The evolutionary origin of turtles is one of the last unanswered questions in vertebrate evolution. Paleontological and morphological studies place turtles as either evolving from the ancestor of all reptiles or as evolving from the ancestor of snakes, lizards, and tuataras. Conflictingly, genetic studies place turtles as evolving from the ancestor of crocodilians and birds.

Having recently looked at more than a thousand of the least-changed regions in the genomes of turtles and their closest relatives, a team of Boston University researchers has confirmed that turtles are most closely related to crocodilians and birds rather than to lizards, snakes, and tuataras.

The study is the first genomic-scale analysis addressing the phylogenetic position of turtles, using over 1000 loci from representatives of all major reptile lineages including tuatara (lizard-like reptiles found only in New Zealand). Earlier studies of morphological traits positioned turtles at the base of the reptile tree with lizards, snakes and tuatara (lepidosaurs), whereas molecular analyses typically allied turtles with crocodiles and birds (archosaurs).

Doesn’t this raise some questions about conventional accounts of evolution? Or do we still pretend we didn’t notice?

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We only ask because … over at Evolution News & Views, they are asking “If Humans Write Genetic Code, Is It Intelligent Design?” (May 22, 2012),

It’s “totally rad,” announced a press release from Stanford School of Medicine: “Scientists from Stanford’s Department of Bioengineering have devised a method for repeatedly encoding, storing and erasing digital data within the DNA of living cells.” After 3 years of work and 750 tries, they found a way to create and erase digital code using DNA molecules.

They’re not using the A-G-C-T bases that the natural genetic code uses to store information. Instead, they use the way a portion of DNA points as the equivalent of a bit: one way indicates a one, the other indicates a zero. It’s rad because they named it that: Recombinase Addressable Data (RAD). It offers the power to use DNA as non-volatile memory and a molecular “switch” to turn on fluorescent proteins in microbes.

Now, the kicker:

If a researcher without foreknowledge of this technology examined a microbe employing it, would he or she be justified in inferring that an intelligent cause played a role in its origin? If so, what’s the difference with inferring an intelligent case for the origin of the “natural” genetic code, since it also involves the encoding and storage of functional information?

The short answer is that it depends on how completely committed to dogmatic materialism one is.

A dogmatic materialist denies that either instance represents actual intelligence in nature. Materialist philosophers argue that the mind is an illusion created by the buzz of neurons. That, indeed, is Francis Crick’s contested Astonishing Hypothesis (“You are nothing but a pack of neurons”).

The dogmatic materialist has the same problem as the multiverse proponent. His position is a dogmatic statement, not evidence. In fact, the more honest materialists admit that.

And that doesn’t stop them from presenting their views as the assured results of modern science or legacy media from unquestionably fronting them as such. At least for now.

And the question hangs: Believe the evidence of one’s senses or an imposing theory, backed by Top People?

From Peter Woit at Not Even Wrong, ”Latest from the Rumor Mill“, (May 16, 2012)

There’s at least one thing about string theory that has changed dramatically since my book was written back in 2002 or so. At the time I accumulated various numbers showing the way hiring in particle theory at leading institutions in the US had been dominated by string theory hires. Overall, at that time about 20 people/year were getting tenure-track positions, roughly half in string theory half in phenomenology. … The number of string theorists getting positions had come down to about 2/year, then down to only one last year.

This is consistent with the fact that the popular science media seem to be back to fronting the multiverse, acknowledging the lack of evidence.

The hiring season is not yet over and not all the data is in, but so far the Rumor Mill shows no job offers to string theorists at all. …

If the multiverse – or anything associated with it – was a pharmaceutical, it would have been pulled from the shelves long ago. They had a long enough run for what they were offering: A fantasy escape from the fact of fine-tuning of the universe.

On a sobering note, however,

One thing hasn’t changed though since 2002: there’s a much larger number of talented and accomplished candidates than there are jobs, and departments are playing it safe, offering the few jobs available only to people working in a small number of areas that are conventionally agreed to be “hot”. As always, if you’re working on some idea that’s not in the narrow mainstream, there’s no chance you’ll get hired into a permanent position at a US institution.

The comments are a solid contribution to the post.

One problem with hiring on the basis of perceived hotness is that it is not an investment in the future. Pardon the analogy, but what’s “hot” today is not within a few fashion seasons. Solid growth requires a long term approach, insulated against the shocks of fad.

See also: The multiverse: Just an excuse to sell books now?

Here.

Michael Ruse, considered one of the world’s leading Darwinian philosophers, has said that very thing in a 1985 article co-authored with Harvard biologist E. O. Wilson:

Ethics as we understand it is an illusion fobbed off on us by our genes to get us to co-operate.

and he continues to be a keynote speaker at prestigious conferences. He restated this position in a book published in 2011:

The thought that there is something more—the thought needed to make normative ethics function—is an illusion.(1)

So if Carson thinks that “Darwinian evolution, or any form of pure materialism, undermines the basis of ethics,” he could call Ruse as a witness. I have looked into this subject in depth and find that most Darwinist biologists attempt to understand ethics along lines similar enough to Ruse’s view that Carson could call them as witnesses too.

Darwin’s Emory Five Hundred do not like the logical implications of what they believe. As their letter to the Emory Wheel (4/27/2012), originally published by four aggrieved biologists, put it, …

More.

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DNA molecule unwinding/National Human Genome Research Institute

From “RNA: From Messenger to Guardian of Genome Integrity” (ScienceDaily, May 23, 2012), we learn,

For decades the scientific community has attributed a role to RNA that is subordinate to that of DNA: the functional processes of expression of genetic information into proteins. With some known exceptions, such as the classes of tRNA and rRNA involved in the synthesis of proteins, RNA molecules were considered “fleeting” messengers necessary to carry genetic instructions from the nucleus, site of the genome, to the cytoplasm where proteins, the scaffolding of living organisms, are produced.

In recent years, this simplistic view has given way to an increasingly complex scenario, with the identification of new RNA classes involved in numerous cellular events.

One in particular, however, had never been identified or described to date: it is DDRNA, a class of non protein-coding RNAs that are generated every time the genome is damaged. They originate from the same sequence of DNA damaged and have the essential task of launching the molecular alarms through which the cell detects the problem and resolves it by repairing the damage.

So let’s see: DNA used to be full of junk  (alleged evidence for Darwinism). RNA used to be gofer (alleged evidence for an RNA world).

The best solution for Darwin’s establishment is to get the concept of evidence undermined.

Oh, wait …

The “radicals” of his title are scientists with an unwavering belief in the truth of their ideas and no compunction about breaking the rules to prove it. They fight, they try to block colleagues’ progress, they commit fraud, they deceive and manipulate others.

Yes, but so do tenured non-entities. So do administrative careerists.

Scientists overlook inconvenient results, writes Mr. Brooks, a British science writer who holds a doctorate in quantum physics and writes a weekly column for The New Statesman. They ignore data that conflict with their ideas.

Ditto.

Something is missing from this picture. Going bad didn’t make the science stars good; it just didn’t stop them from winning.

Interestingly, Brooks tells us that the image of the scientist as someone responsible and safe was invented postwar, to counter the Hiroshima “mad scientist” persona. And, here’s the kicker, he’d like to change that. According to Bouton, he thinks that, to fight “the unprecedented threat from global climate change,” scientists should change their image, and “speak up” – because the scientists he writes about are winners, and history belongs to the winners.

From this desk, it’s hard to see how scientists in a field known for scandal (cf. Climategate and Memogate) will convince more people by sounding a little deranged.

Put another way: it’s okay to look and sound deranged if you are already a winner. Otherwise, recheck those calculations, pronto.

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Well, the team is now producing > documentaries presenting intelligence in nature, daid to be of a similar calibre:

Stanley Salthe, a known dissenter from Darwin, trashed by Darwinists, appears in the film.

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Like the latest doom scenario and the health scare of the decade? Get ‘em all and you get free shipping? Proceed to Checkout … .

Recently, we noted Brian Greene’s honest report on the state of the evidence for his multiverse theory (there is no actual evidence). Which prompted an interesting discussion at Peter Woit’s Not Even Wrong blog, for example, Bernhard:

The only purpose of the multiverse seems again to sell books and make headlines. I never went to a conference where I saw a speaker talking seriously about it. It does not explain anything and is completely shielded from experiment. Brian Greene used to promote string theory, but with no advances, no chances of telling if the theory is write or wrong, and the cherry on top: no signs of SUSY, the multiverse is what is left. The only thing I am amazed is how long are these guys going to repeat the same story again and again and still find suckers that are “fascinated” with it.

Actually, it is not merely fascination; it is fear.

Fear? As Marcus Chown put it,

But the main reason for believing in an ensemble of universes is that it could explain why the laws governing our Universe appear to be so finely turned for our existence … This fine-tuning has two possible explanations. Either the Universe was designed specifically for us by a creator or there is a multitude of universes—a multiverse. – “Anything goes,” New Scientist (June 6, 1998)

There are many similar examples.

We had no idea it was that bad. We thought their hat had way more rabbits in it.

He even found a seat in the overcrowded flight lounge.

In “Confessions of an Atheist Darwin-Doubter”( Evolution News & Views, May 21, 2012), James Barham explains why a reasonable atheist can easily doubt Darwin:

By the 1980s, I had become conversant with the standard critiques of neo-Darwinism, such as Karl Popper’s. Also, from my classical studies, I was familiar with Aristotle. So, I knew there were problems with Darwinism as a metaphysical system, and that alternatives existed. Gradually, too, I became conscious of a growing cognitive dissonance between my Darwin-inspired philosophical materialism and reductionism, and my first-person experience of the fundamental importance of purpose, value, and meaning for human existence. I was familiar with various schemes that had been proposed for explaining away the latter, such as Daniel Dennett’s “intentional stance,” but I could see they were just evading the issue. So, I was left with a contradiction between two aspects of my mental life that I had no idea how to resolve.

Then, one day while browsing in the stacks — this was around 1988 — I stumbled across an essay collection entitled Self-Organizing Systems: The Emergence of Order (ed. F. Eugene Yates; Plenum Press, 1987). This volume was devoted to efforts that were then underway to use dynamical systems theory as a means of modeling the operation of various physiological systems. I immediately had the experience of the scales falling from my eyes. I saw in a flash that the concept of a nonlinear oscillator — and its associated “basin of attraction” — might be a way to model the end-directed, or teleological, feature of biological functions. (A basin of attraction — or “attractor,” for short — is a mathematical representation of dynamical behavior as a “trajectory” through an abstract multidimensional space.) And upon this foundation, I could already vaguely see that an emergentist metaphysics might be erected which might provide a robustly realist, yet rigorously scientific, account of the phenomena of purpose, value, and meaning.

I was aware of well-known criticisms of both of the then-current reductionist accounts of function: the “causal-role” theory and the Darwin-inspired “selected-effects” theory. In a nutshell, the problem is that neither theory can explain the normative character of biological processes in a coherent manner. (Biological processes are “normative” in the sense that they may either succeed or fail in fulfilling their functions.) With respect to the “causal-role” theory, there is no way to distinguish between functional and non-functional parts of a biological system without presupposing the normative character of the overall system as a whole — which begs the question at issue. … More.

Actually, it seems to be a trend. One thing the New Atheists have done, for which the public is surely in their debt, is to render atheism and Darwinism so odious that people who would not have questioned the Darwinists’ circled wagons and circular reasoning before now find that they must.

See also: There are now hopeful signs of a backlash against the brain

"Flowers make certain that gamete fusion has successfully occurred before other pollen are repelled."/Mike Cohea, Brown University

From “Pollination With Precision: How Flowers Do It” (ScienceDaily, May 17, 2012), we learn

Pollination could be a chaotic disaster. With hundreds of pollen grains growing long tubes to ovules to deliver their sperm to female gametes, how can a flower ensure that exactly two fertile sperm reach every ovule? In a new study, Brown University biologists report the discovery of how plants optimize the distribution of pollen for successful reproduction.

…

In pollination, hundreds of sperm-carrying pollen grains stick to the stigma suspended in the middle of a flower and quickly grow a tube down a long shaft called a style toward clusters of ovules, which hold two female sex cells. This could be a chaotic frenzy, but for the plant to succeed, exactly two fertile sperm should reach the two cells in each ovule — no more, no less. No ovule should be left out, either because too many tubes have gone elsewhere, or because the delivered sperm don’t work.

In the journal Current Biology, Brown University biologists report that flowers have evolved an elegant safeguard system to ensure that only the minimum necessary number of pollen tubes will reach each ovule.

“There is a mechanism that prevents too many pollen tubes from delivering too many sperm,” said Mark Johnson, associate professor of biology at Brown and senior author on a new paper detailing the discovery. “But the other cool thing is that there is also a way to salvage fertilization if the first father is a dud.”

The critical question isn’t how this degree of precision could be achieved – in flowering plants, known only from the Mesozoic era to today (if that long), but how it could have been achieved without intelligent guidance during such a period.

As long as Darwinism is not forced to submit to reality-based calculations of probability, there will be no shortage of fanciful ideas getting in the way of serious inquiry.

Incidentally, Despite a concerted effort by evolutionary developmental (evo-devo) biologists and paleontologists the origin of angiosperms remains enigmatic and mysterious (Frohlich and Chase 2007). Further, certain paleobotanists regard the problem of flowering plant origins, “as intractable a mystery today as it was to Darwin 130 years ago” (page 318, Rothwell et al. 2009).