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Pushback against “deep evolution” (we are descended from complex ancestor) and HGT

Also, doubts about horizontal gene transfer persist. First, from Suzan Mazur earlier at Huffington Post on deep evolution:

I recently had a three-way phone conversation with Swedish deep evolution investigators Charles Kurland and Ajith Harish about their phylogenomic Tree of Life (ToL) based on protein structure, which shows that we are descended from a “complex” ancestor — MRUCA (most recent universal common ancestor) — not a simple bacteria. Kurland and Harish think a ToL paradigm shift may be in order. What’s more, Kurland and Harish figure that MRUCA was not the first ancestor, but represents complex survivors of a now-extinct biosphere.

Now, just recently from Mazur, again at Huffington Post, a report on the pushback:

There has been a vigorous and somewhat sharp response to the Charles Kurland and Ajith Harish Tree of Life interview, reminiscent of the email chain circulated by theoretical biologist Stan Salthe following Jerry Fodor’s article in the London Review of Books, “Why Pigs Don’t Have Wings.” I thought it important to share some of the responses to the Kurland and Harish interview, particularly because comments are no longer attached to Huffington Post stories, except on the HP Facebook page. More.

Mazur is the author of Paradigm Shifters: Excerpts from pushback with your coffee:

Speaking of Ford Doolittle— Because Chuck Kurland during our interview said that Doolittle in a 1999 Science magazine article exaggerated the extent to which horizontal gene transfer is a factor in evolution, and then identified Doolitte as a former postdoc of Carl Woese – Doolittle responded with a slur in an email to me, calling Kurland the “Donald Trump of molecular evolution.” (That, by the way, was prior to Trump’s speech to Congress and the Dow surging over 21,000.)

and this:

SUPERFAMILY father Julian Gough, a bioinformaticist at MRC Laboratory for Molecular Biology, Cambridge whose database Kurland and Harish relied on to build their ToL, agrees that HGT is overblown. Gough wrote to me:

“I agree strongly with some of their [Kurland & Harish] assertions, such as that horizontal gene transfer has been overblown by some segments of the scientific community (because it’s an engaging story and a good excuse for our shortcomings in untangling evolution). . . . I think you capture in your interview something very important, that ‘it’s important that science not become dogma’ and these guys are calling everyone out on some stuff that really has been insufficiently challenged. So I am really pleased that as a journalist you are helping to air the views.”

This sounds like a serious, if testy, discussion. We were thinking there’d be pushback but maybe keeping trolls off the HP page proper, as noted above, is keeping the discussion fruitful.

It seems like horizontal gene transfer is taking its place in the world of discussible explanations in evolution. Win some, lose some.

See also: Common ancestry: Bioinformaticist Julian Gough on the SUPERFAMILY database on proteins in genomes

Part II of Mazur’s “Kurland and Harish Rethink Deep Evolution” Part I is here.

and

Horizontal gene transfer: Sorry, Darwin, it’s not your evolution any more

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Extraterrestrial life: Genetic code as Wow! signal

A Wow! signal is definite evidence for extraterrestrial life. We missed this from 2013:

The SETI hypothesis of an intelligent signal in the genetic code is tested. The code is shown to possess an ensemble of same-style precision-type patterns. The patterns are shown to match the criteria of an intelligent signal.

It’s apparently still legal to say that. From ScienceDirect at Icarus:

Abstract: It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but stronger in noise immunity is the genetic code. The code is a flexible mapping between codons and amino acids, and this flexibility allows modifying the code artificially. But once fixed, the code might stay unchanged over cosmological timescales; in fact, it is the most durable construct known. Therefore it represents an exceptionally reliable storage for an intelligent signature, if that conforms to biological and thermodynamic requirements. As the actual scenario for the origin of terrestrial life is far from being settled, the proposal that it might have been seeded intentionally cannot be ruled out. A statistically strong intelligent-like “signal” in the genetic code is then a testable consequence of such scenario. Here we show that the terrestrial code displays a thorough precision-type orderliness matching the criteria to be considered an informational signal. Simple arrangements of the code reveal an ensemble of arithmetical and ideographical patterns of the same symbolic language. Accurate and systematic, these underlying patterns appear as a product of precision logic and nontrivial computing rather than of stochastic processes (the null hypothesis that they are due to chance coupled with presumable evolutionary pathways is rejected with P-value < 10–13). The patterns are profound to the extent that the code mapping itself is uniquely deduced from their algebraic representation. The signal displays readily recognizable hallmarks of artificiality, among which are the symbol of zero, the privileged decimal syntax and semantical symmetries. Besides, extraction of the signal involves logically straightforward but abstract operations, making the patterns essentially irreducible to any natural origin. Plausible ways of embedding the signal into the code and possible interpretation of its content are discussed. Overall, while the code is nearly optimized biologically, its limited capacity is used extremely efficiently to pass non-biological information. (public access) – Vladimir I. shCherbaka, , Maxim A. Makukov Acorus, The “Wow! signal” of the terrestrial genetic code, Volume 224, Issue 1, May 2013, Pages 228–242 More.

From the paper:

To be considered unambiguously as an intelligent signal, any patterns in the code must satisfy the following two criteria: (1) they must be highly significant statistically and (2) not only must they possess intelligent-like features (Elliott, 2010), but they should be inconsistent in principle with any natural process, be it Darwinian (Freeland, 2002) or Lamarckian (Vetsigian et al., 2006) evolution, driven by amino acid biosynthesis (Wong, 2005), genomic changes (Sella and Ardell, 2006), affinities between (anti)codons and amino acids (Yarus et al., 2009), selection for the increased diversity of proteins (Higgs, 2009), energetics of codon-anticodon interactions (Klump, 2006; Travers, 2006), or various pretranslational mechanisms (Wolf and Koonin, 2007; Rodin et al., 2011). The statistical test for the first criterion is outlined in Appendix B, showing that the described patterns are highly significant.

See also: NASA’s mission to find life on Jupiter’s promising moon, Europa

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Design Disquisitions: Jeffrey Koperski on Two Bad and Two Good Ways to Attack ID (Part 2): Two ‘Good’ Ways

Part two of my series looking at Jeffrey Koperski’s paper ‘Two Bad Ways to Attack Intelligent Design and Two Good Ones’ is now up on my blog. This one is quite in depth, but a couple of interesting issues come up along the way. I examine the concept of soft and hard anomalies in scientific theories and how they might affect theory change. I then look at the claim that ID’s scientific core is too meagre to be considered serious science. The final objection I analyse is the claim that ID violates a metatheoretic shaping principle known as scientific conservatism.

In part one of this series looking at Jeffrey Koperski’s paper, Two Bad Ways to Attack Intelligent Design and Two Good Ones, I focussed on the two arguments he thinks fail as good critiques of design. The first argument, if one could call it that, is the claim that ID is merely repackaged creationism. The second was the claim that ID fails to meet the criteria of science because it doesn’t adhere to methodological naturalism. I considered Koperski’s criticisms of those arguments and found them to be persuasive. In the second part of the paper, he takes a look at two more arguments. He sees these as being good reasons to reject ID. In this article I’ll be considering the two arguments put forward, suggesting that they fail as affective counter arguments, concluding that ultimately, the four arguments looked at in his paper all fall in to the category of bad arguments against design.

Read more here.

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The high cost of marchin’, marchin’ for “Science”: If female, you could be road kill yourself

Political correctness decreed that there were no important brain differences between men and women but tests were done mainly on male animals. And, because the resulting problems didn’t help various political causes, they were dangerous to publicize. From Claire Lehmann at Commentary:

The insistence that gender differences were and are immaterial to the proper functioning of a free society has been a feature of our common conversation since the 1970s. It was the key to “second-wave feminism,” the political and social movement that took women’s liberation beyond issues of suffrage and wages and employment to the question of how a just society orders itself.

By the close of the 20th century, however, the insistence that gender differences be treated as inconsequential had ossified into orthodoxy precisely at the moment when the biological sciences were uncovering differences between the sexes that had hitherto been unknown. An ongoing tug-of-war has resulted between scientists who investigate sex differences and activists who oppose such research. This battle over theory has had horrific real-world consequences. The minimizing of sex differences in areas of health and medicine in particular has led to sweepingly harmful and often fatal results, especially for women.

I’d always wondered about that. I remember suffering through laborious explanations in social psychology texts that I proofread and indexed, as to how all such differences were artifacts of sexist bias in testing. For example, even differences in violent crime rates might just be bias…

Everyone on the project knew that such claims could not possibly be true because the ordinary experience of survivors, not their biases, contradicted it. Survivors of violent crime worked among us! Yet no one dared say a thing.

It’s good that social sciences are not really sciences anyway. But seeing how their point of view has spread into medical sciences, which can actually help people, is disconcerting:

It’s worth noting that historically, the hostility toward such research came not from the laboratory but from the humanities and social sciences. A 1986 paper in American Psychologist titled “Issues to Consider in Conducting Nonsexist Psychological Research” gives us a snapshot of the attitudes prevalent at the time. The authors state that “[sexist] bias need not be introduced into research intentionally or consciously” and that “even well-established findings can harbor unsuspected sexism.” They question whether objective scientific methods were even appropriate for use on women as women. Perhaps most troubling was their assertion that a male scientist studying female subjects is, by definition, “sexist.” Consider the following fiasco. More.

Well, if naturalism rules, maybe it is science’s destiny to be governed by cranks, crackpots and ideologues. We did not evolve so as to perceive reality, right?

See also: Blinkers Award goes to… Tom Nichols at Scientific American! On why Americans “hate science”

Objectivity is sexist.

Marchin’, marchin’ for Science (Hint: the problems are back at your desk, not out in the streets)

and

Even Michael Shermer thinks social science is politically biased

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Albert Einstein: Pantheist or deist?

From writer and filmmaker Paul Ratner at BigThink:

ome (including the scientist himself) have called Einstein’s spiritual views as pantheism, largely influenced by the philosophy of Baruch Spinoza. Pantheists see God as existing but abstract, equating all of reality with divinity. They also reject a specific personal God or a god that is somehow endowed with human attributes.

Himself a famous atheist, Richard Dawkins calls Einstein’s pantheism a “sexed-up atheism,” but other scholars point to the fact that Einstein did seem to believe in a supernatural intelligence that’s beyond the physical world. He referred to it in his writings as “a superior spirit,” “a superior mind” and a “spirit vastly superior to men”. Einstein was possibly a deist, although he was quite familiar with various religious teachings, including a strong knowledge of Jewish religious texts. More.

It does not sound as though Einstein was a metaphysical naturalist, as are large numbers of elite scientists today. Could naturalism be one reason some fields are basically stuck? (“We need fresh thinking here but humans did not evolve so as to perceive reality”)

In this connection, does anyone remember Antony Flew? Antony Flew died at 87 in 2010:

Roy Varghese has just notified me of the death of Professor emeritus Antony Flew, the rationalist philosopher who died on April 8 aged 87, spent much of his life denying the existence of God, and then in 2004, dramatically changed his mind.

See also: Antony Flew considered Richard Dawkins a bigot.

and

Evolution bred a sense of reality out of us

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One suspects no further information will ever be available. Here is a Dawkinsian take on the subject.

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Theologian Hans Madueme on BioLogos’s Adam: A stumbling block to faith?

Reviewing Adam and the Genome: Reading Scripture after Genetic Science, at Gospel Coalition:

The book is well-written, informative, engaging, and relentlessly provocative. Despite these strengths, however, the book failed to convince me. It exemplifies what many Christians on the sidelines find concerning as they watch these science-theology debates unfolding. And once again—to borrow a Mark Twain misquote—rumors of Adam’s demise have been greatly exaggerated.

We shouldn’t miss the deep irony. One of the authors’ main motivations for writing this book is to remove a stumbling block for young people. McKnight goes on to tell us, repeatedly and insistently, that most lay believers consider the “historical” Adam central to the faith. As we’ve seen, his main thesis is that there is no historical Adam in the Bible and that Adam, contrary to what most Christians believe, plays no central role in Scripture’s redemptive-historical structure. But in doing so, he places a massive stumbling block to their understanding of the faith. The pastoral dilemma cuts both ways. More.

One wonders whether, these days, Adam and Eve are as hot a topic in faith struggles as they were decades ago. Science’s reputation has taken a beating (often for good reasons). So, for many people, “scientists now think” is right up there with “The New York Times’ editorial board now thinks,” in terms of how it should influence their own view. Readers?

See also: “Adam never existed” theologian responds to critics

and

Blinkers Award goes to… Tom Nichols at Scientific American! On why Americans “hate science”

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Denis Noble’s new book calls for “fundamental revision” of neo-Darwinian theory

From David Klinghoffer at Evolution News & Views, on Denis Noble’s new book, Dance to the Tune of Life: Biological Relativity,

Here is a new book from Oxford University biologist Denis Noble, Dance to the Tune of Life: Biological Relativity. He is one of the Third Way of Evolution folks, and no advocate of intelligent design.

In the book, published by Cambridge U Press, he argues for a “fundamental revision” of neo-Darwinian theory.

Noble was among the organizers and participants at the Royal Society meeting in London that we’ve talked so much about here.

Evolutionary biology is in a state of ferment verging, in some quarters, on open rebellion. Don’t let Darwin apologists tell you otherwise. More.

Darwin apologists can probably convince the New York Times but these days that’s only a participation trophy.

See also: Why the sea is boiling hot

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Can chimpanzees be non-human persons?

From George Johnson at Undark:

In November, Judge María Alejandra Mauricio of the Third Court of Guarantees in Mendoza decreed that Cecilia is a “nonhuman person” — one that was being denied “the fundamental right” of all sentient beings “to be born, to live, grow, and die in the proper environment for their species.”

Agreeing to a petition by animal rights lawyers in Argentina for a writ of habeas corpus — a demand that a court rule on whether a prisoner or inmate is being legally detained — the judge ordered that the chimpanzee be freed from the zoo and transferred to a great ape sanctuary in Brazil.

In an earlier case, an appeals court in Buenos Aires upheld a judge’s demand that the city zoo provide an orangutan named Sandra with a way of life consistent with her “well-being, behavioral complexity, and emotional states.”

It has never been necessary to make claims about the “personhood” of animals in order to secure their humane treatment. But in an age when the internet has left many law offices hurting for work, expect a vast increase in creative litigation.

Though the science is far from settled, and probably will never be, the idea that something resembling a subjective, contemplative mind exists in other animals has become mainstream — and not just for apes. Recent popular science books include “What a Fish Knows: The Inner Lives of Our Underwater Cousins,” “The Soul of an Octopus: A Surprising Exploration Into the Wonder of Consciousness” and “Other Minds: The Octopus, the Sea, and the Deep Origins of Consciousness.” More.

It’s not really all that difficult. An animal who lacks reason and moral sense often has, nevertheless, a sense that an experience is happening to itself. The dog who is informed that he is a “Good dog!” is the subject of an experience. He perceives that the approval is happening to him. But if subjectivity (“well-being, behavioral complexity, and emotional states”) is the criterion for personhood, why not dogs and ravens as well as great apes?

Actually, personhood is a concept developed for how humans relate to each other. Applying it to animals will likely diminish the concept for humans without helping the animals. In any event, there is no evidence of the claimed “continuum” between human and animal intelligence. It has been an abrupt break.

See also: Animal minds: In search of the minimal self

Are apes entering the Stone Age?

and

Furry, feathery, and finny animals speak their minds

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Common ancestry: Bioinformaticist Julian Gough on the SUPERFAMILY database on proteins in genomes

In an interview with Suzan Mazur at Huffington Post. Mazur explains,

Plug certain information into SUPERFAMILY and it can analyze a vast assortment of genomes and assist you in building a Tree of Life using superfamilies — i.e., domains with an evolutionary relationship — and the conserved part of thousands and thousands of protein structures called protein domains.

…

Suzan Mazur: Do protein Superfamilies represent the current limits of our ability to identify common ancestry?

Julian Gough: Yes. That is exactly what their definition is. So if you want to group two protein structural domains into the same Superfamily, the question that you ask is whether there is structural sequence and functional evidence for common evolutionary ancestry. So they’re classified based on that.

The most powerful part of that classification comes from the structure. Structure is far more conserved than sequence and so the knowledge of the structure allows you to classify very distantly related things that have no apparent or detectable similarity in sequence.More.

Suzan Mazur is the author of Public Evolution Summit.

See also: Axe on specific barriers to macro-level Darwinian Evolution due to protein formation (and linked islands of specific function)

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