The new wild west?

Mass Human Cloning May Soon Be Upon Us
Wesley J. Smith

Human cloning has been accomplished, but the field remains generally stalled because of a shortage of human eggs — one needed per cloning attempt — and eggs for use in research are hard to come by.


That impediment may soon be overcome. Scientists have changed human blood cells into immature egg cells. The next steps should go even farther, eventually allowing for the eventual mass lab-creation of eggs capable of being fertilized or used in cloning.. From the Motherboard story:

The eggs produced by [Mitinori] Saitou and his colleagues are far too immature to be fertilized, much less grow into a human child. Still, they open the door for babies made from the genetic material of relatives, dead or alive. They could also provide a way for infertile people or same-sex partners to produce a child made from their own DNA.


The next step, according to the researchers, is to apply a similar process to the production of human sperm and to create egg cells that are mature enough to be fertilized. This will not only require a lot more research, but creating viable human eggs in a lab is also sure to be incredibly controversial.

Ya think?

And Here’s the Thing

It isn’t just eggs and cloning. Biotechnology researchers are creating the most powerful technologies invented since the splitting of the atom. For example:

CRISPR allows any cell or life form to be genetically engineered, potentially used in life-saving genetic therapies or the unleashing of a genetically altered viral pandemic.
Three parent embryos are being created in labs to be brought to birth.
Artificial life forms are being created with no predicate in creation or evolution.
Researchers are putting human stem cells into mouse brains and making other forms of chimeric lab animals.
The list goes on and on.


Yet, there are few concerted national and international discussions outside the research community to find ways to govern these experiments or to draw firm boundary lines. Indeed, other than some government funding restrictions, scientists are generally ethically bound only by their own consciences. That is unacceptable.

Missing: A Systematic Ethical Conversation

George W. Bush’s President’s Council on Bioethics attempted to carry on a systematic ethical conversation about these crucial issues. But the Council was roundly attacked in the media and among mainstream bioethicists for daring to have a conservative perspective and, as a consequence, much of its intellectually sterling work is too often ignored.

Time and scientists wait for no one! Yet our leaders dither. There is no serious discussion that I can discern within the current Administration about gathering a bioethics/biotechnology advisory council together.

We need a robust societal debate, led, I believe, by a council with members holding various, even conflicting, ethical and political perspectives — I call it a populist bioethics council — to duke it out publicly. Nothing attracts media attention or public interest like a good policy donnybrook, out of which we can hope to achieve at least some policy and societal consensuses.


It’s time to focus! Anything goes, or leaving our biotechnological future “up to the experts,” is not a wise or sustainable approach.

A clash of Titans.LXXVI

Bad design or bad logic?

Critic of Intelligent Design Acknowledges: “Bad Design” Arguments Don’t Work
David Klinghoffer | @d_klinghoffer

It’s good to be able to report progress. Nathan Lents, whose name you’re probably tired of hearing, wrote a Wall Street Journal article and a whole book

themed on the idea of “poor design” in the human body. In the book, he included one section about the sinuses and their supposedly “suboptimal design” (pp. 8-13). Lents is a biologist and college professor who, to judge from the language he used in fighting this out with us, apparently didn’t know some basic terminology about the anatomy of the sinuses.

Writing here, here, here, and here,neuroscientist Michael Egnor responded to Lents on a range of topics, which to me seemed like a proper job of “shellacking” Professor Lents, as I wrote in a tweet. Lents was still smarting about that when he agreed to participate in a forum at the Peaceful Science blog administered by computational biologist Josh Swamidass. To make a long story short, Lents accused Egnor of making an elementary error and refusing to acknowledge it. But But Evolution News demonstrated that it was Lents, not Egnor, who was wrong. It was not a matter of opinion or interpretation.

A Mere Quibble?

Now Swamidass, a prominent critic of intelligent design, acknowledges as much. See, “Who Is Right About Sinuses?” So does Lents, while nevertheless brushing off the whole matter as a quibble over terminology: “They did correctly [point] out one mistake I made in terminology, which they make a huge deal out of, and which I have corrected in the text below.” So when he thought he had caught an unacknowledged error on our end, it was a big deal. Now, it’s not. Hey, why fuss about a bit of mistaken terminology? Well, it wasn’t anyone around here who wrote a section of a book, asserting the poor design of the human sinuses, only to have it shown that we didn’t understand that “the maxillary sinus is in fact one of the paranasal sinuses.”

A small point? You decide. But this is interesting. As Swamidass notes, the argument from “bad design” is commonplace, however as he goes on to say, it’s also invalid.

    Though it is not the focus or precise argument of his book, Dr. Lents is often making a “bad design” argument for evolution. This is a common argument offered to support evolution, and Dr. Lents is certainly not the first to make it.

Having recognized that Dr. Lents holds to a very common view, I confess that I do not personally think the bad design argument is valid. In my view, it mistakes the quirks and “seams” in our body as errors, and makes a theological argument that extends beyond science. In contrast with the bad design argument, I prefer to insist science remain neutral and silent on theological arguments such as these, and see these quirks as biological mysteries that often reveal evidence of common descent, and non-intuitive details of how our bodies work. I know I may be in the minority among biologists in disputing the bad design argument, but I hope that could shift in the future. Nothing intrinsic to evolutionary science requires us to make those arguments. 

     Very good — I like the language about “seams.” I am looking right now at the sweater I’m wearing, and it too has “seams” while at the same time reflecting someone’s intelligent design. Thank you, Dr. Swamidass!

Swamidass adds, “Though the acrimony is not necessary, it is not surprising. These are the grand questions we are facing, and they are important.” Yes, they are both grand and important. Speaking only for myself, though, I think the reason for the “acrimony” is that ID scientists are routinely misrepresented, to malign, dismiss, and often to harm them professionally. This pressure to conform or be punished comes from both named opponents and unnamed ones (e.g., Wikipedia editors). Evolutionists face no parallel dynamic.

I do not like to see that happen to respected colleagues. Using the medium we have available to us to forcefully resist these efforts is not only “not surprising.” It’s the correct thing to do.

    

National insecurity?:Pros and cons.

More on lady justice broken scales.

The universe finetuned for furries?

Was Universe Designed for Hairy-Nosed Wombats?
David Klinghoffer | @d_klinghoffer

Professor David Barash of the University of Washington is an evolutionary biologist known for delivering a yearly talk to his students disabusing them of the idea that science can reasonably be reconciled with religious faith. He boasted about this in the New York Times. He calls it The Talk.

Writing today over at Aeon, he offers an essay on “Anthropic arrogance,” arguing that, “Claims that the Universe is designed for humans raise far more troubling questions than they can possibly answer.” He begins by cracking wise.

Welcome to the ‘anthropic principle’, a kind of Goldilocks phenomenon or ‘intelligent design’ for the whole Universe. It’s easy to describe, but difficult to categorise: it might be a scientific question, a philosophical concept, a religious argument — or some combination. The anthropic principle holds that if such phenomena as the gravitational constant, the exact electric charge on the proton, the mass of electrons and neutrons, and a number of other deep characteristics of the Universe differed at all, human life would be impossible. According to its proponents, the Universe is fine-tuned for human life.

This raises more than a few questions. For one, who was the presumed cosmic dial-twiddler? (Obvious answer, for those so inclined: God.) Second, what’s the basis for presuming that the key physical constants in such a Universe have been fine-tuned for us and not to ultimately give rise to the hairy-nosed wombats of Australia, or maybe the bacteria and viruses that outnumber us by many orders of magnitude? In Douglas Adams’s antic novel The Hitchhiker’s Guide to the Galaxy (1979), mice are ‘hyper-intelligent pan-dimensional beings’ who are responsible for the creation of the Earth. What if the Universe isn’t so much anthropic as mouse-thropic, and the appearance and proliferation of Homo sapiens was an unanticipated side effect, a ‘collateral benefit’?

Did I say he cracks “wise”? Wrong word.

A Puerile Challenge

This is well-timed because Ann Gauger’s beautiful essay this morning, “Beyond Adapation: The Human Brain Is Something New,” answers the puerile challenge very nicely. In a universe “designed” for mice or hairy-nosed wombats (which, by the way, are a lot cuter than they sound) it would be mice or wombats writing poetry by Elizabeth Barrett Browning.

The human brain, whether you believe it channels the soul or not, is undoubtedly unique in the world of life.

With our brains we write music, dance the ballet, paint landscapes, play chess, and do theoretical physics. We send men to the moon and then bring them back. We contemplate our origin, what and who we are, and give thanks. Non-human primates [like wombats and mice] don’t do these things. Furthermore, these abilities far exceed what is needed for survival, and at least in the case of theoretical physics and traveling to the moon, are not useful for finding true love. The verdict on chess is still out.

The key point that Gauger makes is that of all the exceptional things that humans can do with our minds, the most exceptional are not explained by adaptation, and so can’t be explained by the evolutionary biology that Dr. Barash teaches. 

Yes, “bacteria and viruses…outnumber us by many orders of magnitude,” but I’m not able to see the sense or wisdom in privileging sheer numbers as a mark of cosmic significance over, for example, the utterly exceptional ability — unique in the universe, as far as we know — of a human being to say and mean, “Thank you.”

Nature's navigators v. Darwin.

Marvelous Migrations at All Scales
Evolution News | @DiscoveryCSC

Think of the simple reasons for animals to migrate back and forth from one area to another. They might need to look for food. They might need to get away from cold or heat as the seasons change. They might want to get away from predators or parasites. If any of these were universal natural laws, though, we wouldn’t find so many exceptions.

Picture the bison in Yellowstone suffering through some of the harshest winters in America, yet enduring hot August days in their shaggy coats as tourists snap pictures. The swans stay, but the sandhill cranes migrate. The coyotes and rabbits stay, while their fellow mammals, the elk and deer, migrate off the plateau in winter. Some crows migrate, but others do not. Is there a design story in this mixture of phenomena?

As we recently shared in a post about a European bird, technology is opening new windows on animal migratory habits that were never before possible. Let’s begin by looking at a few of the more spectacular examples of animal Olympians:

Homing pigeons can find home when released from an unfamiliar location.

The bar-tailed godwit, a shore bird, can fly 11,000 km, the longest known example of non-stop flapping flight.

The globe skimmer dragonfly completes a 15,000 km circuit in four generations.

Monarch butterflies cover 9,000 km in four generations; painted lady butterflies fly almost 10,000 km from England to Africa and back.

15 million free-tailed bats migrate up to 1,500 km each year between Mexico and the US.

Zebras make the longest walking migration in Africa: 500 km (longer than wildebeest circuits).

The arctic tern flies from pole to pole each year, a circuit of 50,000 km.

Sea turtle hatchlings can find their nesting beach after 30 years away. Loggerhead turtles cross the entire Pacific from Australia to South America.

Whales, tunas, eels and turtles cross ocean basins during their life cycles.

The greatest biomass movement on earth is the daily swimming up and down in the water column of billions of planktonic animals. (Cyrus Martin, Current Biology) 

That’s a lot of targeted motion! Migrating animals come in all sizes, from the mightiest whales to the smallest copepods in ocean plankton. Even bacteria can cover relatively large distances with their flagella.

In September, Current Biology published a special issue on migration. Migrating animals appear in a wide variety of animal groups:

Vertebrates: salmon, eels, tunas, sea turtles, numerous bird species, wildebeest, zebra, deer, bats, whales

Arthropods: butterflies, moths, dragonflies

Crustaceans: copepods and other zooplankton

Plants: the seeds of plants can “migrate” through air and water, sometimes crossing oceans. It’s a fascinating topic, but this article will focus mainly on animal migration

Mechanisms for navigation are also very diverse. Bees and flies use a sun compass. Salmon and sea turtles guide by the earth’s magnetic field and also use olfaction. Dung beetles navigate at night by the Milky Way Current Biology.Birds use landmarks, sun angles and stars, and olfactory cues. Mammals and birds can “follow the leader,” staying with an individual that has made the trip before. Whales may use infrasound. Animals coordinate the external cues with their internal circadian clock; for instance, monarch butterflies time their migrations to the angle of the sun. Some animals, like birds and eels, migrate in massive flocks; others, like sea turtles, go it alone but end up together at the same places.

Involves or Evolves

Kenneth Lohmann, an expert on sea turtles, notes that long-distance migration “involves considerable costs in terms of energy and risk. Thus, for such behavior to evolve, the benefits must be high.” Even if a large benefit were easily discernible, though, Darwinians face high hurdles explaining particular cases:

Different species that are closely related evolutionarily, and sometimes even different populations of the same species, exhibit very different scales and patterns of migration. Much of this variation is under genetic control, but the genes involved are largely unknown. A new and burgeoning field of migration research seeks to unravel the genetic architecture of migration. This is challenging because migration involves a complex, interrelated suite of physiological, morphological and behavioral traits that are mediated by an inherited ‘migratory gene package’, which in turn can be viewed as part of a ‘migratory syndrome’

Some aspects of migration appear to be genetically inherited, because Pacific golden plover chicks can find the Hawaiian islands from Alaska over the trackless ocean, and butterflies can find the same trees their great-grandparents did, never having flown there before. The fact that sea turtles can find their feeding grounds as hatchlings implies they are born with an inherited genetic map. But routes can also adapt quickly to changes in the environment. Lohmann points out two cases of rapid alteration of inherited maps:

Migratory adaptations arise and vanish rapidly. For example, monarch butterflies were introduced into Australia only about a century ago, but now have a migration in which the timing and direction are altered by 6 months and 180° relative to the North American population from which they presumably descended Another interesting example involves the central European population of a migratory bird, the blackcap (Sylvia atricapilla), which evolved a new migration route to the British Isles in only three decades. The direction of first migration appears to be encoded by at most a few genes and the new route appears to be based on a novel, genetically programmed orientation preference that is spreading rapidly through the population.

Evolution: Explanation or Assumption?

Most of the articles in this special edition of Current Biology invoke the phrase “has evolved” as a magic wand, never explaining how things evolved. Other than asserting that migration “has evolved repeatedly in numerous species occupying diverse ecological niches,” Lohmann has little to say about evolution. Migration might keep parasites from evolving more virulent forms, he says, and might increase the health of the migrating population; but other than those suggestions, he offers no explanation for the origin of precision mechanisms that make migration possible: celestial navigation hardware and software, olfactory organs with accuracies of parts per trillion, and sensors that can detect the intensity and angle of the earth’s magnetic field lines. Merely possessing the equipment, though, would never provide an advantage for animals physically incapable of long distance travel. Evolution needs to explain the whole animal as a migration-capable machine.

In their article on “The Ecology of Migration,” Alerstam and Bäckman agree that migration offers various “selective advantages” to animals, “like exploitation of seasonal and ephemeral resources, and avoidance of predators, diseases and competitors.” But a potential selective advantage does not create the tools to exploit it. Instant long-distance communication across the globe could be called an advantage to humans, but would that account for the emergence of the iPhone? The authors say that populations that migrate reproduce better than those that don’t, but they fail to explain how magnetic maps and olfactory systems as sensitive as those in Pacific salmon came to be.

The Closest Attempt

The closest attempt to invoke a neo-Darwinian explanation for any aspect of animal migration can be seen in Reppert and de Roode’s entry, “Demystifying Monarch Butterfly Migration.” Those who remember Illustra’s film Metamorphosis, with its multiple challenges to Darwinism, will want to watch this show! Reppert and de Roode link specific mutations with selective advantages:

Monarchs have become a textbook example of warning coloration and plant-derived toxicity to predators. Monarch larvae sequester cardenolides from their milkweed diet, and broadcast their toxicity through the black, white and yellow stripes in larvae, and the bright orange marked with black and white accents in adults. Classical studies have demonstrated that avian predators quickly learn to associate the bright colors with bitter taste and emesis, leading to prey avoidance.

Cardenolides exert their toxic effects in most animals by interfering with the Na+/K+-ATPase sodium pumps, but monarchs and other milkweed specialists have mutations that reduce cardenolide binding. Evolution of cardenolide insensitivity evolved in a step-wise manner during the macroevolution of milkweed butterflies, with monarchs having at least two non-conservative mutations that strongly reduce their sensitivity to cardenolides…

The high level of resistance to cardenolides allows monarchs not only to feed on milkweeds, but also to sequester cardenolides for their own defenses. Although the sequestration of cardenolides by monarchs has been mostly studied in the context of predation, recent studies suggest that these toxins also provide protection against infection with a virulent protozoan parasite…. Monarchs reared on milkweed species with higher concentrations of heart-arresting cardenolides experience lower infection rate, less parasite growth and fewer disease symptoms than those reared on milkweeds with lower concentrations. Furthermore, when given a dual choice between milkweeds that vary in their anti-parasitic effects, infected female monarchs prefer to lay their eggs on the anti-parasitic species…, thereby reducing infection and disease symptoms in their offspring. These studies have also shown that despite their high level of insensitivity, monarchs are not fully resistant to cardenolides, with highly toxic cardenolides reducing adult monarch lifespan.

That’s it. In the whole series of articles, that is the closest that any author comes to an actual neo-Darwinian explanation for any trait in any species, other than to tell us, over and over, that everything “has evolved.” But notice: this example says nothing about navigation or migration itself. It only talks about how mutations in the butterfly allow it to ingest cardenolides without dying of heart attacks. And they got this ability by breaking things: breaking the binding link that makes the toxin interfere with the sodium pump. That may protect them from birds, but doesn’t account for the origin of the time-compensated sun compass, the inherited map, and the ability to fly unerringly 3,000 miles to the exact trees where their ancestors roosted three generations back.

Design advocates agree that the innate mechanisms for migration can adapt to changing environments, as shown in the Australian monarch butterflies. You can call that “evolution” in a limited microevolutionary sense. But in the only cases we know of where navigation equipment and the ability to use it came into being, it was designed by intelligent minds. Try telling our ace fighter pilots or ship captains that the radar instruments that allow them to go far afield and back again “have evolved” simply because they possess a “selective advantage.” If their routes change, they will most likely tell you that the capability to modify routes is built into the system.

And still yet further continuing to rethink the unrethinkable.

On staying alert in the marketplace

Introducing the Richards Scale – Your Tool for Evaluating Grounds for Science Skepticism
David Klinghoffer | @d_klinghoffer

Writing at the NPR science blog 13.7, U.C. Berkeley psychology professor Tania Lombrozo is concerned about “skepticism.”

Calling someone a “skeptic” can be a term of praise or condemnation.
That is true, and interesting. When is skepticism appropriate, and when not? Sometimes it’s an easy call. Hearing that someone doubts the moon landing, for example, and thinks it’s some sort of U.S. government conspiracy, I would rapidly lose interest in whatever he had to say after that. Where do you draw the line, though?

Lombrozo says of herself, “I might praise skepticism towards homeopathic medicine, but disdain skepticism towards human evolution.” “Disdain” is a strong word, and a telling one.

To skepticism, she prefers “truth-tracking and humility.”

Truth-tracking is about getting things right: identifying the signal amidst the noise. We don’t want to be fooled by noise (about a link between vaccines and autism, for example), but we also don’t want to miss out on signal (about the real benefits of vaccination). Truth-tracking isn’t (only) about rejecting noise, but about differentiating signal from noise.

Humility is about recognizing the possibility for error, and therefore holding beliefs tentatively (or “defeasibly“). But recognizing uncertainty doesn’t mean that all bets are off. Some bets are still much better than other bets. You don’t know who will win the next horserace, for example, but that doesn’t mean that you’d assign equal probabilities to all contenders. Similarly, we can quantify uncertainty by assigning degrees of belief to different propositions. I might think that life on other planets is unlikely, and that ESP is unlikely, yet assign a much higher probability to the former than to the latter. Similarly, I might think that rain tomorrow and human evolution are highly likely, but assign a much higher probability to the latter than to the former.
“Getting things right,” and “recognizing the possibility for error.” That’s very nice. We should all strive for both…but they’re a bit vague for practical implementation. Where would those virtues leave you, confronted with the question of, for instance, the scientific “consensus” on Darwinian evolution?

Speaking at the Heritage Foundation recently, Discovery Institute Senior Fellow Jay Richards addressed the topic, offering a much more practical set of guidelines for deciding when doubt is in order. It’s a new podcast episode of ID the Future.  Listen to it here, or download it here.

Dr. Richards, who leads the excellent news site The Stream, has 12 triggers for your skepticism. Think twice about a “proposed consensus”:

“When different claims get bundled together”
“When ad hominem attacks against dissenters predominate”
“When scientists are pressured to toe the party line”
“When publishing and peer review in the discipline is cliquish”
“When dissenters are excluded from the peer-reviewed journals not because of weak evidence or bad arguments but to marginalize them”
“When the actual peer-reviewed literature is misrepresented”
“When consensus is declared before it even exists”
“When the subject matter seems, by its nature, to resist consensus”
“When ‘scientists say’ or ‘science says’ is a common locution”
“When it is being used to justify dramatic political or economic policies”
“When the ‘consensus’ is maintained by an army of water-carrying journalists who defend it with partisan zeal, and seem intent on helping certain scientists with their messaging rather than reporting on the field as fairly as possible”
“When we keep being told that there’s a scientific consensus”
He elaborates on these further, here. I love this as a practical tool for the citizen and science consumer. In fact, with a tip of the hat to Jay, I would propose a scale for quantifying grounds for skepticism – the Richards Scale. For any controversial scientific claim, you count up the clicks on those 12 reasons for doubt, giving you a number between 1 and 12. An idea could register, for example, 3 or 4 on the Richards Scale – prompting mild doubt – or an 11 or 12 – where something fishy is almost certainly going on.

Richards observes:

There’s always this crank somewhere available immediately online that doubts any particular scientific idea, and so the fact that there’s skeptics is not itself an argument against the proposed consensus.
Right, and one does not want to be that crank. Which is why, as he says, you need to examine the sociological dynamics underlying the “consensus.” Tania Lombrozo with her “disdain” for doubts about evolution doesn’t help much with that. The Richards Scale does!

Yet more explaining (away?) of discontinuity in the history of life.

Still More Excuses for Cambrian Non-Evolution
Evolution News | @DiscoveryCSC

Physical Foundations of Biological Complexity

A non-typical, out-of-the-box thinker, Eugene Koonin is often fun to read, at least compared to the typical Darwin apologist. With two co-authors in  PNAS last month, the evolutionary biologist set out to explore “The Foundations of Biological Complexity.” His topic is broader than the Cambrian explosion, but entails it. 

Living organisms are characterized by a degree of hierarchical complexity that appears to be inaccessible to even the most complex inanimate objects. Routes and patterns of the evolution of complexity are poorly understood. We propose a general conceptual framework for emergence of complexity through competing interactions and frustrated states similar to those that yield patterns in striped glasses and cause self-organized criticality. We show that biological evolution is replete with competing interactions and frustration that, in particular, drive major transitions in evolution. The key distinction between biological and nonbiological systems seems to be the existence of long-term digital memory and phenotype-to-genotype feedback in living matter.

Design advocates may wish to look more deeply into Koonin’s paper, but after you simplify the jargon and restate the basic ideas, he seems to be saying that biological matter is just a special case of non-biological matter with memory. As for “competing interactions and frustration,” is that like squeezing long balloons so that a dog shape pops out? Surely there must be more to the “emergence of complexity” than this! Even if the long balloon can remember what happened in the previous “frustrated” state, you won’t get trilobites this way.

Biological systems reach hierarchical complexity that has no counterpart outside the realm of biology. Undoubtedly, biological entities obey the fundamental physical laws. Can today’s physics provide an explanatory framework for understanding the evolution of biological complexity? We argue that the physical foundation for understanding the origin and evolution of complexity can be gleaned at the interface between the theory of frustrated states resulting in pattern formation in glass-like media and the theory of self-organized criticality (SOC) .… We unify these two faces of SOC by showing that emergence of complex features in biological evolution typically, if not always, is triggered by frustration that is caused by competing interactions at different organizational levels. Such competing interactions lead to SOC, which represents the optimal conditions for the emergence of complexity. Competing interactions and frustrated states permeate biology at all organizational levels and are tightly linked to the ubiquitous competition for limiting resources. This perspective extends from the comparatively simple phenomena occurring in glasses to large-scale events of biological evolution, such as major evolutionary transitions. Frustration caused by competing interactions in multidimensional systems could be the general driving force behind the emergence of complexity, within and beyond the domain of biology.

“Competition for limiting resources” sounds a bit Malthusian. But does competition really “drive” innovation like a physical “force”? Extinction seems an easier way out. As for SOC, If biological systems are “nothing but” physical systems, we should see trilobites emerge from molten metal as it hardens, or from the Mandelbrot set. Koonin and his friends admit that the kind of self-organizing and fractal patterns which can emerge in non-biological systems don’t qualify:

However, contrary to some general statements, there is more to the evolution of complexity than SOC. Importantly, SOC does not lead to hierarchical complexity: Fractal patterns produced by SOC are not genuinely complex because, by definition, they appear the same at all spatial and/or temporal scales.

Try as he might to make biology a special case of physics, Koonin cannot get hierarchical complexity (the “functional wholes” Doug Axe writes about in Undeniable), by the mere operation of fundamental physical laws. The missing ingredient is information from an intelligent source. Only that is able to use physical laws to organize matter for functional ends. Specialists may wish to investigate other ideas in the paper for their philosophical entertainment value. In the final analysis, though, Koonin and friends confess, “the level of complexity and elaboration characteristic of living things is unmatched by anything outside biology.” So what has this paper contributed to understanding the Cambrian explosion and all the other explosions(Bechly, “which are the rule”) from the origin of life till now? Nothing. Frustrating, indeed.

What Does It Mean to Be an Animal?

One last idea comes from a “technology feature” in the Nature journal Lab Animal.In her essay “What is a lab animal,” Ellen P. Neff complains that researchers tend to have a “bilaterian-biased” perspective of animal life. She recommends that biologists consider three very different phyla to answer her opening question, “What does it mean to be an animal?” Those phyla would be:

 placozoans, ctenophores, and sponges. Each of them dates back to the Cambrian.

  Neff describes many of the peculiarities of these creatures that make them just as interesting as lab rats. You can’t model animals without covering these very distinct groups, she argues, even though they share many of the same genes of the familiar model animals.

    The communities studying these three phyla are small and no sponge, ctenophore, or placozoan may ever dethrone the traditional models like the mouse, but putting the time and effort into working with less traditional animals has its place. “We need to keep that breadth, and it’s sort of jolting,” says Leys. “It helps people understand things that are not always typical in mammalian systems.”

    The three phyla each have living representatives, which she says have “continued to evolve solutions to life on Earth.” That diversification of these body plans has continued, nobody disputes. The question Neff avoids is how they came to be in the first place.

If we could interrupt Darwinians every time they say a biological phenomenon “has evolved,” and ask how it evolved, debate about the Cambrian explosion would consist of a series of long pauses. But since journals refuse to give voice to Darwin skeptics due to the arbitrary rule of methodological naturalism, the Darwinians continue to get away with non-answers to the origin of hierarchical complexity. Meanwhile, the trilobites look up silently from their Burgess Shale rock slabs, with sad eyes, asking, “Where did I come from?”

File under "Well said." LX

Proverbs10:3 ASV "Jehovah will not suffer the soul of the righteous to famish; But he thrusteth away the desire of the wicked."

When lady Justice's scales malfunction.

Researchers: More than 2,000 false convictions in past 23 years

NBC News:

In 1984, two North Carolina girls, age 4 and 6, were molested. They told police their abuser was Sylvester Smith, who was dating the mother of one of the girls, and he went to prison for the crime. 

Twenty years later, the victims recanted, saying their grandmother told them to blame Smith, and his conviction was overturned.

But the person they say who really molested them -- their cousin, who was nine at the time -- could not be prosecuted because he was under age at the time of the alleged crime. He is, however, serving a life sentence for another crime he committed in the meantime: murder.



Smith's case illustrates the fallout from false convictions: He lost roughly 20 years of his life to prison, while the alleged perpetrator was free to commit other crimes.

Smith's discarded conviction is one of nearly 900 such cases filed in the National Registry of Exonerations, a database of prisoners exonerated in the U.S. of serious crimes since 1989, that was made public on Monday. To qualify as an "exoneree," an individual must have been convicted and later relieved of all the legal consequences.

In compiling the database, researchers became aware of more than 1,100 other cases in which convictions were overturned due to 13 separate police corruption scandals, most of which involved the planting of drugs or guns on innocent defendants. Those exonerations are not included in the registry. 
  ExonerationRegistry.org is the largest database of its kind ever assembled, according to its creators from the University of Michigan Law School and the Center on Wrongful Convictions at Northwestern University School of Law. Nonetheless, researchers are not able to say what percentage of convictions in the U.S. are false, in part because it can take so long for new evidence to come to light. There are currently about 2.5 million people in prison in the United States.

The earliest cases in the database date back to 1989, when DNA evidence freed its first two prisoners.

"We can figure that as sort of the modern period in exonerations because DNA was a big game-changer," said University of Michigan Law Professor Samuel Gross, one of the registry's creators. "It provided a scientific instrument for reviewing cases and providing a different type of evidence about those cases because the technology didn't exist."

But DNA doesn't actually account for the majority of the exonerations in the database, after an initial wave in the early 1990s, he said.

"DNA is a fairly narrow-gauged tool. It only fits particular type of crimes," Gross said, noting that only 37 percent of the people in the database were cleared with the help of DNA evidence. "In the public mind, exoneration became identified with DNA... Most of these cases -- DNA and non-DNA -- everybody agrees there was a mistake; frequently because the criminal was caught, often because we agree there was no crime at all."

Gross co-authored a report on the database that pulls together statistics on exonerations from January 1989 through February 2012. While the database is constantly updated and new exonerations are being added all the time, the report focuses on the 873 individuals whose cases had been filed before March. 

Gross and his report co-author, University of Michigan law school graduate Michael Shaffer, discovered correlations in the types of crimes and reasons for wrongful convictions.

Fabricated crimes. False convictions in child sex abuse cases were usually due to fabricated crimes; sometimes a divorced parent told a child to make up lies about an ex-spouse abusing them, or police or a therapist convinced a child to say something that wasn't true.
Eyewitness mistakes. In adult rape cases, for example, false convictions were typically based on eyewitness mistakes, "more often than not, mistakes by white victims falsely identifying black defendants," the report said.
Misconduct by authorities. For homicides, misconduct by authorities was the second-biggest cause of false convictions, just behind false eyewitness accounts.
Eyewitnesses are crucial to a trial, experts say, and their mistakes, whether intentional or not, can have a huge impact.

"The bulk of the evidence that is presented in trials in human testimony. Almost all of the time, energy, and effort is spent hearing people's statement in what occurred at a different place and a different time," Dan Simon, a professor of law and psychology at USC, said. "The bottom line is, people are often inaccurate."

Asking an eyewitness to identify a suspect from a lineup demonstrates this.

"There's a nice study that shows slight variations in the way the lineup is conducted can result in swings of accuracy from as low as 14 percent to as high as 86 percent," Simon said.
   Confessing to a crime you didn't commit
Another factor in false convictions is what happens in the interrogation room. The report tracks 135 people who falsely confessed to a crime, and went to prison as a result.

"Why would anyone ever admit doing a terrible crime they didn't do?" Gross said. "The first thing to note is the risk false confessions goes up rapidly when the suspects are either juveniles or mentally handicapped or both."

In other cases in the database, a comment made to authorities was misinterpreted as a confession, or police pressure led to the false confession.

How effective are police lineups? Take our test

"Some people are being interrogated at a time of extreme mental anguish and distress," Gross said. "There was a very depressing case from Lake County, Illinois. He confessed to raping and murdering his young daughter, 8 or 9 years old, and a friend of hers. But consider the circumstances. He was being interrogated by the police, probably for 10 or 20 hours, within a day or two of when his daughter was kidnapped, raped and murdered and then they turned on him."

Exonerees can be found in all parts of the country, but most were concentrated in Illinois, New York, Texas, and California. 

93 percent are men, 7 percent women;
Nearly 50 percent are black, 38 percent white, 11 percent Hispanic and 2 percent Native American or Asian;
48 percent had been falsely convicted of homicides, 35 percent of sexual assaults (23 percent adult, 12 percent child), five percent robberies, five percent other violent crimes, and seven percent drug, white-collar and other non-violent crimes.
As a group, they spent more than 10,000 years in prison, an average of more than 11 years each.

Free from bars, but not from stigma
Smith, the man from North Carolina who was accused of molestation, maintained his innocence all along. He was only freed after one of the victims spoke to the other and decided to come forward in 2004.


Chris Seward/ The News & Observer (Raleigh), file

Sylvester Smith's wife Phillis Smith, right, reacts as Judge William Gore announced that Smith would be granted a new trial after two witnesses recanted their testimony in Bolivia, N.C., Nov. 5, 2004.

"They said they were more or less encouraged to accuse Mr. Smith, but it took a number of years and a great passage of time," Smith's lawyer, Roy Trest, said. "Obviously, he was extremely elated after all the years he had spent in prison."

Smith asked for a pardon from the governor, but was denied.

Now 61 and in poor health, he lives with his wife -- who he was married to but separated from before he went to prison -- in Brunswick County, N.C., and has established a friendship with one of the victims who accused him, his lawyer said.

Not all exonerees who leave prison are able to reintegrate back into society like Smith, despite a court proclaiming them innocent.

"Even if people honestly believe that this person was truly innocent, there is a certain stigma that comes with the mere fact that you were in prison," Simon said. "You were with bad people, you were antisocial, you had to live in the jungle-like societies you often find in prisons."

Sometimes, families break up when a defendant goes to prison. Finding a job after release can be hard too.

"Often times, the state is really unhelpful. There is no automatic method to get your criminal record expunged," Simon said. "And they have huge holes in their results, and often times they lack the skills that would help you get a job. Everyone else was studying while you were stuck in a cell."

Simon believes the registry will help reform the justice system because it helps experts analyze the causes of false convictions. The creators are still adding cases to ExonerationRegistry.org. Gross said he hopes exonerees will contact his team if they had their convictions overturned and don't see their story in the database. 
  

Discontinuity in the history of life explained (away?) once again.

Ignoring Other Research, New Study Explains (Away) the Origin of New Body Plans
Günter Bechly

Every now and then a new scientific paper takes on a particularly daunting challenge. The challenge is to explain the discontinuous origin of new body plans in the history of life on earth, for example, as observed in the sudden appearance of the animal phyla during the Cambrian explosion about 530 million years ago. Most of these attempts fail miserably. That is because the proposed causes are clearly not apt to generate new biologic complexity and diversity. Notorious examples are the slime theory and the oxygen and cancer theories that have already been discussed at Evolution News.

A New Pseudo-Explanation

Recently, a team of British paleontologists added a new pseudo-explanation. Deline et al. (2018) studied the presence and absence of thousands of features from all living animal groups, which allowed them “to create a shape space for animal body plans, quantifying their similarities and differences” (Donoghue in the press release by the  University of Bristol 2018) The authors claim: “Our results show that fundamental evolutionary change was not limited to an early burst of evolutionary experimentation. Animal designs have continued to evolve to the present day — not gradually as Darwin predicted — but in fits and starts, episodically through their evolutionary history.”

This is interesting indeed, because it exactly confirms my own argument (Bechly & Meyer 2017) that the history of life is a series of numerous discontinuous abrupt origins (“explosions”), contradicting the fundamental prediction of gradualism implied by Darwin’s theory of evolution through random variation and natural selection. As Richard Dawkins (2009) emphasized in his bestselling book The Greatest Show on Earth: “Evolution not only is a gradual process as a matter of fact; it has to be gradual if it is to do any explanatory work.” Darwin’s theory does not pass this empirical test of its predictions. So far so good (or rather so bad for neo-Darwinism). We already knew this.

Furthermore, the paper states: 

Our results challenge the view that maximum variation was achieved early in animal evolutionary history by nonuniformitarian mechanisms. Rather, they are compatible with the view that the capacity for fundamental innovation is not limited to the early evolutionary history of clades…. Our mapping of metazoan morphospace has shown that, even though some animal phyla demonstrate maximal initial disparity, others, notably chordates, arthropods, annelids, and mollusks, have progressively expanded on the limits of phylum and kingdom level morphospace post-Cambrian.

Thus post-Cambrian evolution has seen body plan innovation, which is hardly controversial. After all, insects, tetrapods, birds, mammals, and other body plans did not exist 530 million years ago. But this point does not negate at all the crucial fact that extreme biological innovation occurred rapidly in the Cambrian. Nor does it negate the fact that when later body plan innovations appear, they typically also do so abruptly.

However, Deline et al. also claim, “The ‘clumpiness’ of morphospace occupation by living clades is a consequence of the extinction of phylogenetic intermediates, indicating that the original distribution of morphologies was more homogeneous.” In a previous article at Evolution News (Anonymous 2018b) this ad hoc hypothesis has already been criticized, because it unashamedly maintains that exactly where the hypothetical intermediates are proposed to have existed, they remain forever inaccessible. How convenient!

An Even More Fundamental Problem

But there is an even more fundamental problem with this new study. As one of their major results, the authors claim that the origin of new body plans did not require the origin of new DNA code for new proteins. Instead, tweaking gene regulatory networks has been a main causal factor in the origin of metazoan disparity. Strangely, the authors completely ignore the work of Paps and Holland (2018) and do not even cite this important paper in their references section. Deline et al. submitted their manuscript on June 26, but the Paps & Holland study was published on April 30, allowing plenty of time to incorporate, or at least to mention those new results, unless these were too inconvenient truths that would have blown their own paper out of the water. 

Paps and Holland reconstructed the ancestral genetic nodes at which different types of animals diverged, and showed that those nodes involved major genetic and genomic innovations compared to other nodes. This clearly refutes one of the major conclusions of Deline et al.’s paper! Thus, Deline et al. are following in the path of Charles Marshall’s failed attempt to downplay the degree of genetic innovation that was necessary in the Cambrian (see Anonymous 2018a). The omission of Paps and Holland gets a truly bizarre twist in the review of Deline et al.’s work by Paps (2018) himself, who praises the new paper to the skies, but does not bother to mention the omission of his own contradicting study. This is a bit fishy.

A Classical Fallacy

The paper also seems to commit the classical fallacy of confusing correlation with causation. It states: “Causal hypotheses of morphologic expansion include time since origination, increases in genome size, protein repertoire, gene family expansion, and gene regulation.” The authors find a correlation with genome size and microRNA repertoire, but no correlation with protein domain diversity, and they conclude that gene regulation was more influential in shaping metazoan disparity. This of course overlooks that the lack of a general correlation between increasing morphological disparity and protein domain diversity does not imply that novel proteins do not play a crucial role in the origin of new body plans, as suggested by Paps and Holland. Apart from that, like all cladistic studies, this paper suffers from the general problem of biased and more or less arbitrary character selection and delimitation (Bechly 2000) in its data for measuring the disparity morphospace in the first place.

Last but not least, the new paper of course does absolutely nothing to explain how on earth random changes in gene regulatory networks could ever produce highly integrated and complex novel organ systems such as arthropod compound eyes, bird feathers, or the countercurrent heat exchange cooling system for the testes in whales. As a causal process, it is as unlikely to generate the phenomenon in question as oxygen levels or cancer.

In short: While certainly an interesting study, Deline et al. delivers just another failed attempt at an explanation for the origin of new body plans and biological disparity. Next?

Literature:

• Anonymous 2018a. “Groundbreaking Paper Shows Thousands of New Genes Needed for the Origin of Animals.” Evolution News June 7, 2018.
• Anonymous 2018b. “A Beautiful, Wonderful Solution to the Cambrian Puzzle?” Evolution News, September 7, 2018.
• Bechly G 2000. “Mainstream Cladistics versus Hennigian Phylogenetic Systematics.” Stuttgarter Beiträge zur Naturkunde Serie A 613, 1–11. (PDF)
• Bechly G, Meyer S 2017. “The Fossil Record and Universal Common Ancestry.” Chapter 10 in Moreland JP et al. (eds). Theistic Evolution: A Scientific, Philosophical, and Theological Critique. Crossway, Wheaton, pp. 331–362.
• Deline B, Greenwood JM, Clark JW, Puttick MN, Peterson KJ, Donoghue PCJ 2018. “Evolution of metazoan morphological disparity.” PNAS preprint, September 4, 2018.
• Paps J 2018. “How animals went from single cells to over 30 different body types.” The Conversation, September 4, 2018.
• Paps J, Holland PWH 2018. “Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty.” Nature Communications 9:1730. (PDF)
• University of Bristol 2018. “Evolutionary origins of animal biodiversity.” Science Daily, September 3, 2018.