Michael J. Behe's Blog, page 586

High tech viewers vs. troll reviewers: Who will win?

Locally, we refer to people who review books without reading them as noviewers. Mostly, they want to encourage others to follow their example and not read the book either.

The usual low-tech technique for spotting noviewers in the review stream is that they engage with the text only via canned talking points at best. They show little interest in the ideas as such. But how to prove that?

From Dave Lee at BBC we learn,

So imagine my delight today when, via the excellent Nieman Lab, I read about Norwegian broadcaster NRK.

The tech section of its site, NRKBeta, is trying a simple experiment. You can’t leave a comment unless you’ve read the story. How will they know? There’s a test!

“If you spend 15 seconds on it, those are maybe 15 seconds that take the edge off the rant mode when people are commenting,” suggested the site’s editor, Marius Arneson, in Nieman Lab’s interview.

It’s only being trialled on a small number of stories at the moment – typically tech stories that have broken out into the main news agenda. The quizzes are written by the reporters, and the questions aren’t too taxing, just enough to show you’ve at least glanced at the text before rushing to the bottom. More.

The rush to the bottom will likely continue, we suspect, because some people read in order to rant – and that’s their right. But it’s the authors’ and other commenters’ right to know if that’s all they’re doing. For sure.

See also: What do we call people who refuse to read books the are attacking

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RVB8 and the refusal to mark the difference between description and invention

. . . (of the concept, functionally specific, complex organisation and associated information, FSCO/I)

Sometimes, a longstanding objector here at UD — such as RVB8 — inadvertently reveals just how weak the objections to the design inference are by persistently clinging to long since cogently answered objections. This phenomenon of ideology triumphing over evident reality is worth highlighting as a headlined post illustrating darwinist rhetorical stratagems and habits.

Here is RVB8 in a comment in the current Steve Fuller thread:

RVB8, 36: >> for ID or Creationism, I can get the information direct from the creators of the terminology. Dembski for Specified Complexity, Kairos for his invention of FSCO/I, and Behe for Irreducible Complexity.>>

For a long time, he and others of like ilk have tried to suggest that as I have championed the acrostic summary FSCO/I, the concept I am pointing to is a dubious novelty that has not been tested through peer review or the like and can be safely set aside. In fact, it is simply acknowledging that specified complexity is both organisational and informational, and that in many contexts it is specified in the context of requisites of function through multiple coupled parts. Text such as in this post shows a simple form of such a structure, S-T-R-I-N-G-S.

Where of course, memorably, Crick classically pointed out to his son Michael on March 19, 1953 as follows, regarding DNA as text:

Crick’s letter

Subsequently, that code was elucidated (here in the mRNA, transcribed form):

The Genetic code uses three-letter codons to specify the sequence of AA’s in proteins and specifying start/stop, and using six bits per AA

Likewise a process flow network is an expression of FSCO/I, e.g. an oil refinery:

Petroleum refinery block diagram illustrating FSCO/I in a process-flow system

This case is much simpler than the elucidated biochemistry process flow metabolic reaction network of the living cell:

I have also often illustrated FSCO/I in the form of functional organisation through a drawing of an ABU 6500 C3 reel (which I safely presume came about through using AutoCAD or the like):

All of this is of course very directly similar to something like protein synthesis [top left in the cell’s biochem outline], which involves both text strings and functionally specific highly complex organisation:

Protein Synthesis (HT: Wiki Media)

In short, FSCO/I is real, relevant and patently descriptive, both of the technological world and the biological world. This demands an adequate causal explanation, and the only serious explanation on teh table that is empirically warranted is, design.

As the text of this post illustrates, and as the text of objector comments to come will further inadvertently illustrate.

Now, I responded at no 37, as follows:

KF, 37: >>Unfortunately, your choice of speaking in terms of “invention” of FSCO/I speaks volumes on your now regrettably habitual refusal to acknowledge phenomena that are right in front of you. As in, a descriptive label acknowledges a phenomenon, it does not invent it.

Doubtless [and on long track record], you think that is a clever way to dismiss something you don’t wish to consider.

This pattern makes your rhetoric into a case in point of the sociological, ideological reaction to the design inference on tested sign. So, I now respond, by way of addressing a case of a problem of sustained unresponsiveness to evidence.

However, it only reveals that you are being selectively hyperskeptical and dismissive through the fallacy of the closed, ideologised, indoctrinated, hostile mind.

I suggest you need to think again.

As a start, look at your own comment, which is text. To wit, a s-t-r-i-n-g of 1943 ASCII characters, at 7 bits per character, indicating a config space of 2^[7 * 1943) possibilities. That is, a space with 2.037*10^4094 cells.

The atomic and temporal resources of our whole observed cosmos, running at 1 search per each of 10^80 atoms, at 10^12 – 10^14 searches per s [a fast chem reaction rate] for 10^17 s [time since big bang, approx.] could not search more than 10^111 cells, a negligibly small fraction. That is, the config space search challenge is real, there is not enough resource to search more than a negligibly small fraction of the haystack blindly. (and the notion sometimes put, of somehow having a golden search runs into the fact that searches are subsets, so search for a golden search comes from the power set of the direct config space, of order here 2^[10^4094]. That is, it is exponentially harder.)

How then did your text string come to be? By a much more powerful means: you as an intelligent and knowledgeable agent exerted intelligently directed configuration to compose a text in English.

That is why, routinely, when you see or I see text of significant size in English, we confidently and rightly infer to design.

As a simple extension, a 3-d object such as an Abu 6500 C3 fishing reel is describable, in terms of bit strings in a description language, so functional organisation is reducible to an informational equivalent. Discussion on strings is WLOG.

In terms of the living cell, we can simply point to the copious algorithmic TEXT in DNA, which directly fits with the textual search challenge issue. There is no empirically warranted blind chance and mechanical necessity mechanism that can plausibly account for it. We have every epistemic and inductive reasoning right to see that the FSCO/I in the cell is best explained as a result of design.

That twerdun, which comes before whodunit.

As for, oh it’s some readily scorned IDiot on a blog, I suggest you would do better to ponder this from Stephen Meyer:

The central argument of my book [= Signature in the Cell] is that intelligent design—the activity of a conscious and rational deliberative agent—best explains the origin of the information necessary to produce the first living cell. I argue this because of two things that we know from our uniform and repeated experience, which following Charles Darwin I take to be the basis of all scientific reasoning about the past. First, intelligent agents have demonstrated the capacity to produce large amounts of functionally specified information (especially in a digital form). Second, no undirected chemical process has demonstrated this power. Hence, intelligent design provides the best—most causally adequate—explanation for the origin of the information necessary to produce the first life from simpler non-living chemicals. In other words, intelligent design is the only explanation that cites a cause known to have the capacity to produce the key effect in question . . . . In order to [[scientifically refute this inductive conclusion] Falk would need to show that some undirected material cause has [[empirically] demonstrated the power to produce functional biological information apart from the guidance or activity a designing mind. Neither Falk, nor anyone working in origin-of-life biology, has succeeded in doing this . . . .

The central problem facing origin-of-life researchers is neither the synthesis of pre-biotic building blocks (which Sutherland’s work addresses) or even the synthesis of a self-replicating RNA molecule (the plausibility of which Joyce and Tracey’s work seeks to establish, albeit unsuccessfully . . . [[Meyer gives details in the linked page]). Instead, the fundamental problem is getting the chemical building blocks to arrange themselves into the large information-bearing molecules (whether DNA or RNA) . . . .

For nearly sixty years origin-of-life researchers have attempted to use pre-biotic simulation experiments to find a plausible pathway by which life might have arisen from simpler non-living chemicals, thereby providing support for chemical evolutionary theory. While these experiments have occasionally yielded interesting insights about the conditions under which certain reactions will or won’t produce the various small molecule constituents of larger bio-macromolecules, they have shed no light on how the information in these larger macromolecules (particularly in DNA and RNA) could have arisen. Nor should this be surprising in light of what we have long known about the chemical structure of DNA and RNA. As I show in Signature in the Cell, the chemical structures of DNA and RNA allow them to store information precisely because chemical affinities between their smaller molecular subunits do not determine the specific arrangements of the bases in the DNA and RNA molecules. Instead, the same type of chemical bond (an N-glycosidic bond) forms between the backbone and each one of the four bases, allowing any one of the bases to attach at any site along the backbone, in turn allowing an innumerable variety of different sequences. This chemical indeterminacy is precisely what permits DNA and RNA to function as information carriers. It also dooms attempts to account for the origin of the information—the precise sequencing of the bases—in these molecules as the result of deterministic chemical interactions . . . .

[[W]e now have a wealth of experience showing that what I call specified or functional information (especially if encoded in digital form) does not arise from purely physical or chemical antecedents [[–> i.e. by blind, undirected forces of chance and necessity]. Indeed, the ribozyme engineering and pre-biotic simulation experiments that Professor Falk commends to my attention actually lend additional inductive support to this generalization. On the other hand, we do know of a cause—a type of cause—that has demonstrated the power to produce functionally-specified information. That cause is intelligence or conscious rational deliberation. As the pioneering information theorist Henry Quastler once observed, “the creation of information is habitually associated with conscious activity.” And, of course, he was right. Whenever we find information—whether embedded in a radio signal, carved in a stone monument, written in a book or etched on a magnetic disc—and we trace it back to its source, invariably we come to mind, not merely a material process. Thus, the discovery of functionally specified, digitally encoded information along the spine of DNA, provides compelling positive evidence of the activity of a prior designing intelligence. This conclusion is not based upon what we don’t know. It is based upon what we do know from our uniform experience about the cause and effect structure of the world—specifically, what we know about what does, and does not, have the power to produce large amounts of specified information . . . .

[[In conclusion,] it needs to be noted that the [[now commonly asserted and imposed limiting rule on scientific knowledge, the] principle of methodological naturalism [[ that scientific explanations may only infer to “natural[[istic] causes”] is an arbitrary philosophical assumption, not a principle that can be established or justified by scientific observation itself. Others of us, having long ago seen the pattern in pre-biotic simulation experiments, to say nothing of the clear testimony of thousands of years of human experience, have decided to move on. We see in the information-rich structure of life a clear indicator of intelligent activity and have begun to investigate living systems accordingly. If, by Professor Falk’s definition, that makes us philosophers rather than scientists, then so be it. But I suspect that the shoe is now, instead, firmly on the other foot. [[Meyer, Stephen C: Response to Darrel Falk’s Review of Signature in the Cell, SITC web site, 2009. (Emphases and parentheses added.)]

Let me focus attention on the highlighted:

First, intelligent agents have demonstrated the capacity to produce large amounts of functionally specified information (especially in a digital form). Second, no undirected chemical process has demonstrated this power. Hence, intelligent design provides the best—most causally adequate—explanation for the origin of the information necessary to produce the first life from simpler non-living chemicals.

The only difference between this and what I have highlighted through the acronym FSCO/I, is that functionally specific organisation is similarly reducible to an informational string and is in this sense equivalent to it. Where, that is hardly news, AutoCAD has reigned supreme as an engineers design tool for decades now. Going back to 1973, Orgel in his early work on specified complexity, wrote:

. . . In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity . . . .

[HT, Mung, fr. p. 190 & 196:] These vague idea can be made more precise by introducing the idea of information. Roughly speaking, the information content of a structure is the minimum number of instructions needed to specify the structure. [–> this is of course equivalent to the string of yes/no questions required to specify the relevant “wiring diagram” for the set of functional states, T, in the much larger space of possible clumped or scattered configurations, W, as Dembski would go on to define in NFL in 2002, also cf here, here and here (with here on self-moved agents as designing causes).] One can see intuitively that many instructions are needed to specify a complex structure. [–> so if the q’s to be answered are Y/N, the chain length is an information measure that indicates complexity in bits . . . ] On the other hand a simple repeating structure can be specified in rather few instructions. [–> do once and repeat over and over in a loop . . . ] Complex but random structures, by definition, need hardly be specified at all . . . . Paley was right to emphasize the need for special explanations of the existence of objects with high information content, for they cannot be formed in nonevolutionary, inorganic processes. [The Origins of Life (John Wiley, 1973), p. 189, p. 190, p. 196.]

So, the concept of reducing functional organisation to a description on a string of y/n structured questions — a bit string in some description language — is hardly news, nor is it something I came up with. Where obviously Orgel is speaking to FUNCTIONAL specificity, so that is not new either.

Likewise, search spaces or config spaces is a simple reflection of the phase space concept of statistical thermodynamics.

Dembski’s remarks are also significant, here from NFL:

p. 148:“The great myth of contemporary evolutionary biology is that the information needed to explain complex biological structures can be purchased without intelligence. My aim throughout this book is to dispel that myth . . . . Eigen and his colleagues must have something else in mind besides information simpliciter when they describe the origin of information as the central problem of biology.

I submit that what they have in mind is specified complexity, or what equivalently we have been calling in this Chapter Complex Specified information or CSI . . . .

Biological specification always refers to function. An organism is a functional system comprising many functional subsystems. . . . In virtue of their function [[a living organism’s subsystems] embody patterns that are objectively given and can be identified independently of the systems that embody them. Hence these systems are specified in the sense required by the complexity-specificity criterion . . . the specification can be cashed out in any number of ways [[through observing the requisites of functional organisation within the cell, or in organs and tissues or at the level of the organism as a whole. Dembski cites:

Wouters, p. 148: “globally in terms of the viability of whole organisms,”

Behe, p. 148: “minimal function of biochemical systems,”

Dawkins, pp. 148 – 9: “Complicated things have some quality, specifiable in advance, that is highly unlikely to have been acquired by ran-| dom chance alone. In the case of living things, the quality that is specified in advance is . . . the ability to propagate genes in reproduction.”

On p. 149, he roughly cites Orgel’s famous remark from 1973, which exactly cited reads:

In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity . . .

And, p. 149, he highlights Paul Davis in The Fifth Miracle: “Living organisms are mysterious not for their complexity per se, but for their tightly specified complexity.”] . . .”

p. 144: [[Specified complexity can be more formally defined:] “. . . since a universal probability bound of 1 [[chance] in 10^150 corresponds to a universal complexity bound of 500 bits of information, [[the cluster] (T, E) constitutes CSI because T [[ effectively the target hot zone in the field of possibilities] subsumes E [[ effectively the observed event from that field], T is detachable from E, and and T measures at least 500 bits of information . . . ”

So, the problem of refusal to attend to readily available, evidence or even evidence put in front of objectors to design theory is significant and clear.

What it in the end reflects as a case of clinging to fallacies and myths in the teeth of correction for years on end, is the weakness of the case being made against design by its persistent objectors.

Which is itself highly significant.>>

Now, let us discuss, duly noting the highlighted and emphasised. END

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Another stab at whether viruses are alive…

Laura Geggel interviews virologists at LiveScience, who offer arguments against the idea, for example:

“Take a cat, a plant and a rock, and leave them in a room for days,” said Amesh Adalja, an infectious disease physician and an affiliated scholar at the Johns Hopkins Center for Health Security in Baltimore. “Come back, and the cat and the plant will have changed, but the rock will essentially be the same,” he said.

Like a rock, most viruses would be fine if they were left indefinitely in a room, Adalja said. In addition, he noted that living beings have self-generated and self-sustaining actions — meaning they can seek out sustenance and behave in self-preserving ways. In other words, “they’re taking actions to further their lives, [such as] a plant sprouting its roots to find water or an animal looking for food,” Adalja said. More.

Dr. Adalja thinks that the fact that viruses can be inert like rocks until they come into contact with a living cell means that they do not “qualify as being alive.”

But wait. The rock cannot be “ert,” so to speak. The virus can be “ert” or inert. Does the ability to be inert for long periods – but suddenly “ert” when an opportunity beckons – show that the virus is not alive?

Anyway, can we be sure that all viruses fit this description? Only recently, we discovered giant viruses, for example. Did anyone predict them? What criteria are we sure they will follow? What rules are we sure they will keep?

This is one of those increasingly numerous situations where an open-ended discussion would serve us better just now than an attempt to enforce boundaries and rules.

Boundaries and rules are great when we know exactly what we are dealing with (think: ice hockey). Otherwise, they just add to the noise, as people rush to defend criteria nature doesn’t appear to have noticed.

See also: Phil Sci journal: Special section on understanding viruses

Why “evolution” is changing? Consider viruses

The Scientist asks, Should giant viruses be the fourth domain of life? Eukaryotes, prokaryotes, archaea… and viruses?

Viruses are alive.

and

Are viruses nature’s perfect machine? Or alive?

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Bees, the New York Times, and claims about “truth”

Vs. tailoring science news while claiming to be a neutral arbiter. From Jon Entine at Genetic Literacy Project, on the New York Times’ Oscar-worthy protestations that it presents “the truth:

Whether a journalist presents a story in good faith but wrongly can be a matter of healthy debate. But increasingly, a more troubling ethical line is being crossed: some writers choose to arrange facts, or even invent them, in ways that grey out nuances to advance a storyline arrived at before independent reporting even commences.

…

Two recent Times articles on the swirling farm controversy about bee health and food—one two years ago and another last week—raise serious questions about whether the paper’s editors are still wearing ideological blinders on stories involving ‘villainous’ agri-businesses.

In 1994, the Times wrote an editorial about “The Bee Crisis,” in which it noted an alarming 50% crash in feral bees in New York state. It blamed that primarily on pesticides. The next year, the phase out began of the most common pesticides—pyrethroids and organophosphates—used to protect crops pollinated by bees. While effective, these chemicals were known to kill beneficial insects and pose serious human health hazards.

They were replaced by what then and now were considered by most entomologists to be a far safer alternative—neonicotinoids, a class of insecticides whose introduction in the mid-1990s coincided with a stabilization of the global bee population. While sometimes sprayed for particular fruit, vegetable or landscape applications, the most overwhelmingly prevalent use of neonics is as a coating for seeds, which then grow into plants that systemically fight pests.

The bee health and pesticide issue faded from the headlines until the winter of 2006-2007, when some US beekeepers began discovering that many of their bees had mysteriously abandoned their colonies. The bees left behind the queen bee, attended by too few, immature worker bees to sustain the colony, yet with ample viable brood and stored food. This was dubbed Colony Collapse Disorder (CCD).

CCD is a periodic but still inexplicable ecological phenomenon that’s been around since at least the 1800s, predating the modern, post-World War II use of synthetic pesticides, says University of Maryland entomologist Dennis vanEngelsdorp, who along with agricultural department researcher Jeff Pettis coined the term a decade ago. vanEngelsdorp, now head of the Bee Informed Partnership, has told me and other reporters, repeatedly, that there have been no instances of CCD over the past five years except cases linked to the Nosema fungus.

But you wouldn’t know that if you depend on the Times as your paper of record. More.

Actually, fewer people every year regard the Times as a paper of record. That’s a feedback loop, really: The fewer the readers, the more of a group mindset the readers have and the more the paper will cater to it.

It’s unfortunate that ecology, despite its importance to us all, tends to attract secular doomsday crackpots. One wishes they would all get religion (an obscure Gaia project on a desert island is what we have in mind) and leave the management of ecologies to people with a more pragmatic, less apocalyptic mindset. People capable of balancing goals, for example.

Note: Curiously, a widespread superstition that persisted quite late into modern times held that one must tell bees about major events such as the death of a member of one’s household; otherwise, they would suddenly swarm away. This implies that bees sometimes departed for no apparent reason centuries ago, leaving people free to speculate as to whether they might have missed something without really knowing much about bees. There is lots we still don’t know.

See also: 2016 worst year ever for “fake physics”?

and

New York Times Markets The “Truth”

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The fact that the Times had to put this on YouTube helps us understand why their doom probably isn’t reversible:

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Origin of life requires “a privileged function?”

From Journal of Molecular Evolution:

ABSTRACT: A general framework for conventional models of the origin of life (OOL) is the specification of a ‘privileged function.’ A privileged function is an extant biological function that is excised from its biological context, elevated in importance over other functions, and transported back in time to a primitive chemical or geological environment. In RNA or Clay Worlds, the privileged function is replication. In Metabolism-First Worlds, the privileged function is metabolism. In Thermal Vent Worlds, the privileged function is energy harvesting from chemical gradients. In Membrane Worlds, the privileged function is compartmentalization. In evaluating these models, we consider the contents and properties of the Universal Gene Set of life, which is the set of orthologous genes conserved throughout the tree of life and found in every living system. We also consider the components and properties of the Molecular Toolbox of Life, which contains twenty amino acids, eight nucleotides, glucose, polypeptide, polynucleotide, and several other components. OOL models based on privileged functions necessarily depend on “takeovers” to transition from previous genetic and catalytic systems to the extant DNA/RNA/protein system, requiring replacement of one Molecular Toolbox with another and of one Universal Gene Set with another. The observed robustness and contents of the Toolbox of Life and the Universal Gene Set over the last 3.7 billion years are thought to be post hoc phenomena. Once the takeover processes are acknowledged and are reasonably considered, the privileged function models are seen to be extremely complex with low predictive power. These models require indeterminacy and plasticity of biological and chemical processes. (public access) – Lanier, K.A. & Williams, L.D. Journal of Molecular Evolution, articles in press: “The Origin of Life: Models and Data,” J Mol Evol (2017). doi:10.1007/s00239-017-9783-y More.

Let’s see: These “privileged” functions require “indeterminacy and plasticity of biological and chemical processes.” It sounds as though they require design.

Question: Would these subjects be easier to sort out if we just assume that the functions are designed and proceeded to investigate on that basis? As opposed to trying to figure out some way it all just sort of happened? Would it save time?

See also: Origin of life: We are all descended from a “complex” ancestor? In the biosphere we know, there was probably never any such thing as a “simple” cell, which is the likely reason the innumerable “it all comes down to” theories of the origin of life don’t work. But now, how can we research pre-Snowball Earth?

and

What we know and don’t know about the origin of life

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So Earth has a “unique” iron signature?

From Sciencedaily:

New research from The University of Texas at Austin reveals that the Earth’s unique iron composition isn’t linked to the formation of the planet’s core, calling into question a prevailing theory about the events that shaped our planet during its earliest years.

Lin said that one of the most popular theories to explain the Earth’s iron signature is that the relatively large size of the planet (compared with other rocky bodies in the solar system) created high pressure and high temperature conditions during core formation that made different proportions of heavy and light iron isotopes accumulate in the core and mantle. This resulted in a larger share of heavy iron isotopes bonding with elements that make up the rocky mantle, while lighter iron isotopes bonded together and with other trace metals to form the Earth’s core.

But when the research team used a diamond anvil to subject small samples of metal alloys and silicate rocks to core formation pressures, they not only found that the iron isotopes stayed put, but that the bonds between iron and other elements got stronger. Instead of breaking and rebonding with common mantle or core elements, the initial bond configuration got sturdier..

…

Lin said it will take more research to uncover the reason for the Earth’s unique iron signature, and that experiments that approximate early conditions on Earth will play a key role because rocks from the core are impossible to attain. Paper. (public access) – Jin Liu, Nicolas Dauphas, Mathieu Roskosz, Michael Y. Hu, Hong Yang, Wenli Bi, Jiyong Zhao, Esen E. Alp, Justin Y. Hu, Jung-Fu Lin. Iron isotopic fractionation between silicate mantle and metallic core at high pressure. Nature Communications, 2017; 8: 14377 DOI: 10.1038/ncomms14377More.

Hey, they’re probably not even rocks, right? Liquid, they say.

See also: Atheist cosmologist warns “deeply religious” people not to put their faith in “apparent” fine-tuning

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Do extinct Neanderthals control human gene expression?

Neanderthal/Photaro

From Andy Coghlan at New Scientist:

A study has now revealed how this genetic legacy is still controlling how some people’s genes work, with possible consequences for their health.

But note this:

Tellingly, the Neanderthal influence has waned fastest in parts of the body that evolved most rapidly around that time, especially the brain. It suggests that once our direct human ancestors had evolved the equipment for sophisticated language and problem-solving, mating with Neanderthals – and the DNA that came with it – rapidly fell out of fashion.

That’s a vast speculation based on minimal evidence about a subject on which we know very little, charitably put. The most reasonable explanation for what happened to the Neanderthals is that they were assimilated, mostly into the much more numerous western European population. But Darwinian evolution theory has always needed subhumans and so will always find them. If not in nature, then in speculation.

Popular Darwinism has always needed extermination stories too because that’s the philosophy. But assimilation is not necessarily forcible. The underlying problem is arithmetic: Members of the minority group enjoy a wider choice of partners if they assimilate than if they don’t. Time does most of the rest.

But Neanderthal control of human genes endures, some of it positive and some negative. Evidence comes from an in-depth analysis of DNA from 214 people in the US, focusing on individuals of European ancestry. By comparing their modern DNA with that from Neanderthals -– whose genome was sequenced in 2008 -– a team led by Joshua Akey at the University of Washington in Seattle was able to identify which Neanderthal gene fragments had survived and were still active in 52 different types of human tissue.

…

“Strikingly, we find that Neanderthal sequences present in living individuals are not silent remnants of hybridisation that occurred over 50,000 years ago, but have ongoing, widespread and measurable impacts on gene activity,” says Akey. More.

We have hardly begun to clear away the nonsense produced by previous generations of Darwinian thinking, upended by genetic studies. But the things we really learn might be quite valuable.

See also: New York Times: Why did we get the Neanderthals so wrong?

Neanderthal Man: The long-lost relative turns up again, this time with documents

and

A deep and abiding need for Neanderthals to be stupid. Why?

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Similarities Between the Debates Over Evolution and Global Warming

For years I have closely followed both the evolution debate and the global warming debate.*  There are some important differences between the two debates, which may be the subject of a subsequent post.  However, the number of similarities is striking.  Enough so that for some time I have seriously considered writing a book detailing the parallels.  I believe it would be highly instructive for many– particularly for those who accept the party line of one of the theories but not the other – to recognize the many similarities between the two debates.

Given the realities of other time commitments, however, I suspect my nascent efforts will never make it to publication before catastrophic global warming either fades with a whimper or results in our apocalyptic demise.

As a result, I offer this exceedingly more modest contribution.  A short collection of preliminary notes and observations, if you will.  If anyone wants to take these observations and turn them into a published tome, please feel free to do so.  All I ask is a simple acknowledgement and, at my treat, a chance to sit down over lunch to discuss the fruits of your labor.

One key caveat for this post:  This post is not primarily about the science.  Nor, as I mentioned above, is it about the differences.  This is primarily about the rhetorical, social, academic, and political similarities of the two debates – not the substance of detailed observations and mathematical calculations, but the underlying framework within which the debates take place.  As always, I am happy to discuss the science in detail, but that is for another thread and another time.

Some of the observations listed below may apply with slightly more force to one topic than the other, but the observation is still readily apparent in both debates, I believe.  If any of the stated observations are unclear, let me know and I will attempt to clarify.

Feel free to add additional observations of your own in the comments.

—–

Without further ado then, here is my bullet-point list of similarities between the evolution debate and the global warming debate – in some rough grouping, but in no particular order:

Approach to the Theory

Failure to clearly define terms and issues.  Imprecise language that shifts meaning as convenient to support the story.
Lack of clear, quantifiable predictions.
Sweeping generalizations about claimed effects, without careful analysis of detailed steps in the physical process that would be required to generate the claimed effect.
Contrary data ignored or re-framed as supporting “evidence” through ad hoc adjustments to the theory.
Heavy reliance on models, instead of real field work.  [Note: Much more problematic in the global warming context, although in the evolution context there is heavy reliance on made-up stories**.]

Behavior of Supporters

Repeated and vociferous claims of “consensus”.
Often refusal to engage in open debate.  Claim that there is no debate, or that the science is already “settled”.
Lack of openness regarding data, assumptions, and the source of conclusions.  [Note: The actual hiding of data and refusal to share with the broader community seems to be much more prevalent in the global warming context.]
Attempts to label skeptics of the theory as “deniers” and as “anti-science”.
Aggressive attempts to prevent opponents from being published; pressure on journal editors and reviewers.
Career protectionism.  Attempts to get skeptics fired, banned, or ostracized.
Vindictive, spiteful, personal attacks, instead of reasoned argumentation.
Bad acting on the part of scientists; inappropriate emails; threats; etc.  [Note: Behavior that actually rises to the level of criminal activity (e.g., stealing board materials, property damage) is more prevalent in the global warming context.]

Socio-Political Aspects

Attempts to protect arguments by academic institutional proclamations, by court cases, by governmental fiat.
Attempts to claim the “scientific” side of the debate and to assert that skeptics are motivated by religious or other non-scientific motives.
Small cabal of outspoken propagandists pushing an agenda, coupled with general silence by the majority of scientists in the field, in some cases due to intimidation or fear of rocking the boat.
High-level political and institutional support, while lacking broad grass-roots support.  This reflects a top-down, “we know best” attitude by politicians and academicians.
Largely the field of academics and lobbyists.  Little practical real-world relevance.  However, strong ideological relevance.
Extensive funding of the consensus side to the tune of many billions of dollars, versus a ragtag bunch of largely self-funded individuals and small organizations on the skeptical side.

—–

Now, skeptics of the theories are not immune to negative behavior either.  Here is a list of some similarities I have observed on the skeptical sides:

Behavior of Opponents

Failure to carefully parse the theory to determine which aspects are supported by the evidence and which are not; tendency to lump everything into a single bucket and dismiss the entire topic.
Assertions that supporters are motivated by anti-religious or cultural-political motives.
Knee-jerk reactions against every aspect of the theory, due to prior bad experiences or assumed motives.
Occasional contrary claims that, similarly, lack evidentiary support.  [Note: This tendency seems to be more prevalent in the global warming context, particularly when discussing negative impacts.]
Tendency to frame the debate into a larger narrative about class dominance, government oppression, or the like.

—–

The number of similarities between the two debates is indeed striking and should provide food for thought — particularly for those who may be skeptical about one of the theories and not the other.

 

Footnotes:

*  The now-popular term “climate change” is really about global warming, the underlying premise being that a rise in the atmospheric concentration of carbon dioxide will cause an increase in the global average temperature.  It is important to keep our eye on this ball when discussing the science and not get misled by the vague term “climate change.”

**  Note again for the record that we are talking about the theory of evolution, not basic biology.  There is a tremendous amount of excellent work being done in the field of biology.  Where evolutionary theory claims relevance is in trying to provide a historical explanation for how biological systems came about and, occasionally, attempting to propose a particular prediction.

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Frog species much younger than thought?

female horned frog, part of “species complex” /Systematics Lab

From ScienceDaily:

These new results indicate that the Asian Horned Frogs family may have originated as recently as 77 million years ago in contrast to 100-126 mya as previously estimated, and suggest that scientists might have been also overestimating the age of many other families of frogs by up to 35%.

The results have completely changed our understanding of how the different Asian Horned Frog species and their species groups are related. Many of the species that look similar, and so were considered to be closely related, were found to be distant relatives of each other, and those that look different were found to be closely related. Paper. (public access) – Stephen Mahony, Nicole M. Foley, S.D. Biju, Emma C. Teeling. Evolutionary History of the Asian Horned Frogs (Megophryinae): Integrative Approaches to Timetree Dating in the Absence of a Fossil Record. Molecular Biology and Evolution, 2017; msw267 DOI: 10.1093/molbev/msw267 More.

Of course, the concept of speciation is in fine shape, right? Always is. No matter what.

See also: Big squawks over bird speciation? Speciation is the Holy Grail of Darwinian evolution. To find an example in action is to find something spectacular.

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Now not 7 but 47 mRNA start codons?!

570% more mRNA start codons have been discovered – with differing expression probability!

Does this reveal another dimension in design of expression rate control?

‘Start Codons’ in DNA and RNA May Be More Numerous Than Previously Thought NIST Feb. 21, 2017

A central principle regarding translation has long held that only a small number of three-letter sequences in mRNA, known as start codons, could trigger the production of proteins. . . . “What if the results indicated that codons didn’t fit a traditional description of start or not, but instead had varying likelihoods to start translation?” . . .“We thought we knew the rules, but it turns out there’s a whole other level we need to learn about. The grammar of DNA might be even more sophisticated than we imagined. . . .“It could be that all codons could be start codons,” Hecht said. “I think it is just a matter of being able to measure them at the right level.”

Measurements of translation initiation from all 64 codons in E. coli

Ariel Hecht Jeff Glasgow Paul R. Jaschke Lukmaan A. Bawazer Matthew S. Munson Jennifer R. Cochran Drew Endy Marc Salit, Nucleic Acids Res gkx070. DOI: https://doi.org/10.1093/nar/gkx070, Published: 21 February 2017

ABSTRACT

Our understanding of translation underpins our capacity to engineer living systems. The canonical start codon (AUG) and a few near-cognates (GUG, UUG) are considered as the ‘start codons’ for translation initiation in Escherichia coli. Translation is typically not thought to initiate from the 61 remaining codons. Here, we quantified translation initiation of green fluorescent protein and nanoluciferase in E. coli from all 64 triplet codons and across a range of DNA copy number. We detected initiation of protein synthesis above measurement background for 47 codons. Translation from non-canonical start codons ranged from 0.007 to 3% relative to translation from AUG. Translation from 17 non-AUG codons exceeded the highest reported rates of non-cognate codon recognition. Translation initiation from non-canonical start codons may contribute to the synthesis of peptides in both natural and synthetic biological systems.

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