Proper science at work:
Prediction: The Fundamental Unity of Life
source:
http://www.talkorigins.org/faqs/comdesc/section1.html#morphological_intermediates_ex3
According to the theory of common descent, modern living organisms, with all their incredible differences, are the progeny of one single species in the distant past. In spite of the extensive variation of form and function among organisms,
several fundamental criteria characterize all life. Some of the macroscopic properties that characterize all of life are (1)
replication, (2)
heritability (characteristics of descendents are correlated with those of ancestors), (3)
catalysis, and (4)
energy utilization (metabolism). At a very minimum, these four functions are required to generate a physical historical process that can be described by a phylogenetic tree.
If every living species descended from an original species that had these four obligate functions, then all living species today should necessarily have these functions (a somewhat trivial conclusion). Most importantly, however, all modern species should have inherited the structures that perform these functions. Thus,
a basic prediction of the genealogical relatedness of all life, combined with the constraint of gradualism, is that organisms should be very similar in the particular mechanisms and structures that execute these four basic life processes.
Confirmation:
The common polymers of life
The structures that all known organisms use to perform these four basic processes are all quite similar, in spite of the odds.
All known living things use polymers to perform these four basic functions. Organic chemists have synthesized hundreds of different polymers, yet the only ones used by life, irrespective of species, are polynucleotides, polypeptides, and polysaccharides.
Regardless of the species, the DNA, RNA and proteins used in known living systems all have the same chirality, even though there are at least two chemically equivalent choices of chirality for each of these molecules. For example, RNA has four chiral centers in its ribose ring, which means that it has 16 possible stereoisomers—but only one of these stereoisomers is found in the RNA of known living organisms.
Nucleic acids are the genetic material of life
Ten years after the publication of The Origin of Species, nucleic acids were first isolated by Friedrich Miescher in 1869. It took another 75 years after this discovery before
DNA was identified as the genetic material of life (Avery et al. 1944). It is quite conceivable that we could have found a different genetic material for each species. In fact,
it is still possible that newly identified species might have unknown genetic materials. However, all known life uses the same polymer, polynucleotide (DNA or RNA), for storing species specific information. All known organisms base replication on the duplication of this molecule. The DNA used by living organisms is synthesized using only four nucleosides (deoxyadenosine, deoxythymidine, deoxycytidine, and deoxyguanosine) out of the dozens known (at least 102 occur naturally and many more have been artificially synthesized) (Rozenski et al. 1999; Voet and Voet 1995, p. 969).
Protein catalysis
In order to perform the functions necessary for life, organisms must catalyze chemical reactions. In all known organisms, enzymatic catalysis is based on the abilities provided by protein molecules (and in relatively rare, yet important, cases by RNA molecules).
There are over 390 naturally occurring amino acids known (Voet and Voet 1995, p. 69; Garavelli et al. 2001); however, the protein molecules used by all known living organisms are constructed with the same subset of 22 amino acids.
The univeral genetic code
There must be a mechanism for transmitting information from the genetic material to the catalytic material.
All known organisms, with extremely rare exceptions, use the same genetic code for this. The few known exceptions are, nevertheless, simple and minor variations from the "universal" genetic code (see Figure 1.1.1) (Lehman 2001; Voet and Voet 1995, p. 967), exactly as predicted by evolutionary biologists based on the theory of common descent, years before the genetic code was finally solved (Brenner 1957; Crick et al. 1961; Hinegardner and Engelberg 1963; Judson 1996, p. 280-281).
The scientists who cracked the genetic code in the 1950's and 1960's worked under the assumption that the code was universal or nearly so (Judson 1996, p. 280-281). These scientists (which included Francis Crick, Sydney Brenner, George Gamow, and several others) all made this assumption and justified it based upon evolutionary reasoning, even in the complete absence of any direct experimental evidence for a universal code.
In 1961, five years before the code was deciphered, Crick referenced Brenner's work in his landmark report in the journal Nature, "General nature of the genetic code for proteins" (Crick et al. 1961). Although the organism used in the paper was the bacterium E. coli, Crick titled the paper "the genetic code for proteins", not "a genetic code" or "the genetic code of E. coli". In this paper, Crick and others concluded
that the code was (1) a triplet code, (2) non-overlapping, and (3) that the code is read from a fixed starting point (i.e. the "start" codon) (Crick et al. 1961). These conclusions were explicitly based on the assumption that the code was essentially the same in tobacco, humans, and bacteria, though there was no direct empirical support for this assumption. These conclusions, when applied to organisms from bacteria to humans, turned out to be correct. Thus, experimental work also assumed a universal code due to common descent.
In fact, in 1963—three years before the code was finally solved—Hinegardner and Engelberg published a paper in Science formally explaining the evolutionary rationale for why the code must be universal (or nearly so) if universal common descent were true, since most mutations in the code would likely be lethal to all living things. Note that, although these early researchers predicted a universal genetic code based on common descent, they also predicted that minor variations could likely be found. Hinegardner and Engelberg allowed for some variation in the genetic code, and predicted how such variation should be distributed if found:
"... if different codes do exist they should be associated with major taxonomic groups such as phyla or kingdoms that have their roots far in the past." (Hinegardner and Engelberg 1963)
Similarly, before alternate codes were found, Francis Crick and Leslie Orgel expressed surprise that minor variants of the code had not been observed yet:
"It is a little surprising that organisms with somewhat different codes do not coexist." (Crick and Orgel 1973, p. 344)
Crick and Orgel were correct in their surprise, and today we know of about
a dozen minor variants of the standard, universal genetic code (see the grey, red, and green codons in Figure 1.1.1). As Hinegardner and Engelberg predicted, the minor variations in the standard genetic code are indeed associated with major taxonomic groups (vertebrates vs. plants vs. single-celled ciliates, etc.).
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I sniffy, stirrer of mankind, doth hazard to predict that in a 'few' years time it will be commonly accepted that there are at least two major trunks on the tree of life, each with its own canopy of branches. I may go so far as to say that there might indeed be (horror or horrors) two separate origin trees.
Hint: Bacteria - 'superbugs' and their potential (evolutionary?) impact on animal biology. Anyone....??
Tsk tsk. :mufc:
Evolution as a process, is already a done deal, methinks.
Hence the ridicule. Rightly or wrongly.
Those who would do ill by Darwin, his original theory, and subsequent developments, do tend to exploit the lack of common understanding in these matters. The onus, therefore, is on proponents to make it understandable to those who lack a Phd in biochemistry or similar....
....and not to get bogged down in arguments regarding ridicule.