Science Literature

The first specimen of Archaeopteryx was discovered in 1861 in Bavaria, Germany, and it quickly made its way into Darwin's Origin of Species as an example of a transitional form. The German name of the fossil was Urvogel ("original bird" or "first bird"), but the English speaking world adopted Archaeopteryx - from the Greek archaios meaning 'ancient' and pteryx meaning 'feather' or 'wing'. The sense of the German name, however, was universally received: this was the first known bird and it displayed sufficient reptilian features to encourage hypotheses about an evolutionary past. This summary is from the University of California Museum of Paleontology: "It has long been accepted that Archaeopteryx was a transitional form between birds and reptiles, and that it is the earliest known bird." The history of evolutionary theory could not be written without the name Archaeopteryx appearing prominently - this is from the National Center for Science Education:

"Archaeopteryx is frequently used for pedagogical purposes because it is easy to recognize its mixture of "bird" and "reptile" features and because it played an historical role in helping to cement Darwin's theory (it was discovered 2 years after publication of the Origin). Textbook authors like Archaeopteryx for these reasons and often illustrate their discussions with pictures of the Berlin specimen, one of the most beautiful fossils ever discovered, and remarkably complete. Textbooks also use Archaeopteryx as an example of how fossils are important for showing transitional features of evolution, and how the fossil record is good evidence that evolution has occurred."

An artist's impression of Xiaotingia zhengi, (credit: Copyright Xing Lida and Liu Yi, source: here)

In recent years, however, the story has become much more complicated, with the finding of the so-called 'feathered dinosaurs' in China, and several Archaeopteryx-like fossils. Lead researcher Xing Xu has reported recently a fossil with the name Xiaotingia zhengi, and published a new phylogenetic analysis which knocks Archaeopteryx off its perch and relocates the animal among a sub-group of dinosaurs. Nature has a news report here, and Discover Magazine here. The latter source has this summary of developments:

"By comparing Xiaotingia's features with those of Archaeopteryx and other related birds and dinosaurs, Xu has drawn up a new family tree. In it, Archaeopteryx sits with Xiaotingia among the deinonychosaurs, a celebrity-filled group of small, predatory dinosaurs that includes Deinonychus and Velociraptor. The lineage that led to modern birds perches on a different branch of the tree."

In view of the iconic status of Archaeopteryx, commentators have been anxious that "creationists" do not gain an advantage from this particular rewriting of the textbooks. When evidence used to prove evolution turns out to be incorrect, there is a danger that people will become disillusioned. Xing Xu knows this: "Because it has held the position as the most primitive bird for such a long time, I am kind of nervous about presenting this result" he said. Consequently, there has been a great deal of damage-limitation activity, pointing out that 'this is the way science works'. This activity is reviewed here, with much of it drawn from Witmer (here):

"In truth, this chapter of the scientific story is just beginning. Just as Xiaotingia moved Archaeopteryx out of the birds, the next find could move it back in - or to somewhere else within this fuzzy tangled knot that makes up the origins of birds and bird-like dinosaurs. That said, during this sesquicentennial anniversary of Archaeopteryx, which is being honoured with exhibits and commemorative coins, the bitter irony may be that it may not have been the bird we've always thought it was. But Archaeopteryx will remain an icon of evolution, perhaps even more so now, providing compelling evidence that, as we should expect, evolutionary origins are rather messy affairs."

One is tempted to say - if the next find could move Archaeopteryx back in, why are people getting so excited about it now? Why can't we treat Xu's approach as a hypothesis that needs to be tested by further analysis and forthcoming discoveries? The answer is that Xu et al. have not presented it like this. Although giving lip-service to tentativeness, they claim that their analysis makes far more sense of the fossil data and that, as Nature News says: "we are about to enter a new era in which Archaeopteryx is considered as distant from the ancestry of modern birds as dinosaurs such as Deinonychus."

The cladistic analysis is recognized as provisional in the abstract: the conclusion has only "tentative statistical support". Animals that deserve to be in the analysis, but are not, are Early Cretaceous birds: Dalianraptor, Jixiangornis, Zhongjianornis; late Jurassic or Early Cretaceous dinosaurs: Pedopenna, Shanag, Sinusonasus, Tianyuraptor, and the enigmatic Jinfengopteryx. Is it possible that the selection of species for inclusion in the cladistic analysis has influenced the outcome? The basal bird species chosen have a stubby snout morphology, and this may have led to those species with a more pointed snout to be shifted over to the deinonychosaurs: namely Archaeopteryx, Anchiornis and Xiaotingia. With additional clear Avialae species, the analysis may come out differently. Witmer writes:

"According to Xu and colleagues' analysis, the most basal fossil birds are forms such as Epidexipteryx, Jeholornis and Sapeornis, all of which were named in the past decade and so comprise new territory even for specialists. Clearly, without the safety net of good old Archaeopteryx at the base of the birds, we've got some fresh work to do."

There is scope also for a discussion of the parameters used within the analysis, although this will have to be pursued by the specialists. Unfortunately, cladistic analyses tend to produce 'black box' outcomes, and there is relatively little attention given to parameter trends within the cladogram and whether these are biologically meaningful. There is also scope for critiquing cladism itself, and whether the underpinning assumptions restrict the scope of the analysis. For more, go here.

According to many commentators, the evolutionary story of the origin of birds is going to be fuzzy:

"The researchers acknowledged that their reclassification was "only weakly supported by the available data," but they said this kind of fuzziness was to be expected when the fossils being analyzed are close to the common ancestor of now-extinct dinosaurs and modern birds. "This phenomenon is also seen in some other major transitions, including the origins of major mammalian groups," they wrote.
Witmer agreed: "We're looking at an origin, and consequently it's going to be messy." [also, he added] "It just shows what evolution is all about. A prediction of evolutionary theory is that it should be really hard for us to figure out what's going on in an origin.""

Interesting. In the past, evolutionists looked for an identifiable trajectory that documented evolution. Now, it is a confused mess which is hard to decipher. Perhaps the most realistic conclusion for the present is that the Late Jurassic-Early Creataceous fossil record shows many features that we do not properly understand, and the most appropriate response is to withhold judgment and await further discoveries and analysis. This applies to the whole of the Birds Are Dinosaurs (BAD) thesis, as is evident here, here, here, here and here.

An Archaeopteryx-like theropod from China and the origin of Avialae
Xing Xu, Hailu You, Kai Du & Fenglu Han
Nature, 475: 465-470 (28 July 2011) | doi:10.1038/nature10288

Abstract: Archaeopteryx is widely accepted as being the most basal bird, and accordingly it is regarded as central to understanding avialan origins; however, recent discoveries of derived maniraptorans have weakened the avialan status of Archaeopteryx. Here we report a new Archaeopteryx-like theropod from China. This find further demonstrates that many features formerly regarded as being diagnostic of Avialae, including long and robust forelimbs, actually characterize the more inclusive group Paraves (composed of the avialans and the deinonychosaurs). Notably, adding the new taxon into a comprehensive phylogenetic analysis shifts Archaeopteryx to the Deinonychosauria. Despite only tentative statistical support, this result challenges the centrality of Archaeopteryx in the transition to birds. If this new phylogenetic hypothesis can be confirmed by further investigation, current assumptions regarding the avialan ancestral condition will need to be re-evaluated.

See also:

Kaplan, M., Archaeopteryx no longer first bird, Nature News (27 July 2011) | doi:10.1038/news.2011.443

Witmer, L.M. An icon knocked from its perch, Nature, 475: 458-459 (28 July 2011) | doi:10.1038/475458a

For 20 years, the National Science Foundation (NSF) has undertaken surveys of science literacy that incorporate these two true-false statements: "Human beings, as we know them today, developed from earlier species of animals", and "The universe began with a huge explosion". Happily, changes have been recommended, but not all have welcomed their suggested replacement wording. The critics say that the revised statements are "surrendering ground to religion". I will suggest below that both the engineers of change and their critics have something to learn about science surveys.

"Two expert panels assembled last year by NSF have suggested qualifying those statements with the phrases "According to evolutionary theory" and "According to astronomers." The board has decided to ask NSF to give the new versions of the questions to half the respondents on its next survey and to analyze the results.
[. . .]
[The second panel advised that] Respondents should also be asked whether they "personally shared this belief.""

The goal: developing a love for science and discovery (source here)

First, what is wrong with the statements as they stand? The first of these concerns the evolution of humans from earlier species of animal. Is this true or false? Is it a statement that will be understood in the same way by the participants? In my view, the statement is problematic. Are we talking about principles here or evidence? If participants are supposed to relate their true/false verdict to evidence, then there are real problems. As Wood and Harrison wrote earlier this year: "Sorting fossil taxa into those that belong on the branch of the tree of life that leads to modern humans from those that belong on other closely related branches is a considerable challenge." Basically, we do not have a clear lineage for human evolution. The reason why many people answer "yes" to the statement is not that they have found the evidence compelling, but that they know that the history of life is framed by evolutionary theory. Ultimately, affirmative responses do not measure scientific literacy, but say something about the worldview of the respondents. (There are other points to make here - linked to whether or not humans are more than animals - but in the interests of conciseness, we move on).

What about the second statement: "The universe began with a huge explosion"? There is a problem with these words - the Big Bang is about the expansion of space as well as the expansion of primordial matter. The word "explosion" is potentially misleading because all familiar explosions are of matter being propelled through existing space. Furthermore, the Big Bang model requires that matter was in a very low-entropy state when it started - consequently it is a misnomer to call the event a "Bang" or an "explosion", because these are words that suggest disorder. The statement, therefore, is OK at a popular level, but the more scientifically-minded participants might find it inadequate. Those who have sympathy with "Big Bang" model dissenters (here and here) may well give the response "false" - and yet this would not be necessarily a sign of poor scientific literacy.

So, the wording of surveys is very important. The researcher writing the questions or statements can unconsciously influence the outcome of the findings. Often, the approach is structured around empirical science (where the problems are much reduced) but then questions or statements about the historical sciences are slipped in as though there is no qualitative difference. The proposed revised wording does improve things significantly. Participants are being asked about their knowledge of what scientists are saying about the past. But what should be more important is whether these scientific ideas are understood and whether the supporting evidence is recognised.

There is a potential problem if respondents are to be asked whether they "personally shared this belief". The advice is sound if participants all recognise that all science is built on presuppositions, many of which cannot be proved scientifically. (It is like having axioms in mathematics). These presuppositions are critically important to the historical sciences. Naturalism is the prime example: the application of naturalism to the history of life leads inevitably to something like Darwinism - as a matter of logic. That humans evolved from apes does not need evidence, because according to the presupposition it must be true - evidence is welcomed as confirming something that is already known. Similarly, on thermodynamic grounds, the universe in its present form must have had a beginning, and the presupposition of naturalism requires that it happened without any specific causation. As New Scientist has expressed it: "Perhaps the big bang was just nothingness doing what comes naturally". Ultimately, naturalism is at the root of a belief system that is expressed in numerous ways. The current "Existence" theme in New Scientist shows where it leads: chance and the multiverse provide the underpinning concepts, leaving humans as zombies existing in a holographic universe, with an illusion of consciousness.

The advocates of naturalism do not accept that their worldview is founded on beliefs. They reserve the word "belief" for superstition and "religion". It is very important to them that a line is drawn between fact/science/knowledge and beliefs. This comes out in Bhattacharjee's report of the proposed modifications to the NSF survey:

"The change infuriates Jon Miller, a science literacy expert at the University of Michigan, Ann Arbor, and architect of the original questionnaire, which is now used by several countries. "If you are altering the questions in that way, you are doing it for religious reasons," he says. "We don't make statements like, 'According to some economists, we had a recession' or 'According to the weatherman, we had a tsunami.'"

Notice that Miller's examples do not relate to the historical sciences. He uses phenomena that can be studied empirically, that relate to contemporary life, and that are defined objectively. From this, conclusions are drawn that go far beyond the point being made. Miller needs to revisit his "religious reasons" claim and start looking at the philosophy of science. Beliefs are of many different types. Yes, there are superstitious beliefs, but there are also beliefs based on evidence and axiomatic beliefs like 2+2=4. For more discussion of these issues, go here.

In defending the recommendation to ask participants whether they "personally shared this belief", Lewenstein appears to put himself on a collision course with the advocates of naturalism. He does not put acceptance of human evolution or the Big Bang in a box marked 'knowledge' but in another marked 'beliefs about knowledge'.

"Bruce Lewenstein, a sociologist at Cornell University who was on the Toumey panel, thinks critics are overreacting. He says the distinction between knowledge and belief is important and must be understood to get a clearer picture of the public's knowledge of science. "Knowledge and belief are not the same," he says. "It might be politically useful for the scientific community to pretend that they are the same, but it would not be intellectually honest.""

This is a debate worthy of our attention. Science needs to be rescued from people who cannot recognise the role presuppositions are playing in their own thinking and from educationalists who think that acceptance of human evolution and the big bang is more important than knowing the evidences on which theories of human evolution and the Big Bang are based. We need to be rescued from people who cannot understand that some beliefs are based on evidence. Most of all, we need to be rescued from people who cannot comprehend that science can be practised without presuming naturalism. Rather, we need a science that is capable, in principle, of falsifying naturalism and which avoids scientists bringing to their work a predetermined vision of what the universe is really like.

New NSF Survey Tries to Separate Knowledge and Belief
Yudhijit Bhattacharjee
Science, 333, (22 July 2011) 394 | DOI: 10.1126/science.333.6041.394

Can a person be scientifically literate without accepting the concepts of evolution and the big bang? To many scientists and educators, the answer to that question is an unqualified "no".

Starting in 1973, Herbert Terrace led an ambitious project to examine the capability of chimps to develop sign language. The chimp participant was born at the Institute for Primate Studies in Oklahoma and was taken from his mother after about a week and handed to Stephanie LaFarge who acted as a surrogate parent. The chimp was effectively adopted. In a recent piece in Nature, Terrace explains why he initiated the project:

"After serving as a graduate assistant at Harvard University with behavioural psychologist B. F. Skinner, I heard that Allen and Beatrix Gardner at the University of Nevada, Reno, were teaching sign language to a chimpanzee named Washoe. But when I looked at their data, I wasn't sure that the chimp's sequences of hand signs were grammatical. I decided to do a study to collect everything a chimp signed, and document the circumstances. We wanted to have full records of the discourse between the infant chimp and the caretaker."

Nim Chimpsky (source here)

The experiment design was based on some important theoretical considerations about the development of language. Influenced by his background in behavioural psychology, Terrace set out to challenge the ideas of the linguist Noam Chomsky - in particular his claim that grammatical speech is uniquely human. Behaviourists tend to the view that animals can be taught to do almost anything, and the Los Angeles Times report says that the "Skinner-Chomsky rivalry framed the Nim project". The new name for Chimp No 37 was Nim Chimpsky, sufficiently distinctive to draw my attention to the project during the 1970s.

To cut a long and fascinating story short, the project ended up supporting the theoretical perspective of Chomsky and underlined the differences between chimp communication and human language. The most influential paper emerging from the project team was published in Science in 1979, with the title: "Can an ape create a sentence?" The answer was no - at every level. Long utterances were not semantic or syntactic elaborations of short utterances - this is quite different from the communications of human children. As the length of utterances of children increase, so also does the complexity of those utterances. This increase in complexity was not observed with Nim. The researchers concluded that all the evidences accumulated in support of apes creating sentences could be explained by reference to simpler non-linguistic processes. They found that animals can learn symbols and signs, but do not show any capability to master the conversational, semantic, or syntactic organisation of language. In answer to the question "Did the experiment meet your expectations?" Terrace replied:

"The language didn't materialize. A human baby starts out mostly imitating, then begins to string words together. Nim didn't learn. His three-sign combinations - such as 'eat me eat' or 'play me Nim' - were redundant. He imitated signs to get rewards. I published the negative results in 1979 in the journal Science, which had a chilling effect on the field."

An interesting follow-up question is: "Why couldn't Nim put a sentence together?" This is particularly important to Darwinists and many other evolutionary thinkers, who go along with Darwin's claim, in The Descent of Man, that there is "no fundamental difference between man and the higher mammals in their mental faculties". Terrace's answer points us to a major difference between humans and animals: only humans have a theory of mind.

"I haven't seen any evidence that a chimp has a theory of mind. It can predict behaviour, but the concept of another individual's thinking is foreign to it. So it is pointless for a chimp to start a conversation: why talk unless you expect a reply?"

After the project, Terrace returned Nim initially to the Institute for Primate Studies. However, after they ran out of funding, he did not want Nim sold as an animal for medical research. Terrace found him a home in a giant cage at a ranch for celebrity animals in Texas where he lived until the year 2000 when he died of a heart attack. But the story does not end there. There are many people who still think of Nim as an adopted human, a chimp who thought he was a boy, an animal that acquired language skills. One of them is Elizabeth Hess, who published a book in 2008 to tell a different story:

"He [Terrace]concluded that Nim and the other chimps who appeared to be communicating were merely mimicking, making fools of the scientists chatting with them. In effect, Terrace had written an obituary for ape-language research. After years of crowing about his achievements with Nim, he leapt into bed with his adversaries and battered other practitioners.
His opponents argued that his failure had been his own. He had been unable to handle his own chimp or provide Nim with consistent teachers. Worst of all, he had ended the study too early to get significant results; at the very least, Terrace's about-face was premature. Then there was the inconvenient fact that once Nim had learnt to sign, he often initiated conversation with humans. Didn't that count?"

The book is now a film. It would appear that the book's agenda resurfaces in the film. Although the science issues are not prominent, viewers are given an emotional roller-coaster as they follow the life of Nim Chimpsky - who is presented as having a theory of mind. Terrace is not happy:

"I'm upset because the film creates the impression the project was a failure because it didn't turn out the way I'd hoped it would when I started," Terrace declared recently in his office at Columbia, where he still runs the Primate Cognition Laboratory. "The only line between success and failure for scientists is really whether they honestly report their results, and I did that."
But that's not all Terrace is displeased about. "The film also suggests I was not affectionately involved with Nim. And that's not true." Marsh, he added, has "made a technically good film, but he's misrepresented me, and he misrepresented the science."

One thing that impresses me about the 1979 paper is the thoroughness with which the data is reported and discussed. The writers are people who started out to challenge Chomsky's theoretical approach, but ended up falsifying their own hypothesis. This is the way science is supposed to work. They impacted the whole field of ape-language studies - but there are other agendas operating. There are people who "know" that there can't be a discontinuity between apes and humans, because that is inconsistent with their understanding of evolutionary theory. So they find ways of undermining the research and promoting their own views. This is ultimately the same problem that we face elsewhere with evolutionary theorists - people confuse theory with fact and see overwhelming evidence where there is plenty of scope for divergent interpretations of the data. Will we ever learn?

Q&A: The interpreter
Jascha Hoffman
Nature, 475, 173 (14 July 2011) | doi:10.1038/475173a

In 1973, Herbert Terrace, a psychologist at Columbia University in New York, embarked on an experiment to teach sign language to an infant chimpanzee named Nim Chimpsky, after linguist Noam Chomsky. On the release of the documentary Project Nim, Terrace talks about research ethics, chimp cognition and the origins of language.

Can an ape create a sentence?
H.S. Terrace, L.A. Petitto, R.J. Sanders and T.G. Bever
Science, 23 November 1979, 206, 891-902 | DOI: 10.1126/science.504995

Abstract: More than 19,000 multisign utterances of an infant chimpanzee (Nim) were analyzed for syntactic and semantic regularities. Lexical regularities were observed in the case of two-sign combinations: particular signs (for example, more) tended to occur in a particular position. These regularities could not be attributed to memorization or to position habits, suggesting that they were structurally constrained. That conclusion, however, was invalidated by videotape analyses, which showed that most of Nim's utterances were prompted by his teacher's prior utterance, and that Nim interrupted his teachers to a much larger extent than a child interrupts an adult's speech. Signed utterances of other apes (as shown on films) revealed similar non-human patterns of discourse.

See also:

Tyler, D. Was Darwin's thinking about continuity of mind well grounded? (ARN Literature blog, 17 April 2009).

For many of us, an important characteristic of science is self-correction. We are proud of the way new findings catalyse re-evaluation and, if corrections are needed, the development of new knowledge. If you are like this, be prepared to be shocked when you read Jonathan Wells' latest book. The concept of Junk DNA was widely held by evolutionary biologists during the 1990s, but only a few were prepared to expose the hypothesis to tests of its validity. Yet this is when publications started to accumulate that reported functionality in genetic material widely regarded as "nonsense". Instead of alerting popularisers of science to be cautious, these writers treated the new data as unrepresentative exceptions. They pressed on with their claim that the bulk of the genome is useless. The trickle of challenging research findings became a stream, but the 'consensus' about junk DNA was not corrected. The stream became a river, but still the much-needed correction was lacking. Here is Richard Dawkins' comment from The Ancestor's Tale (2004, page 22):

"DNA differs from written language in that islands of sense are separated by a sea of nonsense, never transcribed. 'Whole' genes are assembled, during transcription, from meaningful 'exons' separated by meaningless 'introns' whose texts are simply skipped by the reading apparatus. And even meaningful stretches of DNA are in many cases never read -presumably they are superseded copies of once useful genes that hang around like early drafts of a chapter on a cluttered hard disk. Indeed, the image of the genome as an old hard disk, badly in need of a spring clean, is one that will serve us from time to time during the book."

(Source here)

Wells' approach is one of analysing and presenting the evidence for functionality. There are two broad categories to consider. The first concerns the transcription of non-protein coding DNA into various RNAs. The research literature suggests that most of this DNA is transcribed and in many cases, functionality has been confirmed. The second category concerns widespread conserved sequences of non-coding DNA. The very fact of it being conserved in different types of organism is supportive of functionality, even when we do not (yet) know the function.

Wells refers to a hierarchy of three levels for genome functionality. The argument is an interesting one, because it points to genetic information being present in both digital and analogue forms. In some examples discussed, the DNA sequence is in itself not important, but the length of the sequence is critical for successful functioning.

"The genome is hierarchical, and it functions at three levels: the DNA molecule itself; the DNA-RNA-protein complex that makes up chromatin; and the three-dimensional arrangement of chromosomes in the nucleus. At all three of these levels, DNA can function in ways that are independent of its exact nucleotide sequence." (p.93) [. . .]
"At the third level, the position of the chromosome inside the nucleus is important for gene regulation. In most cells, the gene-rich portions of chromosomes tend to be concentrated near the center of the nucleus, and a gene can be inactivated by artificially moving it to the periphery. In some cases, however, the pattern is inverted: rod cells in the retinas of nocturnal mammals contain nuclei in which the non-protein-coding pats of chromosomes are concentrated near the center of the nucleus, where hey form a liquid crystal that serves to focus dim rays of light." (p.94-5)

Junk DNA defenders have argued that junk DNA is supportive of Darwinism and that it refutes ID. This is why design advocates have felt it necessary to engage with these arguments. Well's book is compelling - it demolishes the thesis of junk DNA. If the original argument was logical, then the empirical data that we now have in profusion counts against Darwinism and confirms ID. Wells hastens to say that ID advocates have never suggested that all non-coding DNA is functional, only that it is unlikely that most DNA is non-functional. The design inference leads to the research goal of looking for functionality. This refutes the claim that ID is a science-stopper and does not lead to interesting avenues of research. This case shows that it is the Darwinists who have been guilty of science-stopping by their dogmatic claim that non-coding DNA is "nonsense" and not worth investigating.

Despite the onslaught of new data, with new functionalities being reported each week, there are still die-hards who cannot relinquish the junk DNA thesis. As an example of the intellectual gymnastics that are needed to sustain the myth, Wells refers to the "Onion test" proposed by Ryan Gregory in 2007. He claimed to have a "reality test" for those questioning the junk DNA thesis. "Ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?" (p.85) Wells' discussion of this test is worth reading in full, but his conclusion points to a logical flaw:

"So the onion test is a red herring. Why onion cells have five times as much DNA as human cells is an interesting question, but it poses no challenge to the growing evidence against the myth of junk DNA." (p.87)

Wells points out that the champions of junk DNA should be held accountable for keeping the myth alive and failing to demonstrate the self-correcting character of science. By quoting their arguments, he shows how they all demonstrate a vested interest in a Darwinian approach to evolution (i.e. demonstrating past tinkering that has accumulated nonsense DNA in the genome) and a hostility to ID. The individuals who need to retract erroneous arguments and conclusions are primarily John Avise, Francis Collins, Jerry Coyne, Richard Dawkins, Douglas Futuyma, Philip Kitcher, Kenneth Miller and PZ Myers. Science writers Richard Robinson, Michael Shermer and Carl Zimmer are also named for failing to demonstrate critical thinking skills when writing on this subject. Only Francis Collins has shown signs of revising his thinking - Wells puts it quite strongly: "he subsequently recanted his belief in the myth of junk DNA" (p.98). In an interview for Wired Magazine, he said: "I've stopped using the term" junk DNA (p.99) However, Collins gets only a partial reprieve, because his own baby The Biologos Foundation still promotes the junk DNA myth to argue against ID. (p.100)

Wells communicates very effectively in 114 pages of text plus 54 pages of references. The book could easily have been much larger if there was more background to the research findings and more discussion of the key implications brought out in the last chapter. Wells writes in a very restrained way, sparing us rhetorical flourishes that are often found in books and articles that deal with controversial issues. The writing style is concise, clear and compelling. Wells has chosen to communicate as a scientist and not as a polemicist. Consequently, the book is an invaluable resource as a state-of-the-art review of the issues. It provides a convincing rebuttal to anyone seeking to perpetuate the myth of junk DNA and anyone who suggests that the genome is a product of Darwinian tinkering rather than intelligent design.

Strongly recommended.

See also:

Tyler, D. Does the human genome have "serious molecular shortcomings"? (ARN Literature Blog, 7 May 2010)

Tyler, D. The Molecular Revolution's unfulfilled promises of simplicity (ARN Literature Blog, 11 April 2010)

Tyler. D. Hidden biological information via antisense transcription (ARN Literature Blog, 17 December 2008)

One of the more unusual research papers to be published recently is Phil Senter's use of the baraminological method to analyse morphological continuity within Dinosauria. The paper explicitly refers to "creation science" in the title and makes extensive use of terms familiar only to baraminologists. Senter's main motive, however, is to demonstrate that evolutionary theory is supported by empirical evidence that is recognised as evidence by creation scientists. By publishing his study, Senter hopes to influence the "huge number of voters who believe that the creationist world view has scientific validity and empirical support".

"Because of this onslaught, it is imperative to demonstrate that evolutionary theory is supported by empirical evidence. Towards this end, it is important to use methodology that is endorsed by creation science, so that creation scientists cannot reject the results of such studies without rejecting their own research. Towards that end, here I present a study using methodology endorsed and used in baraminology, the branch of creation science in which organisms are classified into separately created 'kinds' (baramins)."

Creationists point out that the lighter lines are data and the darker lines are inferred from evolutionary theory. (source here)

Although Senter has published before on these issues, he realised that he needed to refine the method of analysis to engage better with baraminologists, and also enhance his data set. The opportunity to do the latter came in 2010 when he visited the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing. The data matrix used in the new paper includes 392 characters and 102 taxa, and Senter claims it is "the most comprehensive phylogenetic data matrix for Coelurosauria yet published". In this blog, we pass over the details of the data and go straight to the discussion. First, Senter has the "good news for the creationist world view":

"First, seven major dinosaurian groups (birdlike coelurosaurs, Tazoudasaurus + Eusauropoda, Stegosauria, Ankylosauridae, Neoceratopsia, Hadrosauridae and basal Hadrosauriformes) are separated from the rest of Dinosauria by morphological gaps. Creationist inferences that [these groups] represent diversification within separately created kinds are congruent with these results. Second, each morphologically continuous group found by taxon correlation includes at least some herbivores. This is congruent with the creationist assertion that all carnivorous animals are descendants of originally herbivorous ancestors. Third, although creationists have answered the problem of room on Noah's ark for multiple pairs of gigantic dinosaurs by asserting that only about 50 'created kinds' of dinosaurs existed, the problem is solved even better by the results of this study, in which only eight dinosaur 'kinds' are found."

However, Senter is not regarding this research as good news for creationists! He points out that the diversity within each group is "enormous". We should recognise that evolutionists also accept this diversity, but they say it happened in millions rather than hundreds of years.

"Acceptance that such diversity arose by natural means in only a few thousand years therefore stretches the imagination. The largest dinosaurian baramin recovered by this study includes Euparkeria, basal ornithodirans (Silesaurus and Marasuchus), basal saurischians, basal ornithischians, basal sauropodomorphs, basal thyreophorans, nodosaurid ankylosaurs, pachycephalosaurs, basal ceratopsians, basal ornithopods and all but the most birdlike theropods in an unbroken spectrum of morphological continuity. The creationist viewpoint allows for diversification within baramins, but the diversity within this morphologically continuous group is extreme."

Senter has other points to make. Arguably, there are taxon correlations between basal members of these groups, so a case can be made for bridging between the groups. More recent finds are helping to fill morphological gaps.

"Therefore, although results of this study identify seven potential morphological gaps that persist within Dinosauria, any creationist celebration of the persistence of such gaps is premature because of the general trend for such gaps to be filled by continued discovery."

The purpose of this blog is to welcome discussion of these issues in the science literature. From the acknowledgements, it is clear that Senter is already finding it possible to have meaningful communications with baraminologists. It will be a good thing if there is a two-way communication in the journals.

"Todd Wood and David Cavanaugh deserve thanks for much useful communication regarding baraminology. Both are congenial and collegial despite occupying the other side of the ideological fence, and I almost feel that I must apologize to both gentlemen that the results of this study are as they are."

It is my view that there are some methodological issues to be addressed even before engaging with fossil data. The significance of the research is that the issue of morphological discontinuities between groups of species is "on the table" for discussion by evolution-orientated scientists. This is important because systematic tools for studying discontinuity have previously not been given a high priority because the focus has been on establishing relationships (for example, using techniques of cladistic analysis). (For further thoughts on addressing discontinuities, go here). From an evolutionary perspective, we already know the answer: all these dinosaur groups are connected by common descent and must demonstrate a continuous morphological spectrum - any apparent discontinuities are a consequence of an imperfect fossil record. It appears that only a design perspective is capable of the data wherever it leads: there are actually two hypotheses to test: one is monophyletic common descent and the other is the diversification of many basic types.

Regarding tools, it is important for methods to allow competing hypotheses to be explored. Cladism needs to be challenged, because evolutionary branching is part of the underpinning philosophy. It should be called "Evolutionary Cladism" and be treated as a suspect tool because all data is viewed from an evolutionary perspective. It cannot avoid coming up with an evolutionary outcome. There was a time when "Transformed Cladism" was proposed to avoid this methodological flaw - but so embedded is evolutionary thinking in the minds of cladists that they cannot see the problem (for more on cladism, go here). The problem for Baraminology is it has the same fundamental problem - although in this case the creation of distinct baramins is the underlying philosophy. We need to develop tools that are our servants, not our guides, in understanding the data. We need tools that allow patterns in the data to emerge independently of the interpretation. Then the modelling work can start.

Using creation science to demonstrate evolution 2: morphological continuity within Dinosauria
P. Senter
Journal of Evolutionary Biology, Article first published online: 4 JUL 2011 | DOI: 10.1111/j.1420-9101.2011.02349.x

Abstract: Creationist literature claims that sufficient gaps in morphological continuity exist to classify dinosaurs into several distinct baramins ('created kinds'). Here, I apply the baraminological method called taxon correlation to test for morphological continuity within and between dinosaurian taxa. The results show enough morphological continuity within Dinosauria to consider most dinosaurs genetically related, even by this creationist standard. A continuous morphological spectrum unites the basal members of Saurischia, Theropoda, Sauropodomorpha, Ornithischia, Thyreophora, Marginocephalia, and Ornithopoda with Nodosauridae and Pachycephalosauria and with the basal ornithodirans Silesaurus and Marasuchus. Morphological gaps in the known fossil record separate only seven groups from the rest of Dinosauria. Those groups are Therizinosauroidea + Oviraptorosauria + Paraves, Tazoudasaurus + Eusauropoda, Ankylosauridae, Stegosauria, Neoceratopsia, basal Hadrosauriformes and Hadrosauridae. Each of these seven groups exhibits within-group morphological continuity, indicating common descent for all the group's members, even according to this creationist standard.

See also:

Walker, M. Can religious teachings prove evolution to be true? BBC Wondermonkey blog (5 July 2011)

Wood, T. Phil Senter does it again, Todd's Blog (7 July 2011)

We have known for many years that the eyes of trilobites, going back to the Early Cambrian, have highly sophisticated optics. Although vision has been invoked as a probable characteristic of many other types of animal, there have been few examples of preserved eyes in the fossil record, even in the Burgess Shale and Chengjiang lagerstatte. However, the Emu Bay Shale, which provides exquisite preservation of Early Cambrian animals, has now supplied us with the earliest example of an non-trilobite arthropod eye. Of the seven specimens recovered to date, three are spectacular for the detail revealed and stunning because they document eyes that "are as advanced as those of many living forms". One of the authors of the research paper, Dr Jim Jago, is quoted in the press release:

"These are by far the most complicated eyes known from this period of earth's history. Each eye is seven to nine millimetres across and comprises over 3000 tiny lenses. As yet, the animal to which these eyes belonged is unknown, but they may have belonged to a large shrimp like animal. However, the rock layers in which the eyes are preserved include a dazzling array of fossil marine animals, many being new to science. They include primitive trilobite-like creatures, bizarre armoured worms and large swimming predators."

One of the newly reported complex eyes from the Emu Bay Shale (source here)

The abrupt appearance of complexity in the fossil record has often been documented in this blog, primarily to raise questions about the relevance of Darwinism for understanding the origins of complexity. Time and time again, Darwinists fill the gaps in knowledge with their theoretical models, but sooner or later, the next generation of scholars will realise that Darwinists have constructed a virtual world that does not match the real world revealed by research. The features that appear abruptly are as follows:
1. Compound eyes with lenses that are larger than any others previously documented in the Cambrian Period. The largest have an elevational diameter of 150 micrometres and the smallest are about half this size.
2. The arrangement of the lenses shows a regional specialisation otherwise unknown in the Early Cambrian. The larger lenses create a "bright zone" and in living animals this generates binocular vision whilst retaining wide peripheral fields. These features are very useful to fast-moving predators.
Here is Jim Jago again:

"The fossil compound eyes have over 3000 lenses, giving them much sharper vision than anything previously found from rocks this old. The eyes are much more complex than anything found previously in rocks of similar age. The newly discovered eyes are as advanced as the eyes in many living insects such as robberflies. The arrangement and size of the lenses indicates that these eyes belonged to an active predator that was capable of seeing in low light."

The significance of the find is that there are no earlier intermediate forms from which to construct an evolutionary scenario, and that the structure of these eyes is essentially modern. The authors of the research paper anticipate this problem for evolutionary theory in their first sentence: "theory suggests that complex eyes can evolve very rapidly" and they cite the well-known 1994 paper by Nilsson and Pelger. They are right to say "theory suggests" because the Nilsson and Pelger paper has no links with empirical data. It is a conceptual model of morphological change - it completely by-passes issues of how light is sensed, transmitted to the brain and decoded. Parameters are introduced that are guesstimates; there is no link to Darwinian mechanisms of mutation and natural selection; assumptions are introduced throughout, with the minimum of justification. The weight that is put on this paper is justifiably called "A Scientific Scandal" by David Berlinski (for his essay, go here). The paper is really a dressed-up "just-so" story - with no link to the real world. Theory is fine as long as it is tested and validated - the problem with Nilsson and Pelger's theory is that it is an exercise in vivid imagination, has not been tested and cannot be regarded in any sense as authoritative.

There is no doubt that the Cambrian Explosion is a puzzle to Darwinists (for the reason why, see here). Many of them still refuse to concede that there was an non-Darwinian explosion of animal forms and they keep looking for ways of stretching out the timescales. However, others look for some strong selection pressures that could drive rapid evolution. The authors of the research paper align themselves with the latter group: "[The eyes] provide further evidence that the Cambrian explosion involved rapid innovation in fine-scale anatomy as well as gross morphology, and are consistent with the concept that the development of advanced vision helped to drive this great evolutionary event." Their reference for this points to Andrew Parker, who has championed this interpretation. The problem is that there are no transitional eyes to give this argument a connection to evidence. In fact, numerous "explanations" have been proposed, but none of them are compelling. It is far better to admit we do not know, as Shu did in 2008:

"Although we remain as blind men interpreting elephants when we search for the origin of metazoans, more and more accumulating data and hypotheses certainly help us with a better understanding the classic can of worms in both biology and geology."

The hypothesis to which I return repeatedly in these blogs is that the fossil record is not so much a record of evolutionary transformation, as a record of ecological transformation. Whilst I cannot claim the new fossil eyes are a proof of the hypothesis, they can certainly be understood in this way. As the Cambrian seas became richer ecosystems, the fauna became more diverse and the food webs more complex. As part of this picture, the arthropods with "modern" eyes do not look out of place at all.

For further reading on this paper, please refer to Darwin's God and Creation-Evolution Headlines.

Modern optics in exceptionally preserved eyes of Early Cambrian arthropods from Australia
Michael S. Y. Lee, James B. Jago, Diego C. Garcia-Bellido, Gregory D. Edgecombe, James G. Gehling & John R. Paterson
Nature, 474, (30 June 2011), 631-634 | doi:10.1038/nature10097

Despite the status of the eye as an "organ of extreme perfection", theory suggests that complex eyes can evolve very rapidly. The fossil record has, until now, been inadequate in providing insight into the early evolution of eyes during the initial radiation of many animal groups known as the Cambrian explosion. This is surprising because Cambrian Burgess-Shale-type deposits are replete with exquisitely preserved animals, especially arthropods, that possess eyes. However, with the exception of biomineralized trilobite eyes, virtually nothing is known about the details of their optical design. Here we report exceptionally preserved fossil eyes from the Early Cambrian (~515 million years ago) Emu Bay Shale of South Australia, revealing that some of the earliest arthropods possessed highly advanced compound eyes, each with over 3,000 large ommatidial lenses and a specialized 'bright zone'. These are the oldest non-biomineralized eyes known in such detail, with preservation quality exceeding that found in the Burgess Shale and Chengjiang deposits. Non-biomineralized eyes of similar complexity are otherwise unknown until about 85 million years later. The arrangement and size of the lenses indicate that these eyes belonged to an active predator that was capable of seeing in low light. The eyes are more complex than those known from contemporaneous trilobites and are as advanced as those of many living forms. They provide further evidence that the Cambrian explosion involved rapid innovation in fine-scale anatomy as well as gross morphology, and are consistent with the concept that the development of advanced vision helped to drive this great evolutionary event.

See also:

Primitive creatures had powerful eyes, University of South Australia, Press Release (30 June 2011).