Dubious Darwinian Inferences Unquestioned

Science was invented to stop jumping to conclusions.  Leaps of faith from small clues to grand explanations were to be replaced by slow, careful, methodical investigations of raw data until rational inferences could be drawn.  Do the following research examples do justice to that ideal?

1. Smelly dinobird air space:  The news media are chortling over the latest idea coming from paleontologists: birds inherited their excellent sense of smell from dinosaurs because it gave them evolutionary fitness (see Science Daily).  Aside from the fact that no scientist has ever tested the smelling ability of dinosaurs, the researchers at Ohio State only had olfactory bulb cavities to measure – empty spaces devoid of the brain hardware and software needed to know how good it was.  “Of course the actual brain tissue is long gone from the fossil skulls,” Lawrence Witmer admitted.
       The researchers measured 157 olfactory bulb cavity sizes in birds and dinosaurs, but what inferences can be drawn from volume alone?  Scientists can compare olfactory bulb size in living birds and test their smelling ability; the article said that larger size in birds and mammals tend to correlate with smelling ability.
       That may be, but exceptions are common in biology, and nothing is known about dinosaur olfaction.  Insects arguably have some of the most sensitive smelling organs in the animal kingdom, but their equipment is smaller than the head of a pin.  If brain size is not a clear indicator of intelligence, it would seem olfactory bulb cavity size alone cannot be used as a proxy for smelling ability, particularly among a whole class of extinct reptiles (cf. 10/06/2010).
       Nevertheless, the Ohio State team let their imaginations take flight into the skies of data-challenged inference, drawing a grand scenario of evolution covering millions of unexperienced years, while the press release cheered them on:

   The study revealed details of how birds inherited their sense of smell from dinosaurs.
       “The oldest known bird, Archaeopteryx, inherited its sense of smell from small meat-eating dinosaurs about 150 million years ago,” said Fran?ois Therrien, curator of dinosaur palaeoecology at the Royal Tyrrell Museum and co-author of the study.  “Later, around 95 million years ago, the ancestor of all modern birds evolved even better olfactory capabilities.”
   

   Witmer speculated about the smelling ability of T. rex and other dinosaurs, but then the press release caught him in a potentially falsifying catch-all hypothesis: “Witmer noted that the ancient beasts most likely exhibited a range of olfactory abilities.”
       If so, it would seem no evolutionary inference could be drawn (cf. 12/21/2010).  Witmer drew one anyway: “T. rex had large olfactory bulbs, which probably aided the creature in tracking prey, finding carcasses and possibly even territorial behavior, while a sense of smell was probably less important to dinosaurs such as Triceratops, he said.”  But couldn’t that point be made about birds as well?  Indeed, it can, and they did:

   If early birds had such powerful sniffers, why do birds have a reputation for a poor sense of smell?  Witmer explained that the new study confirms that the most common birds that humans encounter today — the backyard perching birds such as crows and finches, as well as pet parrots – indeed have smaller olfactory bulbs and weaker senses of smell.  It may be no coincidence that the latter are also the cleverest birds, suggesting that their enhanced smarts may have decreased the need for a strong sniffer, he said.

   So far, we have seen a “range of olfactory abilities” in dinosaurs and birds, but the headline promised something else: “Birds Inherited Strong Sense of Smell from Dinosaurs.”  Has anything about that really been discovered in the raw data other than a hodgepodge of varying measurements of empty space where olfactory bulbs once lurked?  Aside from the fact that dinosaur-to-bird evolution remains contentious (09/09/2010), their inferences about bird evolution were held together by a lot of hedging words like probably, might, may, and suggesting, not by empirically justified inferences (for other examples of risky inference, see 01/14/2011 and 10/06/2010).
       Meanwhile, over at Live Science Charles Q. Choi even presented his readers with a cartoony dinosaur proud of his opossum-like prey, sporting some kind of incipient wings.  His inference was even bolder: “The ancestors of modern birds might have survived the mass extinction that wiped out their dinosaur forebears by having a better sense of smell, researchers suggest.”
       From the idea that olfactory bulbs grew in early birds then shrank again, he drew this inference: “This improved sense of smell, as well as larger brains overall, might have provided an edge that could explain why modern birds are still around and their dinosaur and archaic bird relatives are not.”

2. Missing dinobird link:  Cross out the missing in missing link: Science Daily rejoiced to announce, “New Species of Dinosaur Bridges Gap in Dinosaur Family Tree.”  The congratulatory headline was accompanied by a picture (artist drawing, not photo) of a dinosaur found in New Mexico, claimed to be 230 million years old (labeled late Jurassic).
       What was the gap?  “The evolutionary position of these early predatory dinosaurs was contentious because there was a gap in the fossil record between them and later theropod dinosaurs.”  What were the data?  “A team of scientists led by the Smithsonian Institution has discovered a fossilized dinosaur skull and neck vertebrae that not only reveal a new species, but also an evolutionary link between two groups of dinosaurs.”
       Actually, the data stop at the word vertebrae in the prior sentence; the rest is inference.  “Because only the skull and neck of Daemonosaurus were found, the total length of the new species is unknown.”  How much can be inferred from a skull and a few vertebrae?  Possibly that these bones differed enough from those of other known dinosaurs to justify classifying it as a new species (although changes in morphology during development should not be ignored; see 07/14/2010).  But without a traceable pedigree, the story about ancestry has to be inferred:

   “Various features of the skull and neck in Daemonosaurus indicate that it was intermediate between the earliest known predatory dinosaurs from South America and more advanced theropod dinosaurs,” said Hans Sues, curator of vertebrate paleontology at the Smithsonian’s National Museum of Natural History and lead author of the team’s findings.  “One such feature is the presence of cavities on some of the neck vertebrae related to the structure of the respiratory system.”

   Once again, a research team used air space as data.  Assuming Dr. Sues gave his best example, it would seem that cavities in vertebral bones could vary substantially within species, let alone between them.  The respiratory system itself, of course, is not available for study.  But many fossils “indicate” something else – mosaics of traits that do not neatly fit into evolutionary sequences; could that not be the case here?
       Charles Q. Choi at Live Science posted an even larger copy of the artist drawing to start off his cheery, uncritical report, but had to admit, “The formative steps of theropod evolution are still poorly understood.”

3. Parroting the scientists:  It is well known that general science news sites like PhysOrg and Science Daily parrot the press releases from universities and research labs, which parrot the opinions of the research scientists themselves.  After all, no institution wants its staff to look bad.  For institutional prestige, their findings need to be portrayed as significant discoveries.
       In this case, CSIRO (the Commonwealth Scientific and Industrial Research Organization in Australia) announced, “Tiger-parrots show their true evolutionary stripes.”  The predictable echo from PhysOrg was nearly instantaneous.
       In this story, Dr. Leo Joseph of CSIRO promised enlightenment: “This research on tiger-parrots – and some other enigmatic Australian parrots such as the little-known Night Parrot of inland Australian deserts – sheds light on the bigger picture of parrot evolution for Australia and New Guinea.”  Beaming with pride, he continued, “It has shown for the first time, for example, that tiger-parrots represent a very early branch of the parrot evolutionary tree in Australia and New Guinea.”
       On what basis did he show that?  After all, the data were surprising and confusing: “During our research on these oddball parrots of Australia and New Guinea, we affirmed that the Australian parrots are far from one cohesive group,” Dr. Joseph said.  “They appear, instead, to be made up of about five different main branches of the parrot evolutionary tree.”
       That inference was hedged with a bit of non-evolutionary convergence or conservation: “We have shown that the New Guinea tiger-parrots aren’t rosella-like parrots and that their resemblance in some aspects of their appearance to rosellas probably indicates some plumage characters that have been part of the evolution of parrots of Australia and New Guinea for a long time.”  Conservation, though, is not the kind of evolution Darwin was interested in.
       Even more shocking, he upset an apple cart: “We also showed, because we included so many other parrots, they aren’t even part of the Asian and African assemblage with which they have even more often been associated.”  So he replaced one evolutionary story with another that has even more branches, and tossed in some stasis for good measure.
       It’s not clear this is shedding light or stirring the pot: “The researchers found that the tiger-parrots of New Guinea’s rainforests – named for their striped or barred plumage – are not, as has been widely accepted, closely related either to a group of rosella-like parrots found in Australia and Oceania, nor a similar group found in Asia and Africa.”  Nevertheless, readers were promised that the parrots themselves would “show their true evolutionary stripes.”
4. Early enzymes:  With an Easter-like flair, Columbia University heralded revelation and resurrection: “Researchers Resurrect Ancient Enzymes to Reveal Conditions of Early Life on Earth.”  This was no mean resurrection: “for the first time [they] reconstructed active enzymes from four-billion-year-old extinct organisms.” the press release said, shedding light all around the tomb: “The results shed new light on how life has adapted to changes in the environment from ancient to modern Earth.”  Let the world rejoice.
       To pull off this miraculous inference, they engaged in “ancestral sequence reconstruction” by comparing gene sequences of living organisms.  They focused on thioredoxin enzymes that are found in all living cells.  A devilish design idea threatened the inference.  They expected to find the resurrected enzyme would be simple, but “Instead we found that enzymes that existed in the Precambrian era up to four billion years ago possessed many of the same chemical mechanisms observed in their modern-day relatives,” even though the organisms back then supposedly predated the buildup of oxygen in earth’s atmosphere.
       Furthermore, the putative Precambrian proteins were seen to be highly resistant to changes in temperature and acidity – more features indicating advanced early function instead of simplicity.  The team was courageous in the face of these difficulties: “By resurrecting proteins, we are able to gather valuable information about the adaptation of extinct forms of life to environmental alterations that cannot be uncovered through fossil record examinations,” they assured the crowd.  PhysOrg and Science Daily blessed the assembly with a firm Amen.
5. Absolution of flowering plants:  The angiosperms (flowering plants) have acted shamefully by hiding evidence of their evolution from evolutionists since Darwin, who called their sudden appearance an “abominable mystery.”  Scientific bishops at Penn State are ready to forgive them, after their “Study [that] helps to solve Darwin’s mystery about ancient plant evolution” managed to get the penitent petunias to confess their genes.
       And what a confession: “The evolution and diversification of the more than 300,000 living species of flowering plants may have been ‘jump started’ much earlier than previously calculated.”  Apparently they carried on their anti-evolutionary activities a long time – “nearly 200 million years earlier than the events that other research groups had described.”
       The mystery, however, has a strange new twist.  According to their genomic comparisons, some undescribed “upheavals” in the plant genome “produced thousands of new genes that may have helped drive the evolutionary explosion that led to the rich diversity of present-day flowering plants.”  What’s odd is that neo-Darwinists would have stated it the other way around: evolution drove the production of new genes.  The Penn State evolutionists even described this upheaval, whatever caused it, as a series of genetic miracles: “one or more important genetic metamorphoses had occurred in the ancestor of flowering plants,” they said, “and we also knew that these metamorphoses could explain the enormous success of so many species living on the Earth today.”
       Their explanation, however, suggests that the predecessors were not successful.  Conifers and other gymnosperms, had, by any measure, great success already.  Were they able to naturalize their miracles?  Yes; they “examined volumes of molecular evidence,” the press release said, and inferred that said metamorphosis was “a special kind of DNA mutation — called a polyploidy event — that revolutionized the flowering-plant lineage.”
       Such polyploidy mutations are generally lethal in vertebrates, they said, but “Plants, on the other hand, often survive and can sometimes benefit from duplicated genomes.”  The explanation is similar to that of gene duplication, where evolutionists assume that one copy can continue to function while the other finds new things to do, like invent petals, sepals, stamens, veined leaves, and fruit.
   Science Daily dutifully recorded and broadcast the good news.
       Assured that Father Darwin would be pleased to see so much light shed on his mystery, dePamphilis congratulated himself on his inference that polyploidy is the solution.  “The further we push back the date of when these events happened, the more confidently we can claim that not most, but all flowering plants are the result of large-scale duplications of the genome,” he said, turning to Fred Hoyle’s abominable epithet: “It’s possible that the important polyploidy events we’ve identified were the equivalent of two ‘big bangs’ for flowering plants.”
       Hoyle had criticized his rivals’ cosmology as a “big bang” with the explanatory power of an explosion from nothing, so it’s hard to see how dePamphilis can take comfort in the comparison.  The Penn State press release, furthermore, neglected to go into details of how a copy of anything can innovate new things full of functional genetic information.  They apparently left that essay question as an exercise.  It is unclear, though, if the big-bang theory of flowering plant evolution provides understanding on the origin of orchids any more than saying, “stuff happens.”

Some conclusions are admittedly hard to make in science.  The effectiveness of a new pill, for instance, is complicated by many factors: age, sex, genetic condition, allergies, and much more.  When data are hard to come by, particularly in the historical sciences, inference to the best explanation is commonly used.  It requires, however, a detailed examination of all competing hypotheses, as Stephen Meyer performed in his book Signature in the Cell.
    When contrary inferences are ignored, however, anything goes; the sky is the limit on inferences that can be drawn, because there is nothing to compare them to.  It is a risk in “normal science” as Thomas Kuhn described it that no one will be challenged to think outside the box (the paradigm).  Researchers working on the paradigm form a kind of guild of mutually supportive workers who only seek to confirm or fine-tune the paradigm.  They may even be oblivious to the possibility that other paradigms exist – or they may rule them out because of peer pressure.  They can also be oblivious to other interesting questions that the paradigm does not ask.
    Signs that a paradigm is vacuous and due for a scientific revolution may have to come from outside, among observers not beholden to the paradigm, who are able to point out its flaws.  Any paradigm that assumes its own validity could be ruled circular and immune to falsification.  If so, Karl Popper would have said it is not science.

Year after year we have pointed out the shenanigans of the Darwin Party.  They turn emptiness into confidence, air space into data, duplicates into toolkits, science into storytelling.  These blind guides, professing wisdom in folly, promising what they cannot deliver, are driven by pantheistic visions of molecules self-organizing into minds.
    There’s ample enough evidence in 10 years of these pages to convict them of pseudoscience, yet they remain in power – so much so that to question their authority is to risk one’s career (see next entry, 04/11/2011).
    If you are sick of their tactics, and have had it with “stuff happens” as scientific explanation, if you are fed up with totalitarian rule by fools masquerading as scholars, and toady reporters incapable of asking hard questions, then join the resistance.  Arm yourself with truth, answers, wisdom, honesty, and courage.  Have a strategy.  Learn to be effective, not boisterous or careless.  Know what you are up against, and count the cost.  Only by driving the Darwin Party from power will there be hope of a scientific revolution that, once again, is dedicated to following the evidence where it leads.