partial quotes from marginal figures means something, you would hunt up the actual articles and find out what Klein and Dose really said in the rest of their articles (and if Does's article is really from 1988, what relevance is a 15 year old article from before the recent advances in the field? What problems does he identify and which have been resolved - e.g., cytosine synthesis).

>and the science reports from
>newspaper articles are not my preferred source of information. Fair
>enough, to win this argument I concede would need to do better.
>
>I emphasise that my only contention here is that an integrated and
>wodely accepted abiogenesis theory is currently very lacking:

Message-ID: <UqW_7.1932$ko4.205650@nasal.pacific.net.au> "This author at least acknowledges that abio is still closer to the speculation rather than solution end of the scale:" [followed by a quote which showed no such thing]

I'm now going to go into "philosophy of science mode", and I am going to use the term "research program", do not be alarmed.

While the basic concept of abiogenesis can be stated simply (development of life from non-living substances), and is often referred to as a theory or hypothesis, abiogenesis isn't a really a theory per se (this is not unique to abiogenesis, it is true of most other "big" theories as well). What it is, is a well defined research program with a number of defined and well connected sub-domains (origin of building blocks, origin of polymers, self-replicator dynamics, transition of a self replicator system to a genetic system, origin of the genetic code, origin of metabolic systems from prebiotic precursors). There is a master theoretical statement that defines the research program [simple chemicals -> basic building blocks -> catalytic polymers + abiotic metabolism pre-RNA world -> RNA world -> DNA/protein world]. This is well and widely accepted (otherwise there wouldn't be a research program).

In each of the subdomains is a number of hypotheses and theories (basic building blocks [heterotrophic theory, autotrophic theory], RNA world theory [pure RNA, cofactor catalysis, ribopeptide world]), each of these theories is then subject to a number of experimental and observational programs, and some have far more support than others (e.g., heterotrophic theory has a large body of experimental support vs. autotrophic theory [although it looks as if both will operate in any plausible prebiotic world]). The RNA world has experimental support and support from "molecular fossils". In each of the subdomains there is a variety of levels of detail and support, where things are sorted out on a broader level, but require lots more work in the fine detail [e.g., what is the relative role of thioesters and pyrophosphate in the prebiotic world].

And guess what, scientists in these subdomains actually test their hypotheses, discard ideas on the basis of experimental evidence and so on. Just like the rest of science.

Abiogenesis is not at the "solution end of the scale". No one ever said it was. Neither is it at the speculation end of the scale. It is a defined but developing research program (unlike a mature research program).

You seem to be under the impression that if every subdomain of a research program hasn't been sorted out in all but minor detail it must be "speculation". It doesn't work like that. As an example, when first proposed as a hypothesis in 1986, the RNA world could have been described as "speculation"; now, after significant experimental effort, more refined theoretical considerations and observation work, the RNA world is an established, well-accepted theory with a wide body of supporting evidence, some of which points to the organization of the genetic code, some of which points back into the pre-RNA world. However, the RNA world is not a completed research program (or even a mature research program), far more experimental work is needed, and there are many areas where more detail is needed.

Science is like that; co-transmitter theory (where my early research was) took over 30 years to fill in the basic outlines, yet nobody called it speculation because the full details of the subdomains [synthesis][distribution][reaction] had not been fully worked out nor the links forged in detail.

Consider the polypetide agmatine, first found by a mate of mine in cow brain, it's been painfully characterized, located in nerve terminals, determined that it is released from nerve terminals, its biosynthesis worked out .. and we still have not the foggiest idea what it actually does. If I took you back to the early days of agmatine research, where we had only a few clues about its biology, but a well defined research program, what would you say about agmatine research?

Now we have a far more integrated view (it has all the hallmarks of a co-transmitter, nerve specific synthesis, granule storage and de-polarization induced release, but doesn't seem to do anything), but are frustrated by a complete lack of clues as to its actual role in the nervous system. What do you make of our "frustration"? That agmatine doesn't exist? That we will never work out what it does?

Abiogenesis is a broadly supported and integrated research program. By no means are all the details filled in, and many unresolved questions remain. In the various sub-domains, alternate hypotheses and theories are undergoing tests (and it looks like heterotrophic theory is winning out over autotrophic theory). This is one aspect that might be confusing Mark, as he seems to find reports of experimental tests of particular theories or hypotheses in a given subdomain as evidence that the research program is not widely supported.

[snip a combination of purple prose journalism, "gritted teeth" indeed, Miller never talks like that; a fairly decent Science News overview of Wactherhauser's ideas on autotrophy; and a report that shock horror researchers are actually conducting tests to determine if heterotrophic theory or autotrophic theory is correct. Gee, scientists testing theories, who would have thunk it.]

This all started when Mark asked if there had been any progress in abiogenesis research since Miller and Fox. When I replied with a list of progress, Mark felt he had to "balance" this with some quotes that purportedly showed lack of progress. Progress in a research program, or the robustness of the research program itself, is not judged by soundbites, but by the accumulation of data and theories in peer-reviewed journals, where people put in the hard yards and have their ideas and experiments open to criticism. And people do criticize them, and more experiments are done, more detailed theories emerge. That is how science is done.

In the 5 years since the RNA world was first published (in a peer-reviewed journal), there was a number of publications; some criticized the idea, others did experimental tests. By the end of 1991 there was a solid body of experimental work that confirmed that RNA was a broad activity catalyst, a broad theory of conversion of a tRNA-like ribozyme to an mRNA based translation system, and the discovery of the sunY self-replicator system (all in peer-reviewed journals). Now compare this with ID. In the 5 years since the first general-audience books on ID were published there has been ... well, nothing. There have been no peer-reviewed publications of any level of detail at all. Heck, not even an academic-grade book which provides reasonable details of the ideas.

The RNA world was a controversial idea; the idea that RNA could be a catalyst, and a broad range catalyst at that was astounding to say the least. But this originally unpopular idea did get published, and has founded a research program in its own right, which has exploded in the last 5 years. ID'ers don't publish in peer-reviewed journals and occasionally write books with fuzzy details and sometimes completely incorrect biology.

Again, I wish to emphasize that we don't know how life started on this planet, and that abiogenesis research has a long, long way to go. Nonetheless abiogenesis is a coherent, broadly supported research program, with broadly supported research domains, and substantial progress has been made in some key questions.

To repeat a question from a previous post. Because we struggle to explain ball lightning, do you feel it reasonable to claim that non-natural mechanisms must be involved?

[1] As TO's foremost typo-maker after Danny Niccoli, I really shouldn't base puns on typos, but wode seemed so appropriate [wode - blue dye - feeling blue]

Cheers! Ian
=====================================================
Ian Musgrave Peta O'Donohue,Jack Francis and Michael James Musgrave
reynella@werple.mira.net.au http://werple.mira.net.au/~reynella/
Southern Sky Watch http://www.abc.net.au/science/space/default.htm

Progress in Abiogenesis Research

Post of the Month: January 2002