What Mean These Observations?

Science news outlets report many interesting findings every week.  It’s not always clear, though, whether the conclusions drawn from them are warranted by the data.  Here are some recent cases:

1. Jaws of steel:  A skull labeled Australopithecus robustus was studied for the force its jaws could generate.  Interpretation: “Early humans had jaws of steel.”  With this title, Science Daily is assuming this skull tells us about our ancestry, even though it is similar to apes and the linkage to human evolution is questionable at best.  Researchers at Arizona State assume this animal’s teeth could really crack a nut.  What does it mean?  “New research … reveals nut-cracking abilities in our 2.5-million-year-old relatives that enabled them to alter their diet to adapt to changes in food sources in their environment.”  It is not clear that they found any fossil nuts or fossil menus, but one of the researchers knew just what our great-great-grandparents were facing in their own great depression: “These fall-back foods – hard nuts and seeds – were important survival strategies during a period of changing climates and food scarcity.”  Apparently they had not yet evolved the ability to hit the big nuts with a rock and save their teeth.
2. Spongy Cambrian fuse:  Since the time of Darwin, the Cambrian explosion has been one of the biggest problems for the theory of evolution.  All the animal phyla appear abruptly in the fossil record without ancestors, despite over a century of looking for precursors.  This week in Nature,¹ researchers reported traces of a steroid in Precambrian rock in Oman said to be 635 million years old.  They said this chemical (24-isopropylcholestane, or lpc24) is diagnostic of sponges, and must mean that true sponges had evolved 100 million years before the Cambrian explosion.
       Brocks and Butterfield pointed out, though, in the same issue of Nature,² that the claim by the discoverers that the steroids indicate the presence of mature sponges “overlooks the evolutionary nature of biological taxa and the incremental assembly of defining characteristics along (now-extinct) ‘stem lineages’.”  In the evolutionary world view, one cannot assume the existence of mature sponges in rocks 100 million years earlier.  They must have been 100 million years less evolved.  Did the assumed ancestors even have the same characteristics of Cambrian sponges?  No clear evidence of spicules, for instance, has been found in the periods prior to the Cambrian.  “The absence of convincing spicules in the Ediacaran or Cryogenian fossil record implies that the modern poriferan classes were not fully defined until the Cambrian,” they said.  So not only was the original paper vulnerable to charges of question-begging, the criticism by Brocks and Butterfield was similarly theory-laden with Darwinian ideas.  Nevertheless, the news media jumped on the evolutionary interpretation with dramatic headlines like “Oldest Fossil Evidence for Animals Found” (Live Science), “Ancient sponges leave their mark” (BBC News, and “Earliest Evidence for Animal Life Discovered” (Science Daily).
3. Bible food fight:  Last month a theologian at the University of St. Andrews announced that the Biblical diet was unhealthy.  PhysOrg reported him claiming that people living in Bible times did not enjoy a balanced diet, contrary to portrayals of Israel as a land flowing with milk and honey.  This conclusion was based on his comparison of Biblical texts, comparative anthropological evidence, and archaeological finds.  He admitted that Biblical texts were not necessarily intended to give dietary advice, but left unanswered the question whether the land was capable of providing a balanced diet, and even if so, whether the practices of the people matched the precepts of the Old Testament.  Even today, many people do not eat what they know they should.  To what extent modern conceptions of what constitutes a good diet should be imposed on ancient people seems also open to question.  Every so often the modern “food pyramid” gets rearranged.  And some living tribes, like Eskimos, seem to get along fine with diets that contradict modern notions of the balanced diet.  The judgment call in the article, therefore, seems moot on several counts.
4. Tranquil flood:  A report on Science Daily called into question the Black Sea Flood theory for the origin of legends of Noah’s Flood.  Sediment cores on the Danube River were adduced to cast doubt on the Ryan-Pitman hypothesis that was popular a few years ago (04/21/2001, 04/26/2002).  Their questioning suggests additional questions, though.  Did the Ryan-Pitman hypothesis even qualify as an explanation for a Biblical flood that is described in Genesis 6-9 as covering all the high mountains?  And can sediments limited to a small region such as the Danube inform any interpretation of a flood of much vaster extent?  National Geographic interpreted this, anyway, to cast doubt on the Bible: “‘Noah’s Flood’ Not Rooted in Reality, After All?”  The only thing it was casting doubt on was the Ryan-Pitman hypothesis.  In that regard, yes, it could be called a “mythical flood,” but not necessarily a “Nail in Noah’s-Flood Coffin” like National Geographic intimated.
5. Protein evolution:  Pyrrolysine, an amino acid outside the standard 20-amino-acid library of “letters” making up life’s protein code, has been studied in more detail by researchers at Yale.  This uncommon amino acid, found in only 7 microbes, is modified after the protein has been translated in the ribosome.  Science Daily said the research team feels this fact “gave the researchers a molecular handle by being an extreme example of an amino acid that evolved to serve a highly specific need.”  Apparently the microbes have molecular systems that manage this particular amino acid.  To the reporter, this can only mean that “these molecules have evolved to work together.”  Teleology is supposed to be forbidden in Darwinian explanations.
6. Monkey politics:  Some chimpanzees are big and use physical attacks to get their way.  Others are smaller and more docile, grooming others to win favor.  One chimpanzee named Freud in Tanzania was observed to use both strategies.  According to Science Daily, this can only mean one thing: monkeys evolved politics.  The brief article did not mention this as evidence for the origin of human politics, but the lead author is the McKnight Distinguished Professor in the College of Biological Sciences’ department of ecology, evolution and behavior (EEB) at the University of Minnesota.  The human-evolution angle is apparently part of the motivation for the study, because she said, “We plan to study more alpha males to determine if grooming is a common strategy that small-bodied males use to placate rivals or cultivate cooperative alliances.” 
7. Red message:  Some ochre-colored markings were found on a cave wall in Africa said to be 100,000 years old.  This must mean that human culture evolved 70,000 years earlier than thought, reported Michael Balter in Science last week.³  One researcher nearly “fell off his chair” at the suggestion that the simple cross-hatched lines represented deliberate, symbolic designs.  “If so,” Balter commented, “the timeline for the earliest known symbolic behavior must once again be redrawn,” even if scientists don’t know what they symbolized, or even if they were symbols in the first place.  What “If not so”?
8. RNA world lines:  Mexican researchers publishing in PLoS One think they found fossils of the long-lost RNA world in the genetic code.⁴  How did they discern this?  They modeled on a computer the kinds of relationships of purines and pyrimidines in the DNA and RNA in some species of Archaea and bacteria.  “Remarkably,” they remarked, “the scaling properties of the distance series of some codons from the RNA code and most codons from both extended RNA codes turned out to be identical or very close to the scaling properties of codons of the SGC” [standard genetic code].  What does this mean?  “Therefore, we conclude that most current prokaryotes may still contain relics of the primeval RNA World and that both extended RNA codes may well represent two plausible evolutionary paths between the RNA code and the current SGC.”  This, of course, assumes that the RNA World even existed.  They referred to it as a “possible” thing and a “notion.”  The word notion appeared six times in the paper, most notably here: “The notion that present genomes may still retain remnants of their ancestry for more than three billion years has been a subject of controversy.”  Nevertheless, they concluded, “Our results support the notion that evolution did not erase all vestiges typical of the RNA World in today prokaryote genomes, not only in terms of an enrichment of RNY codons, but also revealing the existence of an underlying ancient fractal structure.”  The notion of a fractal structure in DNA played heavily in the paper.
9. Snakes alive:  A giant boa fossil has been discovered in Colombia.  Matthew Huber in Nature took this to mean that “tropical climate in the past was not buffered from global warming.”⁵  He did ask some questions about this inference proposed by discoverers Head et al in the same issue,⁵ namely:
   

   All that said, these implications are based on a new type of proxy: Head and colleagues’ findings are the result of probably the first study in ‘snake palaeothermometry’, and as such must be viewed with caution.  Is the empirical link between size and temperature really generalizable and accurate?  Could the ability to lose heat be an important limitation for these giant snakes, rendering Head and colleagues’ extrapolations moot?  Can a few vertebrae truly provide accurate estimates of snake size?  Why have similarly giant snakes not been found in other warm intervals?

   The popular press, however, did not hesitate to say that the giant snake fossil is a lesson for humans about global climate change (see National Geographic).

Mistakes in explanation happen.  Observations cannot speak for themselves.  There will always be some slippage between what we see and what it means.  For example, in Nature this week,⁶ Laurence Hurst bemoaned the fact that a diagnostic marker for positive selection in genes may be due to other causes not so benign.  Genes with “accelerated evolution” have been long inferred to be hotspots where positive natural selection is working overtime.  Berglund et al in PLoS Biology,⁷ proposed, instead, that hotspots may be artifacts of biased gene conversion (BGC) – the leftover damage from repair processes trying to correct mutations.  It leads to mutations getting fixed in the genome due to biased interactions between repair mechanisms and “purifying selection” – the genome’s attempt to maintain stability.  This will influence standard tests for positive selection and “possibly lead to false inference of positive selection at the protein level,” they said.
    Hurst said the work “undermines the assumed connection between fast evolution and pervasive positive selection.  Instead, it seems that hotspots have probably accelerated evolution by means of a biased DNA repair process, not because the changes were good for us.”  This new inference is 180 degrees out of phase with the old one.  It means we are devolving: “Indeed, many changes are probably detrimental.”  As a result, inferring positive natural selection in the genes will require more rigor:

More disturbingly, the results bring into question the usefulness of the standard tool kit for identifying hotspots of changes that are beneficial to organisms.  Convincing demonstration of positive selection now requires both evidence that the changes were not caused by BGC and scrutiny of the impact of the amino-acid changes.

That last sentence implies that evolutionists had looked for rapid change in a gene, without tying it to some functional benefit for the organism (see 09/05/2008).  The take-home lesson: don’t assume an observation has one and only one interpretation.  A corollary is that competing explanations may all be wrong.

1.  Love et al, “Fossil steroids record the appearance of Demospongiae during the Cryogenian period,” Nature 457, 718-721 (5 February 2009) | doi:10.1038/nature07673.
2.  Jochen J. Brocks and Nicholas J. Butterfield, “Biogeochemistry: Early animals out in the cold,” Nature 457, 672-673 (5 February 2009) | doi:10.1038/457672a.
3.  Michael Balter, “Early Start for Human Art? Ochre May Revise Timeline,” Science, 30 January 2009: Vol. 323. no. 5914, p. 569, DOI: 10.1126/science.323.5914.569.
4.  Marco V. Jos�, Tzipe Govezensky, Jos� A. Garc�a, Juan R. Bobadilla, “On the Evolution of the Standard Genetic Code: Vestiges of Critical Scale Invariance from the RNA World in Current Prokaryote Genomes,” Public Library of Science One, 4(2): e4340. doi:10.1371/journal.pone.0004340.
5.  Head et al, “Giant boid snake from the Palaeocene neotropics reveals hotter past equatorial temperatures,” Nature 457, 715-717 (5 February 2009) | doi:10.1038/nature07671.
6.  Laurence D. Hurst, “Evolutionary genomics: A positive becomes a negative,” Nature 457, 543-544 (29 January 2009) | doi:10.1038/457543a.
7.  Berglund, Pollard and Webster, “Hotspots of Biased Nucleotide Substitutions in Human Genes,” Public Library of Science: Biology, Vol. 7, No. 1, e26 doi:10.1371/journal.pbio.1000026.

Evidence can be badly misinterpreted, as any lawyer knows.  What do observations mean?  Humans are prone to jumping to conclusions.  Science is supposed to be a more rigorous process of linking causes to effects, in hopes of providing reliable explanations for natural phenomena.  Scientific reasoning usually does a better job than intuition, but it is not infallible.  A lot of questions have been raised about scientific reasoning over the last century.  Radicals have questioned the connection between scientific reasoning and “the real world” as it is “out there” apart from our sensations of it.  Most scientists today help themselves to the concept of “scientific realism” which assumes a connection.  The Stanford Encyclopedia of Philosophy says, “Scientific realists hold that the characteristic product of successful scientific research is knowledge of largely theory-independent phenomena and that such knowledge is possible (indeed actual) even in those cases in which the relevant phenomena are not, in any non-question-begging sense, observable.”  But how justified is scientific realism?  Scientists may assume it, but on what grounds?  Are they just begging deeper questions, even when they claim something as an “observation”?  Notice the article’s conclusion:

Scientific realism is, by the lights of most of its defenders, the sciences’ own philosophy of science.  Considerations of the significant philosophical challenges which it faces indicate that it can be effectively defended only by the adoption of a metaphilosophical approach which is also closely tied to the science, viz., some version or other of philosophical naturalism.

Metaphysics is unavoidable, therefore.  Can it be minimized?  Science does have a lot of success stories to its credit.  If scientists can fly a spacecraft around Saturn, applying widely varying findings accumulated through years of careful research in disparate fields, they must be doing something right.  There’s a strong link, however, between the successful explanations and phenomena that are observable, testable, and repeatable.  Origin stories are in different domain.  How successful can a theory about a universal common ancestor be if no observer was present?
    Early scientists were scrupulous in cashing out their explanations in empirical evidence.  Darwin came along and relaxed the rules.  In the Origin, he made “one long argument,” employing analogies, using, for instance, artificial selection (a form of intelligent design) as a proxy for natural selection (chance masquerading as law of nature).  He also pieced together widely disconnected snippets of observation into a grand mythical story that merely sounded “plausible.”  There are no laws of plausibility.  How do you test plausibility?  If the intellectual world gets swept off its feet by the apparent plausibility of Darwin’s Myth because it fits with their Victorian values of progress in an age of criticism of establishment religion, does that make it the Truth?
    Darwin got away with substituting hypothesis and narrative for scientific explanation.  He did so, ironically, by helping himself to moral and intellectual concepts not derivable from his universal law of natural selection.  This intellectual coup, achieved more through rhetoric than demonstration, prostituted the noble advance of science that had long sought understanding through rigorous observation and testing.  These articles (above) are examples of that legacy.  Getting science back to its founding principles is as difficult as getting America’s entitlement-minded culture back to the limited government specified in the Constitution.  Without it, though, any justification for reliable inference about the world and its natural history is compromised.
    Letting storytellers in science is like letting hackers on the internet.  When hackers run rampant on the science network, it’s hard to tell what is real anymore.  Only suckers broadcast excited messages that shout, “Send this to everyone you know!”