Posted on 08/01/2009 7:57:05 AM PDT by GodGunsGuts
With the advent of modern biotechnology, researchers have been able to determine the actual sequence of the roughly three billion bases of DNA (A,T,C,G) that make up the human genome. They have sequenced the genomes of many other types of creatures as well. Scientists have tried to use this new DNA data to find similarities in the DNA sequences of creatures that are supposedly related through evolutionary descent, but do genetic similarities provide evidence for evolution?...
(Excerpt) Read more at icr.org ...
Sadly, not on these threads...
His PhD appears to be in Genetics, go look it up to double check. If it is, then it would make highly qualified to speak on this subject.
Yup, in typical liberal fahion they dissect the background of their targets in order to avoid the actual subject.
But this is necessary when you have no coherent argument.
Well, since nucleotides form a natural polymer (they inherently link to one another) they are far, far, far more likely than scrabble pieces, which only assort randomly, don't polymerize, and don't have the complex properties that a polymer has, to form meaningful arrangements.
What's the meaning? Initially it's only, "how well do I reproduce myself." Probably some sequences will be more easily reproduced than others. If that's the case, you're off from there with few limitations. Every time some slight change improves reproduction fecundity and fidelity, it will be preserved in future copies, and subject to further improvement.
So the problem is not the origin of information. Information is there once you have a polymer with a definite primary sequence that gets copied accurately. Meaningfulness is there so long as some sequences copy better than others, at that's certain to be the case because different primary sequences will have different secondary (bonding) and tertiary (3-D) structures.
The problem is how do you get an accurately reproducing bio-polymer in the first place. In fact it can't be DNA because DNA can't reproduce by itself. It needs RNA and proteins to reproduce. So, the original reproducer was certainly something other than DNA, and DNA latter piggybacked on it. For instance RNA, which can have enzymatic properties, and therefore could conceivably facilitate it's own reproduction, almost certainly preceded DNA. There may well have been one or more reproducing molecules (or molecular systems) which preceded RNA, but haven't been retained by organisms the way RNA was.
Whatever. I don't know the answer. But I do know the question. It's not, "how do you get information?" That's easy. It's, "how do you get reproducing bio-polymers?" That's the hard part.
So, we are left with asking ourselves, what is the only known source of information? The answer is, of course, an intellect. It is beyond the realm of empirical science to determine the identity and nature of that intellect. Even so, an intellect is the best explanation by far of the origin of the information embedded in DNA.
Again, I disagree.
Funny, however, that I agree there are significant difficulties with the naturalistic origin of life. It's just that the part you think is hard is actually very easy, and happens as a matter of course once given reproduction, while the part that's really hard you pass over.
More specifically, it's simply not true that "an intellect ... is the only known source of information." Any time you have nonrandom structure you have information, and the world is full of nonrandom structure created naturally without "intellect". For instance the various layers of sand, gravel and rock in a river bed contain information. They tell you actual things about the river. When sand was deposited it means the river was flowing slowly. Gravel means faster flow, and rocks mean the flow was torrential. There are innumerable examples. The size of hail pellets, and the number of ice layers, for example, record information about the thermal layers in the clouds that produced them. Um, O.K., it's early and I'm caffeineless, so I'm not thinking of more examples right now, but you must realize on refelction that they are endless.
Why do you say, "like Dr. Tomkins," when Dr. Tomkins himself has not done so? He's been at the ICR for 18 months, and has published no technical or research articles for them. Only short, fluffy popular pieces like the present article.
Nor do any of his previous research articles, while at Clemson, appear to come anywhere near to engaging a crucial test between creation/design and evolution/descent explanations of biochemical data. They all seem to deal with the sorts of adaptations to local environments which creationists allow within "kinds".
If he's competent to address it, why do you think Dr. Thomkins has been consistently avoiding the issue since he received his Ph.D. 13 years ago?
" Animal relationships derived from these new molecular data sometimes are very different from those implied by older, classical evaluations of morphology. Reconciling these differences is a central challenge for evolutionary biologists at present. Growing evidence suggests that phylogenies of animal phyla constructed by the analysis of 18S rRNA sequences may not be as accurate as originally thought. Inaccuracies may occur in molecular phylogenies for a variety of reasons.
Prior to analysis, the sequences of corresponding genes from each animal must be placed in register (aligned) with each other so that homologous sites within each sequence can be compared. However, sequence divergences may be sufficiently large that unambiguous alignments cannot be achieved, and different alignments may lead to different inferred relationships. Additionally, the data are often sufficiently noisy that there may be a lack of strong statistical support for important groupings. 1
The article then discusses a figure detailed similarities and differences in 18s rRNA sequences which show that mollusks (scallops) are more closely related to deuterostomes (sea urchins) than arthropods (brine shrimp). Of course, this is not too surprising. Intuitively, a scallop seems more like a sea urchin than a shrimp. So, the 82% correlation between the scallop and sea urchin is not surprising. However, in this light it is surprising is that a tarantula (also an arthropod) has a 92% correlation with the scallop. Here we have two different arthropods, a shrimp and an tarantula. How can a scallop be much more related to one type of arthropod and much less related to the other type of arthropod? This troubling thought led the authors of the Science article to remark:
Different representative species, in this case brine shrimp or tarantula for the arthropods, yield wildly different inferred relationships among phyla. Both trees have strong bootstrap support (percentage at node). . . The critical question is whether current models of 18S rRNA evolution are sufficiently accurate to successfully compensate for long branch attraction between the animal phyla. Without knowing the correct tree ahead of time, this question will be hard to answer. However, current models of DNA substitution usually fit the data poorly . . .
There are many other interesting little problems concerning commonly used phylogenic tracing genes and proteins. For example, mammalian and amphibian "luteinizing hormone – releasing hormone" (LHRH) is identical. However, birds, reptiles, and certain fish have a different type of LHRH. Are humans therefore more closely related to frogs than to birds? Not according to standard evolutionary phylogeny trees. Again, the data does not match the classical theory in this particular situation.15" [LINK]
Yep- Phylogeny- manipulate the data to suit hte hypothesis- if the data refutesd the hypothesis, just ignore it (or better yet- just simpyl attack the credentials of anyone that bring the data to the table- that's always a winning tactic amoung those who don't like the data- Ah- shallow victories- but I guess shallow is betterthan bnothing if that's what gets one up in the am)
What are your credentials? Other than owning a keyboard?
"The "origin of life" (OOL) is best described as the chemical and physical processes that brought into existence the first self-replicating molecule. It differs from the "evolution of life" because Darwinian evolution employs mutation and natural selection to change organisms, which requires reproduction. Since there was no reproduction before the first life, no "mutation - selection" mechanism was operating to build complexity. Hence, OOL theories cannot rely upon natural selection to increase complexity and must create the first life using only the laws of chemistry and physics.
If the origin of life took place in the pre-biotic soup, then it took place in an aqueous (i.e. water-based) solution of pre-biotic monomers. According to Le Chateliers Principle, one of the basic laws of chemistry, the presence of a product (in this case, water) will slow the reaction. If one tries to polymerize monomers into polymers in an aqueous solution (one where water is the solvent), it not possible to obtain any appreciable amount. The bottom line, the polymerization step in the chemical origin of life could never take place in water—this step is impossible in the primordial soup.
Step 3: Pre-RNA World: Getting A Sufficient Self-Replicating Molecule
Though the OOL appears to be dead in the water, because of the lack of evidence for a "primordial soup" and the problems facing polymerization, let’s assume that those hurdles could be overcome. What would happen next? Many researchers have hypothesized that once polymers somehow formed, some of them came together to form the first self-replicating molecules. Somewhere within this step--the Pre-RNA world--the true origin-of-life occurred. However, nothing even close to a complete scenario by which polymers can naturally form a self-replicating molecule has ever been put forth. Chemists can artificially synthesize some self-replicating molecules in the lab, but they are not synthesized under conditions resembling the early Earth. Essentially, this is an appeal to a miracle.
...One commentator noted that these self replicating molecules contain vastly less information compared to what is necessary for even the most primitive cell:
"This system carries very little information, in contrast to even the simplest cell. Mycoplasma gentalium has the smallest known genome of any living organism, which contains 482 genes comprising 580,000 bases. This organism is an obligate parasite. A free-living organism would need many more genes."19
Step 4: RNA World
Some time after the first "self-replicating" molecule formed, according to the story, RNA came along. Today, RNA is a genetic molecule in all cells, similar to DNA, but more versatile within the cell. The "RNA World" is essentially a hypothetical stage of life between the first replicating molecule and the highly complicated DNA-protein-based life. The chief problem facing an RNA world is that RNA cannot perform all of the functions of DNA adequately to allow for replication and transcription of proteins. OOL theorist Leslie Orgel notes that an "RNA World" could only form the basis for life, "if prebiotic RNA had two properties not evident today: a capacity to replicate without the help of proteins and an ability to catalyze every step of protein synthesis."41 The RNA world is thus a hypothetical system behind which there is little positive evidence, and much materialist philosophy:
"The precise events giving rise to the RNA world remain unclear … investigators have proposed many hypotheses, but evidence in favor of each of them is fragmentary at best. The full details of how the RNA world, and life, emerged may not be revealed in the near future."41
The best claimed evidence of an "RNA World" includes the fact that there are RNA enzymes and genomes, and that cells use RNA to convert the DNA code into proteins.42 However, RNA plays only a supporting role in the cell, and there is no known biochemical system completely composed of RNA.42
RNA experts have created a variety of RNA molecules which can perform biochemical functions through what is commonly termed "test tube evolution." However, "test tube evolution" is just a description for what is in reality nothing more than chemical engineering in the laboratory employing Darwinian principles; that does not imply that there is some known pathway through which these molecules could arise naturally.
The most interesting RNA molecule synthesized is perhaps an RNA "polymerase" which can replicate 14 base pairs of RNA.42 Yet, the polymerase itself is 200 pairs long.42 As Gerald Joyce noted, OOL theorists are thus 14 / 200 towards achieving a possible model molecule for the RNA World. $2 However, Joyce also noted that the replication accuracy of this molecule is too poor to allow for it to persist as a functional form of life.42
These purely speculative scenarios aren't bad on their own merits, but they are just another reminder of the philosophical presupposition driving this research in the first place: naturalism. Only when scientists assume there must be a natural explanation do they turn to completely unfalsifiable unverifiable and incomplete speculatory hypotheses.
The theory then says that some unknown precursor of RNA turned into RNA through an unknown process. This "RNA-world hypothesis" states that life then arose from a population of self-replicating RNA molecules. RNA is a sister molecule to DNA, used when DNA breaks up to create proteins or replicate. Like a copy from the library, RNA has a complementary code to DNA and goes out to do the dirty work. A few types of RNA have been known to have auto-catalytic self-replicating abilities, however this scenario inevitably encounters a chicken and egg problem18.
But these molecules must be encapsulated within a "cell wall structure" or a small protective enclosure from the outside world. But, the protective cell requires replicating genetic machinery to be created. Thus, we now have a "chicken and egg scenario"--which came first? the self-replicating machinery (which needs a cell to operate), or the cell itself, which protects (and is created by) the cellular machinery? The answer is neither came first for both are required for self-replication. How could self-replicating RNA arise naturally when it essentially is an irreducibly complex system that cannot functionally replicate without other distinct components.
Step 6: Making Proto-cells
Leaving the "chicken-egg" problem aside for a moment, how would we get the first cell-walls for these early replicating sets of molecules? According to one major biology textbook:
"One of the earliest episodes in the evolution of life may have been the formation of a membrane that could enclose a solution of different composition from the surrounding solution, while still permitting the selective uptake of nutrients and elimination of waste products. This ability of the cell to discriminate in its chemical exchanges with the environment is fundamental to life, and it is the plasma membrane that makes this selectivity possible."46 [LINK]
[[What are your credentials? Other than owning a keyboard?]]
Can walk and chew gum at the same time?
You don’t even have to read the article to find the first logical fallacy - they start with the title. It’s a classic false dilemma - it either had to have been designed or it evolved, and those are the only two possibilities and they are mutually exclusive.
‘Synthesis of chiral compounds from achiral reagents always yields the racemic modification.’ and ‘Optically inactive reagents yield optically inactive products.’3
This is a consequence of the Laws of Thermodynamics.
To resolve a racemate (i.e. separate the two enantiomers), another homochiral substance must be introduced. The procedure is explained in any organic chemistry textbook. The idea is that right-handed and left-handed substances have identical properties, except when interacting with other chiral phenomena. The analogy is that our left and right hands grip an achiral (non-chiral) object like a baseball bat equally, but they fit differently into a chiral object like a left-handed glove. Thus to resolve a racemate, an organic chemist will usually use a ready-made homochiral substance from a living organism. The reaction products of the R and L enantiomers with an exclusively right handed substance R', that is R-R' and L-R' (called diastereomers), are not mirror images. So they have different physical properties, e.g. solubility in water, thus they can be separated.
However, this does not solve the mystery of where the optical activity in living organisms came from in the first place. A recent world conference on ‘The Origin of Homochirality and Life’ made it clear that the origin of this handedness is a complete mystery to evolutionists.4 The probability of forming one homochiral polymer of N monomers by chance = 2–N. For a small protein of 100 amino acids, this probability = 2–100 = 10–30. Note, this is the probability of any homochiral polypeptide. The probability of forming a functional homochiral polymer is much lower, since a precise amino acid sequence is required in many places. Of course, many homochiral polymers are required for life, so the probabilities must be compounded. Chance is thus not an option.
A further problem is that homochiral biological substances racemize in time. This is the basis of the amino acid racemization dating method. Its main proponent is Jeffrey Bada of the Scripps Institution of Oceanography in La Jolla, California.5 As a dating method, it is not very reliable, since the racemization rate is strongly dependent on temperature and pH, and depends on the particular amino acid.6 Racemization is also a big problem during peptide synthesis and hydrolysis.7 It shows that the tendency of undirected chemistry is towards death, not life.
A tragic reminder of the importance of chirality is thalidomide. In the early 1960s, this drug was prescribed to pregnant women suffering from morning sickness. However, while the left-handed form is a powerful tranquilliser, the right handed form can disrupt fetal development, resulting in severe birth defects. Unfortunately, the synthesis of the drug produced a racemate, as would be expected, and the wrong enantiomer was not removed before the drug was marketed.8
In my own undergraduate chemistry education, one of the required experiments demonstrated these concepts. We synthesized the dissymmetric complex ion, [Co(H2NC2H4NH2)3]3+,9 from achiral reagents, so a racemate was produced. We resolved it by reacting it with a homochiral acid from a plant source, forming diastereomers that could be resolved by fractional crystallisation. When the resultant homochiral crystals were dissolved, and activated charcoal (a catalyst) added, the substance quickly racemized, because a catalyst accelerates approach to equilibrium.
Origin-of-life researchers have tried to think of other means of producing the required homochirality. There have been unsuccessful attempts to resolve racemates by other means.
Transfer RNAs selected the right enantiomer
One attempt to solve the chirality problem was proposed by Russell Doolittle, a professor of biochemistry at the University of California at San Diego, and an atheist. He claimed: ‘From the start of their [Transfer RNA synthetases’] existence, they probably bound only L-amino acids.’27 He never explains how such complicated enzymes could have functioned unless they were themselves homochiral, or how they would operate before RNA was composed of homochiral ribose. Doolittle’s ‘solution’ is mere hand-waving. It is hardly worth refuting except that it appeared in a well-known anti-creationist book, which says something about the quality of its editing, or the quality of anti-creationist arguments.
It seems like Doolittle was trying to explain away his prior televised evolution/creation debate with biochemist Duane Gish held before 5,000 people at Liberty University on 13 Oct 1981. The pro-evolution journal Science described the debate as a ‘rout’ in favour of Gish.28 The next day, the debate was reported by the pro-evolution Washington Post under the headline ‘Science Loses One to Creationism’. The sub-headline cited Doolittle’s anguished remark: ‘How am I going to face my wife?’ showing that Doolittle himself knew he was defeated.
If we can only ‘speculate’ on the origin of life, why do so many people state that evolution is a ‘fact’? Repeat a rumour often enough and people will swallow it." [LINK]
If anyone is obscuring other possibilites that would be the evo-cultists incapable of tolerating any dissent of their cult.
Either one would be more productive than what he’s doing at present, but we should be patient, it probably is the very best he can do.
Yeah, well, speaking of manipulating dishonestly to suit a hypothesis... I've only checked out one of "your" (Sean D. Pitman's) citations so far, and it isn't pretty. Pitman is either incompetent, or he's lying/hiding something:
There are many other interesting little problems concerning commonly used phylogenic tracing genes and proteins. For example, mammalian and amphibian "luteinizing hormone – releasing hormone" (LHRH) is identical. However, birds, reptiles, and certain fish have a different type of LHRH. Are humans therefore more closely related to frogs than to birds? Not according to standard evolutionary phylogeny trees. Again, the data does not match the classical theory in this particular situation.15" [LINK]
First off (and there doubtless many problems with this which I, as a laymen, am not catching, but I caught enough that it reeks...) the article Pitman cites does NOT say, "mammalian and amphibian "luteinizing hormone – releasing hormone" (LHRH) is identical." It said (underline added):
Mammalian and amphibian hypothalamic immunoreactive LHRH yielded displacement curves parallel to those of synthetic LHRH in assays employing four antisera which recognize different regions of the decapeptide, thus suggesting a similarity in the structure of their LHRH.
An immunoreaction assay, using only four elements against an unsequenced hormone, can't possibly prove it's "identical" with anything.
Turns out, this result doesn't even prove what is claimed about the comparative relationships, because we have no idea if genuinely homologous hormones were being compared. You see, it turns out that LHRH is a whole FAMILY of hormones, with as many as 14 variants in vertebrates alone and with all vertebrates synthesizing at least 2 forms in the brain. BUT THIS WASN'T KNOWN when the paper you/Pitman cite was published IN 1980!
I got an inkling that something was wrong reading the paper, both because it used superseded methods, and because it seemed to be describing something simultaneously familiar and unfamiliar. Aha! Turns out I had read about "luteinizing hormone releasing hormone(s) (LHRH)" before, but didn't realize it because THEY AREN'T EVEN CALLED THAT any longer. Now they're referred to as Gonadotropin-releasing hormone(s) (GnRH)
So it turns out Pitman used an outdated, 1980 reference, in an article he wrote in 2004, and updated in 2008, simply because it said what he wanted it to say.
Since Pitman is an M.D., and GnRH is an important neuronal hormone, one of the most important released by the hypothalamus, it is unlikely that he did this out of ignorance. If not, then he effectively lied, knowingly using the old reference despite reams and reams of later published research, conducted in light of the knowledge of different forms of GnRH, coded by different genes.
If he didn't lie, then he was incompetent, choosing to write about this hormone, and use it to make a key point, while obviously doing no adequate research.
Since the first citation of yours that I pulled out of the hat turned out to be a load of crap, I feel justified in ignoring the rest of your citations, which you have presumably cribbed from equally (dis)reputable sources.
Now, if you want to pick one or more particular articles, and affirmatively lay out the argument(s) which you consider to follow therefrom, that I would be willing to look at. But going through dozens of cites to figure out just how each one is bogus, misrepresented or irrelevant? No thanks.
What's the point? I'm already pretty confident I know the answer, and equally confident he won't be frank with me (or probably even with himself) on this particular subject. Nor is it really my job, as a non-creationist, to implicitly prod "creation scientists" in one direction or another. That's the job of creationists. (Laughable as it is that a rank and file creationist would ever hold a "creation scientist" accountable!!!) And, besides, I'm more curious how rank and file creationists react.
Fact is, however good a scientist Tomkins might be otherwise, he has effectively put science aside, at least so far as his work at the ICR is concerned, since simply by joining the staff he is required to annually sign the ICR Oath, which commits him, in advance of and despite the evidence, to reaching specific, pre-designated "scientific" conclusions. I won't participate in that sham even peripherally.
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