Darwinism,uniformitarianism's fair weather friend.

Is Evolution True? Laying Out the Logic

Ann Gauger December 5, 2014 3:32 AM |

Monday we published a paper in the journal BIO-Complexity demonstrating that enzymes can't evolve genuinely new functions by unguided means. We argue that design by a very sophisticated intelligent agent is the best explanation for their origin. I want to take some time to lay out our argument against Darwinian evolution and for intelligent design. It's important, because it reveals the logical fallacy in most evolutionary thinking.

Just to give an example of the thinking of ID critics, here is a passage from one of the references in our paper (Kherhonsky et al. (2006) Enzyme promiscuity: Evolutionary and mechanistic aspects. Current Opinion in Chemical Biology 10:498-508):

An oft-forgotten essence of Darwinian processes is that they occur gradually, while maintaining organism fitness throughout. Consequently, a reasonable assumption is that, ever since the emergence of the primordial living forms, very little novelty has evolved at the molecular level. Rather, existing genes were modified, or tinkered with', to generate new protein structures and functions that are related to those of their ancestors. Unlike 'out of the blue' scenarios advocated by the 'intelligent design' school, 'tinkering' scenaoirios depend on the availability of evolutionary starting points. The hypothesis that the broad specificity, or promiscuous functions, of existing enzymes provide these starting points was first formalized by Jensen in a review that has inspired many. Jensen proposed that, in contrast to modern enzymes, primitive enzymes possessed very broad specificities. This catalytic versatility enabled fewer enzymes to perform the multitude of functions that was necessary to maintain ancestral organisms. Duplication of genes and divergence led to specialized genes and increased metabolic efficiency. Since Jensen, the structures of >30,000 proteins, and the sequences of hundreds of thousands, have taught us that these processes led to the creation of enzyme families and superfamilies. The vestiges of these divergence processes are the scaffold and active site architecture shared by all family members [6].

To summarize, the key points of that evolutionary argument are:

1. Evolution is true. That is, enzymes have evolved new functions by a process of random mutation and natural selection.
2. Modern enzymes can't evolve genuinely new functions by random mutation and natural selection but can only tinker with existing functions.
3. Therefore, ancient enzymes must have been different, capable of carrying out a broad range of enzyme activities.
4. Those enzymes underwent duplication and diverged from one another, becoming specialized.
5. How do we know this happened? Because we now see a broad array of specialized enzymes. Evolution is the explanation.

This begs the question of whether evolution is true. It is a circular argument unsubstantiated by the evidence and unfalsifiable. No one can know what ancient enzymes actually looked like, and whether they really had such broad catalytic specificities.

In contrast, our argument is as follows:

1. Is evolution true? Test case: Do enzymes evolve by a process of natural selection and random mutation?
2. Modern enzymes are the only thing we can test.
3. No one knows if ancient enzymes were different. They are lost in the deep past, so claims with regard to their promiscuity or ability to evolve are hypothetical and unfalsifiable.
4. Modern enzymes can't evolve new functions, based on our own experiments. 
5. We haven't tested the universe of modern enzymes, so our result is qualified, but the nine most similar enzymes did not change function.
6. Our estimate for the likely waiting time for an enzyme to evolve a new function is at least 10¹⁵ years.
7. Therefore evolution of enzymes is likely to be impossible.
8. Given the sophistication of enzymes and the way they work together, intelligent design is the best explanation for the origin and current diversity of modern enzymes.

You can read the argument in more detail in our paper.

Notice both arguments agree that modern enzymes can't evolve genuinely new functions. The difference is in the conclusion reached. The evolutionary argument assumes what it concludes -- it's a snake swallowing its tail, and goes nowhere.

In contrast, our argument relies on the uniformitarian principle that underlies all science. What is true for modern enzymes was true for ancient ones as well.

From Wikipedia:

Uniformitarianism is the assumption that the same natural laws and processes that operate in the universe now have always operated in the universe in the past and apply everywhere in the universe. It has included the gradualistic concept that "the present is the key to the past" and is functioning at the same rates. Uniformitarianism has been a key principle of geology and virtually all fields of science.

Gradualism has since been discarded in geology and paleontology, and it is not part of our argument. But the part about processes having always operated in the same way does apply: the evolutionary mechanism has always functioned in the same way, with the same limits, and enzymes have always functioned in the same way, with specific, not promiscuous, catalytic activities.

Now here's the point: anyone who wants to make a special case for the non-uniformitarian origin of enzymes (or animal groups) has created a special category to protect the idea that evolution is true. That idea is apparently untouchable. Any hypothesis about the deep past is accepted if it allows an evolutionary explanation for current diversity, and avoids problems with difficult facts. As a consequence, papers on the origin of life, protein evolution, the origin of animal form, and human origins are full of speculation masked as supporting argument, or even as statements of fact.

But the problem remains. If you start with the assumption that evolution is true, and view all evidence through those glasses, you won't even notice that your argument chases its tail.

File under 'well said'

"The best revenge is to be unlike him who 

performed the injury."

Marcus Aurelius, Meditations

Justice trampled underfoot in Azerbaijan

Jehovah’s Witnesses Call for End to Unjust Detention in Azerbaijan

Jehovah’s Witnesses are calling on international authorities to speak out against the unjust detention of Irina Zakharchenko and Valida Jabrayilova. The two women have been in jail since February 17, 2015, when the Sabail District Court sentenced them to three months of pretrial detention for alleged unauthorized distribution of religious literature. The court recently extended their detention by two more months.

Irina Zakharchenko and Valida Jabrayilova

Peaceable Women Treated as Dangerous Criminals

On December 5, 2014, Ms. Zakharchenko and Ms. Jabrayilova were talking to the residents of an apartment complex in Baku about their Bible-based beliefs when police stopped them. The police released the women after a few hours, but investigators repeatedly summoned them for interrogation. On February 17, 2015, agents of the Ministry of National Security (MNS) unexpectedly brought the women to a closed hearing to be criminally charged. The judge characterized them as a “threat to the public” in order to justify their pretrial detention. Immediately, the MNS jailed the women at its headquarters, pictured above.

Since then, agents of the MNS conducted an extensive search of their homes, confiscating religious literature, personal notebooks, a laptop, and a mobile phone. The court has dismissed every appeal on behalf of the women and refuses to grant house arrest as a replacement for pretrial detention.

Great Concern for Health and Well-Being

Lawyers, family, and friends are concerned for the state of health and well-being of the two women, which they believe is worsening. Ms. Zakharchenko is 55 years old. Doctors classify her as being 80 percent disabled because of severe arthritis and a previous injury to her right leg.

There is particular concern about the women’s emotional health. The MNS allows only their attorneys to visit them. Relatives can forward necessary items such as clothes, medicines, and soap only once a month. In an effort to offer comfort, family members have tried to provide them with a Bible, but the MNS has refused permission.

Will Azerbaijan Move to Show Religious Tolerance?

As part of the investigation of Ms. Zakharchenko and Ms. Jabrayilova, the MNS has summoned and interrogated at least 20 other Witnesses and searched at least ten homes. Additionally, officials representing the MNS, agents of the State Committee for Work with Religious Associations, and the police searched the Kingdom Hall where the women worship.

Since Azerbaijan’s authorities have offered them no alternative, Jehovah’s Witnesses have applied to the Office of the High Commissioner for Human Rights and contacted a number of international organizations to call attention to Azerbaijan’s unjust detention and treatment of Ms. Zakharchenko and Ms. Jabrayilova. Azerbaijan has made international commitments to promote human rights and fundamental freedoms and prides itself in its claim of being a country of religious tolerance.

Jehovah’s Witnesses respectfully request that the government of Azerbaijan honor its human rights obligations and permit the Witnesses to worship in peace. They appeal to the government of Azerbaijan to release these innocent women immediately.

Yet more on the tree of life

Do All Life Forms Fall into a Nested Hierarchy?

 

 

Casey Luskin June 11, 2015 4:57 AM |

 

A biology graduate student and alumnus of our Summer Seminar on Intelligent Design recently contacted me to ask where ID comes down on common descent. I explained to him that in the ID camp, some folks accept common descent while others are skeptical. ID proponents can respectfully disagree on that question (and others too), while agreeing on the powerful evidence for design in nature. But my correspondent asked about an argument in favor of common ancestry he had heard that basically went like this:

All life forms fall within a nested hierarchy. Of the hundreds of thousands of specimens that have been tested, every single one falls within a nested hierarchy, or their evolutionary phylogenetic tree is still unknown and not sequenced yet.

This claim (which he wasn't making, by the way) is far from true. We constantly find organisms that don't fit neatly into a phylogenetic tree. Or, what happens is evolutionary biologists attempt to force-fit organisms into the tree only by invoking processes like convergent evolution and loss of traits. In other words, evolutionary biologists are forced to propose that an organism's traits did not arise through common ancestry, because common ancestry fails to explain the data. Does this mean that evolutionary biologists reject common ancestry when they find data that doesn't fit a tree? No, because they assume common ancestry; they aren't interested in testing it. So when they find data that doesn't fit a tree, they just find ways to force-fit the data into the tree. Here's what's going on:
The first and primary assumption of all evolutionary phylogenetic classification methodologies is that common ancestry is true. This assumption nearly always goes unquestioned, even when the data doesn't support it. As Elliott Sober and Michael Steele explain, "It is a central tenet of modern evolutionary theory that all living things now on earth trace back to a single common ancestor," and "This proposition is central because it is presupposed so widely in evolutionary research." They acknowledge that cladistics assumes that a tree exists, and common ancestry is correct:

Whether one uses cladistic parsimony, distance measures, or maximum likelihood methods, the typical question is which tree is the best one, not whether there is a tree in the first place. (Elliott Sober and Michael Steele, "Testing the Hypothesis of Common Ancestry," Journal of Theoretical Biology 218 (2002): 395-408 (emphasis added).)

Likewise, the assumption is made explicit, and primary, in the UC Berkeley Museum of Paleontology's introductory page on cladistics:

What assumptions do cladists make? There are three basic assumptions in cladistics:
1.Any group of organisms are related by descent from a common ancestor.

One textbook cited by Stephen Meyer in Darwin's Doubt concurs about this assumption:

The key assumption made when constructing a phylogenetic tree from a set of sequences is that they are all derived from a single ancestral sequence, i.e., they are homologous. (Marketa Zvelebil and Jeremy O. Baum, Understanding Bioinformatics (New York: Garland Science, 2008), p. 239.)

Together, these authorities make a crucial point: cladistics and other phylogenetics methods do not demonstrate common ancestry; they assume it. In other words, these methods don't test whether all organisms fit into a nested hierarchy (i.e., phylogenetic tree). Rather, evolutionary systematics assumes that common ancestry is true and therefore all organisms belong within a nested hierarchy, and then it uses methods to force-fit any organism into the tree, even if that organisms has traits that don't fit neatly within the tree. Thus, Michael Syvanen -- a rare evolutionary biologist who is open to the possibility that universal common ancestry is false -- laments the pro-tree biases of treebuilding algorithms:

Because tree analysis tools are used so widely, they tend to introduce a bias into the interpretation of results. Hence, one needs to be continually reminded that submitting multiple sequences (DNA, protein, or other character states) to phylogenetic analysis produces trees because that is the nature of the algorithms used. (Michael Syvanen, "Evolutionary Implications of Horizontal Gene Transfer," Annual Review of Genetics, 46:339-356 (2012) (emphases added).)

Common ancestry, therefore, is a starting assumption about the data -- not a conclusion from it. Another key lesson is this: just because you see evolutionary biologists creating an impressive-looking phylogenetic tree doesn't mean that all of the organisms or their traits shown within that tree fit neatly into a nested hierarchy (i.e., a tree structure). One could cite many examples of organisms that don't fit cleanly into a tree. Here are a few: Sahelanthropus tchadensis is widely touted as a human ancestor that lived about 6-7 million years ago, sometime very soon after the supposed split between the human line and the chimp line. But it's rarely mentioned that this specimen doesn't fit into the standard hominin tree at all. Why? Because it has a flat face, a humanlike quality, which shouldn't exist that far back:

If we accept these as sufficient evidence to classify S. tchadensis as a hominid at the base, or stem, of the modern human clade, then it plays havoc with the tidy model of human origins. Quite simply, a hominid of this age should only just be beginning to show signs of being a hominid. It certainly should not have the face of a hominid less than one-third of its geological age. Also, if it is accepted as a stem hominid, under the tidy model the principle of parsimony dictates that all creatures with more primitive faces (and that is a very long list) would, perforce, have to be excluded from the ancestry of modern humans." (Bernard Wood, "Hominid revelations from Chad," Nature, 418 (July 11, 2002):133-35.)

Because of this, some are skeptical that S. tchadensis belongs on the human line. If that's the case then its flat face represents convergent evolution. And if it is on the human line, then you are forced to propose that later species on the human line lost this trait. Either way, S. tchadensis creates major problems for a nice, neat, nested hierarchy of hominins that is consistent with the chronology of the fossil record. Much further back, there are organisms like Diania, thought to be an early arthropod ancestor from the Cambrian period, but which actually cause huge problems for the arthropod tree:

[W]e should caution that dinocaridids, Diania and other potential stem-arthropods typically express mosaics of arthropod-like characters, which makes resolving a single, simple tree of arthropod origins problematic. Indeed, the position recovered here for Diania between Radiodonta and the ostensibly similar-looking Schinderhannes is surprising. Diania, Schinderhannes and the remaining Arthropoda all share the putative apomorphy of jointed trunk appendages, and yet the trunk limbs of Diania resemble the frontal appendages of Anomalocaris and other radiodontans, which themselves lack trunk limbs entirely. If this is a secondary reduction in fossils like Anomalocaris, then Diania may in fact occupy a more basal position with respect to Radiodonta, Schinderhannes and Arthropoda; a scenario that would be more consistent with their fairly simple body morphology. (Liu et al., "An armoured Cambrian lobopodian from China with arthropod-like appendages," Nature, 470 (February 24, 2011): 526-530 (internal citations omitted).)

The reason the authors talk about "mosaics of arthropod-like characters" is that these organisms don't fit into an orderly, sequential, hierarchical, treelike pattern as predicted by common descent. They present a mishmash of traits, not distributed in a treelike pattern that shows some sequential, hierarchy ordering arthropod traits. This is a famous problem in arthropod evolution, rightly described as a mess. As one paper observes: "Arthropod phylogeny is sometimes presented as an almost hopeless puzzle wherein all possible competing hypotheses have support." That's the opposite of a nested hierarchy. Nor is it just within the Cambrian phyla that we find such an array of phylogenetic misfits. Among the animal phyla more generally, we see traits that make it difficult to create a treelike representation of relationships.
The argument cited by the grad student noted that one reason an organism's classification isn't understood is that "their evolutionary phylogenetic tree is still unknown and not sequenced yet." That's a bit of a rudimentary argument, but it probably means that until we sequence an organism's genome, we don't know where it belongs in the tree of life. But sometimes after we sequence an organism's genome we find that its place in the tree of life is even less clear than it was before.
This is exactly what happened after the comb jelly genome was sequenced. As I wrote last year, comb jellies (phylum ctenophora) have muscles and complex nervous systems, but molecular studies suggest they branch off very close to the base of the animal tree. However, sponges -- which branch off later according to molecular data -- lack such structures. This means that either complex muscle and nervous cells were lost in sponges (even though these are complex, useful traits you'd probably want to keep around) or muscles and brains evolved convergently in later animals. Either way, you're left with a situation where comb jellies don't fit neatly into the animal tree. They show a mosaic of traits that shouldn't be the case under common descent.
Here's one more classic example from the animal phyla: symmetry. Animals can be divided up in many different ways. Some display bilateral symmetry, basically meaning they have a right half and a left half. Such "bilaterian" phyla include vertebrates, arthropods, and mollusks. Others have radial symmetry, where their symmetry is distributed in an essentially circular fashion around a central axis. Phyla with radial symmetry include cnidarians (e.g., jellyfish), ctenophores (comb jellies), and echinoderms (e.g., star fish and sea urchins).
From an evolutionary perspective, you might expect an animal tree to divide up neatly according to whether organisms display bilateral or radial symmetry. Not so. Echinoderms are placed much closer to vertebrates than they are to cnidarians and other phyla with radial symmetry. In fact, in another weird twist, vertebrates (with bilateral symmetry) are thought to be much closer to echinoderms (with radial symmetry) than they are to other bilaterian phyla like the arthropods, mollusks, or annelids. This grouping is made on the basis of early developmental processes. Echinoderms and vertebrates are both deuterostomes, meaning that early in development the first opening in the blastopore becomes the anus rather than the mouth. The upshot is this: animal symmetry is not distributed in a treelike pattern.
Yes, a critic might object that larval stages of echinoderms can have bilateral symmetry. But exactly the same can be said of some cnidarians, which are very far from echinoderms in the animal tree -- showing, again, that symmetry is not distributed in a treelike pattern.
In any case, an evolutionary biologist could decide to group phyla according to early developmental processes, or according to symmetry, and that's fine. If you weight one trait heavily, you'll get one tree. But switch that weight to another trait and you'll get another, conflicting tree. Either way, when you use one character set to create your tree, then the other character set is no longer distributed in a treelike fashion, and vice versa. That's a major problem.
Another good example of an organism whose genome posed problems for phylogenetic classification after it was sequenced is birds. As we reported last December, the sequencing of various bird genomes led to the unexpected conclusion that many types of birds that were previously thought to be closely related -- water birds, birds of prey, and songbirds -- evolved their groups' defining traits convergently. As Nature put it, "the tree of life for birds has been redrawn" by this study. The problem was, once genomic data was sequenced and understood, many basic habits and lifestyles of birds no longer fit into a nested hierarchy.
Again, there are innumerable examples of organismal traits that don't fit into a treelike pattern. But here are two more that came out recently.
In April, Science Daily reported a study that looked at how different marine organisms swim ("Convergent evolution: Diverse sea creatures evolved to reach same swimming solution"). The scientists found that organisms as diverse as cuttlefish (a mollusk), the black ghost knifefish (a vertebrate), and the Persian carpet flatworm (phylum platyhelminthes) all use the same method of swimming:

The ability to move one's body rapidly through water is a key to existence for many species on this blue planet of ours. The Persian carpet flatworm, the cuttlefish and the black ghost knifefish look nothing like each other -- their last common ancestor lived 550 million years ago, before the Cambrian period -- but a new study uses a combination of computer simulations, a robotic fish and video footage of real fish to show that all three aquatic creatures have evolved to swim with elongated fins using the same mechanical motion that optimizes their speed, helping to ensure their survival. These three animals are part of a very diverse group of aquatic animals -- both vertebrate and invertebrate -- that independently arrived at the same solution of how to use their fins to maximize speed. And, remarkably, this so-called "convergent" evolution happened at least eight times across three different phyla, or animal groups, supporting the belief that necessity played a larger role than chance in developing this trait.

Now they are welcome to invoke convergent evolution if they like, but it's striking how each of these widely diverse organisms has a very similar mode of swimming, where the length of one undulation of the animal's fins divided by the average amplitude of the corresponding sideways movement gives you a ratio of about 20. You can see how distantly related (according to the usual evolutionary paradigm) these similar-swimming organisms are by looking at a tree diagram from the original paper. Also in April there were striking reports of a new vegetarian theropod dinosaur that had traits that made it very difficult to classify within the standard dinosaur tree:

Although closely related to the notorious carnivore Tyrannosaurus rex, a new lineage of dinosaur discovered in Chile is proving to be an evolutionary jigsaw puzzle, as it preferred to graze upon plants. Chilesaurus boasted a proportionally small skull, hands with two fingers like Tyrannosaurus rex and feet more akin to primitive long-neck dinosaurs.

Theropods, of course, include the meat eaters Velociraptor and T. rex, yet this species was a vegetarian. It thus poses a severe puzzle for evolutionary classification, as an article in The Guardian acknowledged:

Fossil hunters in Chile have unearthed the remains of a bizarre Jurassic dinosaur that combined a curious mixture of features from different prehistoric animals. The evolutionary muddle of a beast grew to the size of a small horse and was the most abundant animal to be found 145 million years ago, in what is now the Aysén region of Patagonia.

The discovery ranks as one of the most remarkable dinosaur finds of the past 20 years, and promises to cause plenty of headaches for paleontologists hoping to place the animal in the dinosaur family tree.

"I don't know how the evolution of dinosaurs produced this kind of animal, what kind of ecological pressures must have been at work," said Fernando Novas at the Bernardino Rivadavia Natural Sciences Museum in Buenos Aires.

The technical paper in Nature puts it this way:

For a basal tetanuran, Chilesaurus possesses a number of surprisingly plesiomorphic traits on the hindlimbs, especially in the ankle and foot, which resemble basal sauropodomorphs. These features are here considered as secondary reversals that might be related to a less-cursorial mode of locomotion. Furthermore, derived features of the dentary and teeth shared by Chilesaurus, sauropodomorphs and therizinosaurs are interpreted as homoplasies related to herbivorous habits. ... Chilesaurus represents an extreme case of mosaic evolution among dinosaurs, owing to the presence of dental, cranial and postcranial features that are homoplastic with multiple disparate groups. Using quantitative morphospace analysis, we explored morphospace occupation of different skeletal regions in Chilesaurus with respect to a variety of avian and non-avian theropods. This shows that Chilesaurus has a ceratosaur-like axial skeleton, a 'basal tetanuran' forelimb and scapular girdle, a coelurosaur-like pelvis, and a tetanuran-like hindlimb. General ankle and foot construction does not group with any theropod clade, probably as a result of the characters shared by Chilesaurus, sauropodomorphs and herrerasaurids.

Science Daily explained in less technical terms why this species, with its set of traits resembling many different types of dinosaurs, is difficult to classify:

Other features present in very different groups of dinosaurs Chilesaurus adopted were robust forelimbs similar to Jurassic theropods such as Allosaurus, although its hands were provided with two blunt fingers, unlike the sharp claws of fellow theropod Velociraptor. Chilesaurus' pelvic girdle resembles that of the ornithischian dinosaurs, whereas it is actually classified in the other basic dinosaur division -- Saurischia. The different parts of the body of Chilesaurus were adapted to a particular diet and way of life, which was similar to other groups of dinosaurs. As a result of these similar habits, different regions of the body of Chilesaurus evolved resembling those present in other, unrelated groups of dinosaurs, which is a phenomenon called evolutionary convergence.
Chilesaurus represents one of the most extreme cases of mosaic convergent evolution recorded in the history of life. For example, the teeth of Chilesaurus are very similar to those of primitive long-neck dinosaurs because they were selected over millions of years as a result of a similar diet between these two lineages of dinosaurs.
Martín Ezcurra, Researcher, School of Geography, Earth and Environmental Sciences, University of Birmingham said: 'Chilesaurus can be considered a 'platypus' dinosaur because different parts of its body resemble those of other dinosaur groups due to mosaic convergent evolution. In this process, a region or regions of an organism resemble others of unrelated species because of a similar mode of life and evolutionary pressures. Chilesaurus provides a good example of how evolution works in deep time and it is one of the most interesting cases of convergent evolution documented in the history of life.

What we see here is a dino that doesn't fit with the dino tree not just because it's a herbivorous theropod, but also because different parts of its body appear similar to different types of dinosaurs. Through convergent evolution and loss of traits, you can always find a way accommodate such quirky data. However the bottom line is that organisms like these are the opposite of finding "All life forms fall within nested hierarchy." We explain further in our curriculum Discovering Intelligent Design:

You may recall the "main assumption," mentioned at the beginning of the chapter, that Darwinian evolutionists use when constructing trees: similarity implies inheritance from a common ancestor. But what about situations where that assumption is clearly untrue -- i.e., when two organisms share a trait that their supposed common ancestor could not have possessed? A striking example is the [skull] similarity between marsupial and placental "saber-toothed cats," which are classified as very different types of mammals due to their two distinctly different ways of bearing young.
According to current evolutionary theory, the common ancestor of these two cats was a small rodent-like mammal with a very different body plan. Thus, their highly similar skull structures had to develop independently and could not have been inherited from a common ancestor.
Common descent does not explain these similarities. Evolutionists try to explain this evidence by claiming these distinctly different cats evolved the same traits independently through convergent evolution.

Does this sort of data absolutely refute universal common descent? Taken on a case-by-case basis, no of course not, and we're not claiming it does. What it shows, collectively, is that the evolutionary case is a lot weaker than is routinely claimed. We commonly -- if not constantly -- find organisms whose traits don't fit into a hierarchical tree.
I like how we conclude on this topic in Discovering Intelligent Design:

Perhaps the main assumption of phylogenetic trees should be rewritten as: "similarity implies inheritance from a common ancestor, except when it does not." Rather than being a helpful solution for neo-Darwinists, convergent evolution undermines the reasoning used to construct phylogenetic trees.

In fact, maintaining that "All life forms fall within a nested hierarchy" requires you to ignore huge amounts of data. ID proponents who doubt common descent have, I would say, ample reason for doing so.

 

For materialists the obvious remains a bridge too far.

Biologist in TEDx Talk: Life's "Complex Interacting Molecular Machines" Appear "Built by an Engineer"

Casey Luskin June 10, 2015 8:02 AM | 

Recently a friend sent me a link to a TEDx talk, "Digital biology and open science -- the coming revolution," which affirms that life's "complex interacting molecular machines" reveal "molecular clockwork is real and pervasive" and appear to be "built by an engineer a million times smarter than" we are. The speaker is biologist and engineer Stephen Larson, who holds a PhD in neuroscience from University of California, San Diego, and is CEO of MetaCell, a systems biology research and consulting company that seeks to understand biology through computation.

Now I don't think that Dr. Larson is pro-intelligent design, which makes his descriptions of biology all the more striking. In fact, after recounting some complex features of biology that appear designed, he immediately throws in the disclaimer that "what we understand of course is that life evolved on the planet over billions of years." Nonetheless he admits that he finds the extremely "well organized" nature of life's "technology" to be "unsettling." He even says, "I've got to be honest with you, I kind of hate this." Here's the transcript of the relevant section, from most of the first 4:30 of the talk:

[A]s science continues to reveal how life works, we find again and again that the magic that seems to distinguish between things that are alive and things that are not [is] actually created by complex interacting molecular machines. These microscopic machines are as precise and intricate as a mechanical watch, but instead of being run on gears and springs, are powered by the fundamental rules of physics and chemistry. Our understanding of the precise coiling and uncoiling of the DNA molecule, or the way that one molecule can literally walk almost robotically along the tightrope of another molecule, continue to show us again and again, this molecular clockwork is real and pervasive.

Now what's most unsettling to me about this is that we didn't build these machines. As someone originally trained as an engineer, I've got to be honest with you, I kind of hate this. As the most clever species on the planet, we kind of like to think of ourselves as the builders of the most sophisticated technology in the entire universe. We invented written language and the printing press. We cured polio and sent a man to the moon. Heck, we even took savage beasts and turned them into kittens, and then built a global communications network to share pictures of them. That's pretty impressive.

And yet when I look through a microscope at a humble bacterium -- by the way its ancestors were on the planet a billion years ago, billions of years ago -- I still wonder how it really works. Because the mechanical watch that is life is not like any watch we've ever built. It is biological gears and springs, but they fill rooms and buildings and cities of a vast microscope landscape that's bustling with activity.

On the one hand it's extremely well organized, but on the other hand the sheer scale of all of this unfamiliar well-organized stuff that happens in there makes me feel that I've stumbled onto an alternate landscape of technology that's built by an engineer a million times smarter than me. The more that I search for principles beyond the ones we've already learned, the more I am overwhelmed with the feeling that this stuff was built by aliens.

OK, not literally. I don't literally mean that I think little green men and women came down to the earth and seeded life here a billion years ago. What we understand of course is that life evolved on the planet over billions of years. But the results of evolution confuse even our smartest engineers when we try to understand how we could build what biology has evolved.

What if life has good engineering principles and we just haven't figured them out yet? Could studying biology give us the ability to extract new engineering principles that maybe then we could use to solve the world's intractable problems? Our experiments only give us glimpses into what happens in these tiny spaces, but what happens there has huge implication for the future, in the 21st century, and beyond.

Now Larson is a systems biologist, which means he is trained to see life from an engineering point of view. In such a perspective, scientists treat biological systems as if they are infused with teleology -- built from the top down to achieve some goal, not blindly from the bottom up as Darwinian evolution sees them. This doesn't mean that systems biologists have doubts about Darwinian evolution (doubts that they'll admit) or that they support intelligent design. They hold their extremely fruitful systems biology viewpoint in tension with the origins-models they otherwise endorse. Here's how physicist David Snoke describes the field with its sense of cognitive dissonance:

Opponents of the intelligent design (ID) approach to biology have sometimes argued that the ID perspective discourages scientific investigation. To the contrary, it can be argued that the most productive new paradigm in systems biology is actually much more compatible with a belief in the intelligent design of life than with a belief in neo-Darwinian evolution. This new paradigm in system biology, which has arisen in the past ten years or so, analyzes living systems in terms of systems engineering concepts such as design, information processing, optimization, and other explicitly teleological concepts. This new paradigm offers a successful, quantitative, predictive theory for biology. Although the main practitioners of the field attribute the presence of such things to the outworking of natural selection, they cannot avoid using design language and design concepts in their research, and a straightforward look at the field indicates it is really a design approach altogether.

(David Snoke, "Systems Biology as a Research Program for Intelligent Design," BIO-Complexity, Vol. 2014 (3).)

Larson talks further about the machine-like nature of many biological systems, how we can use computers and an engineering-based view of biology to better treat diseases, and even how we can understand complex biological mysteries like love. He says we can only understand biological feelings like love as "a series of complex but specific and knowable events that happen inside your body." Complex and specified -- sound familiar?

I highly recommend watching the talk in full.

A flame flickers in the gloom.

JUNE 3, 2015
RUSSIA

Ministry of Justice Registers Jehovah’s Witnesses in Moscow

On May 27, 2015, the Russian Federation Ministry of Justice registered the Local Religious Organization of Jehovah’s Witnesses in Moscow. The registration came nearly five years after the European Court of Human Rights (ECHR) ruled that a Moscow court decision to liquidate the Witnesses’ legal entity was illegal.

After years of legal proceedings, the Golovinskiy District Court of Moscow ruled to liquidate the Witnesses’ legal entity in 2004. In 2010, the ECHR ordered Russia to remedy the violation by restoring the community’s registration and paying moral damages. The Russian government paid the fine but only now registered the religious community.

Fuzzy math or heads Darwinism wins tails I.D. loses.

BIO-Complexity Paper: Why Chaitin's Mathematical "Proof" of Darwinian Evolution Fails

Casey Luskin April 7, 2014 5:08 AM | 

 new peer-reviewed paper in BIO-Complexity, "Active Information in Metabiology," reports on the further investigations of the Evolutionary Informatics Lab into the ability of unguided evolutionary mechanisms to produce new information. This time, authors Winston Ewert, William Dembski, and Robert Marks show that the budding field of metabiology only produces creative outputs through active information -- i.e., informational inputs donated by an intelligent source -- and does not truly demonstrate that unguided processes can produce new information.

What is "metabiology"? According to the paper, it's "a fascinating intellectual romp in the surreal world of the mathematics of algorithmic information theory" where "halting oracles hunt for busy beaver numbers and busy beaver numbers unearth Chaitin's number, knowledge of which in turn allows resolution of numerous unsolved mathematical problems, many of whose solutions would earn large cash bounties." That description may not help most of us very much. The field of "metabiology" was developed by the Argentine-American computer scientist and mathematician Gregory Chaitin. In his 2013 book Proving Darwin: Making Biology Mathematical, Chaitin describes metabiology as an "answer" to David Berlinski's "stinging critique of Darwinism" in The Devil's Delusion. "Metabiology" is Chaitin's attempt to use mathematics and (hypothetical) computer simulations to formally prove that Darwinian theory can create new information. It relies on an inherently gene-centered view of evolution, where a simulated "genetic code" (i.e., a computer program) can be "mutated," and when the program "halts" or stops running, it outputs a number that correlates with the program's "fitness." If the number goes up as the evolutionary simulation proceeds, Chaitin thinks he's shown Darwinian processes can increase fitness over time.

There are many reasons why Chaitin's model does not accurately reflect how Darwinian evolution works, if it does work, in the real world of biology (some of which are summarized nicely over at Theory, Evolution, and Games Group). Not the least of such problems is the fact that the simulation basically grants itself infinite probabilistic resources (actually, computing resources, but that's analogous to probabilistic resources in biology).

As Ewert, Dembski, and Marks explain:

Because metabiology programs have unbounded length and can run for an unbounded amount of time, the unboundedness essentially undermines the creativity required to solve the large-number problem. With unbounded resources and unbounded time, one can do most anything.

In the real world, probabilistic resources are limited. Time is finite, and populations have finite sizes, and this imposes limits on what traits can evolve especially (as Stephen Meyer shows in Darwin's Doubt) when traits require multiple mutations before providing some advantage. Metabiology uses a population of one single "digital organism," which then "evolves" over time, but it grants itself essentially infinite computing resources to do this. With such a generous endowment, sure, anything can eventually evolve. But we don't live in an unlimited world, which is precisely why Darwinian evolution faces major theoretical problems. They thus write:

Although elegant in conception, metabiology departs from reality because it pays no attention to resource limitations. Metabiology's math obscures the huge amounts of time required for the evolutionary process. The programs can run for any arbitrarily large number of steps. Additionally, programs can be of any length with no penalty imposed for longer programs.

Ewert, Dembski, and Marks explain that Chaitin's program uses a halting oracle as a source of "active information." A halting oracle is a hypothetical meta-program that can tell you if a given program will ever stop running. As they explain, such an oracle could be useful in disproving certain mathematical conjectures, such as Goldbach's conjecture, "which hypothesizes that all even numbers greater than two can be written as the sum of two primes." They discuss how a halting oracle could determine if the conjecture was false:

Suppose a program X can be written to test each even number sequentially to see if it were the sum of two primes. If a counterexample is found, the program stops and declares "I have a counterexample!" Otherwise, the next even number is tested. If Goldbach's conjecture is true, the program will run forever.

If a halting oracle existed, we could feed it X. If the halting oracle says "this program halts," Goldbach's conjecture is disproved. A counterexample exists. If the halting oracle says, "This program never halts," then Goldbach's conjecture is proven! There exists no counterexample.

The difficulty for Chaitin is he admits that for metabiology, "[The halting oracle] is where all the creativity is really coming from in our program," but also admits that such an oracle is "mathematical fantasy." Ewert, Dembski, and Marks thus aptly observe, "A computer tool proven not to exist is admittedly at the outset an obvious major strike against a theory purporting to demonstrate reality."

Now at this point, one might reasonably ask, "If a halting oracle is a hypothetical fantasy, how can Chaitin claim to use one in metabiology?" The answer is that Chaitin isn't actually creating a computer program. He's seeking a mathematical proof of the Darwinian model, where he's allowed to indulge thought experiments that invoke hypothetical entities. All he needs to be able to do is to prove what might happen if he theoretically had a halting oracle. But it doesn't help that one could never exist.

That problem aside, they explain that the "halting oracle" used by Chaitin's program has three different options of how to find a search target: "

• Exhaustive Search (poor)
• Random Evolution (good)
• Intelligent Design (better)

Metabiology uses "random evolution" but not in a manner that is biologically realistic. The program is capable of systematically simulating all possible programs, which in effect allows it to totally rewrite itself instantly -- something that simply doesn't happen in biology -- and thereby grants unrealistic access to the equivalent of unlimited resources in an organism's developmental process. This unrealistically guarantees the program could never get stuck on a local fitness peak because it can keep trying out entirely new "genetic codes" indefinitely until a better one is found.

Which, again, is nothing like how the real world of biology, where an organism is forced to rely on the genome it receives, which at best will have just a few small mutational differences from its parents. Darwinian evolution in real biology requires a grueling ascent of mount improbable, but Chaitin's program can fly wherever it wants at any time. To put it another way, metabiology cheats by giving a digital organism unrealistic access to any program at any time which will lead to a higher fitness state. As Ewert, Dembski, and Marks explain:

As any computer programmer will tell you, landscapes of computer program fitness are the opposite of smooth. We would therefore not expect Darwinian evolution to fare well. Chaitin notes this when he writes [3], "The fitness landscape has to be very special for Darwinian evolution to work."

The environment for evolution to occur, therefore, has to be carefully designed. Indeed, in the paradigm of conservation of information, smooth landscapes can be source of significant active information [14]. Metabiology's construction of smooth landscapes is accomplished by running all viable programs, a computationally expensive approach that is only possible because there are no resource limitations.

Chaitin also presents a different model that uses what he calls "intelligent design" to find a search target. This obviously doesn't help show what unguided evolutionary processes can accomplish. The author of the blog "Theory, Evolution and Games Group" critiques Chaitin's model, writing that metabiology uses "a teleological model -- a biologist's nightmare." Ewert, Dembski, and Marks explain:

Like AVIDA and ev, metabiology makes use of external information sources to assist in the search. Like the simple Hamming oracle, the halting oracle can be mined for information with various degrees of sophistication. Evolution thus requires external sources of knowledge to work. The degree to which this knowledge is used can be assessed using the idea of active information.

They conclude: "In order for evolution to occur in these models, external knowledge must be imposed on the process to guide it. Metabiology thus appears to be another example where its designer makes an evolutionary model work. ... Consistent with the laws of conservation of information, natural selection can only work using the guidance of active information, which can be provided only by a designer." Properly understood, in other words, these programs demonstrate that evolution requires intelligent design.

The dead rebuke Darwin defenders

Fossils Don't Lie: Why Darwinism Is False

Jonathan Wells April 27, 2009 3:18 PM 

Coyne goes on to discuss several "transitional" forms. "One of our best examples of an evolutionary transition," he writes, is the fossil record of whales, "since we have a chronologically ordered series of fossils, perhaps a lineage of ancestors and descendants, showing their movement from land to water."⁹

"The sequence begins," Coyne writes, "with the recently discovered fossil of a close relative of whales, a raccoon-sized animal called Indohyus. Living 48 million years ago, Indohyus was... probably very close to what the whale ancestor looked like." In the next paragraph, Coyne writes, "Indohyus was not the ancestor of whales, but was almost certainly its cousin. But if we go back 4 million more years, to 52 million years ago, we see what might well be that ancestor. It is a fossil skull from a wolf-sized creature called Pakicetus, which is bit more whalelike than Indohyus." On the page separating these two paragraphs is a figure captioned "Transitional forms in the evolution of modern whales," which shows Indohyus as the first in the series andPakicetus as the second.¹⁰

But Pakicetus--as Coyne just told us--is 4 million years older than Indohyus. To a Darwinist, this doesn't matter: Pakicetus is "more whalelike" thanIndohyus, so it must fall between Indohyus and modern whales, regardless of the fossil evidence.

(Coyne performs the same trick with fossils that are supposedly ancestral to modern birds. The textbook icon Archaeopteryx, with feathered wings like a modern bird but teeth and a tail like a reptile, is dated at 145 million years. But what Coyne calls the "nonflying feathered dinosaur fossils"--which should have come before Archaeopteryx--are tens of millions of years younger. Like Darwinists Kevin Padian and Luis Chiappe eleven years earlier, Coyne simply rearranges the evidence to fit Darwinian theory.)¹¹

So much for Coyne's prediction that "later species should have traits that make them look like the descendants of earlier ones." And so much for his argument that "if evolution were not true, fossils would not occur in an order that makes evolutionary sense." Ignoring the facts he himself has just presented, Coyne brazenly concludes: "When we find transitional forms, they occur in the fossil record precisely where they should." If Coyne's book were turned into a movie, this scene might feature Chico Marx saying, "Who are you going to believe, me or your own eyes?"¹²

There is another problem with the whale series (and every other series of fossils) that Coyne fails to address: No species in the series could possibly be the ancestor of any other, because all of them possess characteristics they would first have to lose before evolving into a subsequent form. This is why the scientific literature typically shows each species branching off a supposed lineage.

In the figure below, all the lines are hypothetical. The diagram on the left is a representation of evolutionary theory: Species A is ancestral to B, which is ancestral to C, which is ancestral to D, which is ancestral to E. But the diagram on the right is a better representation of the evidence: Species A, B, C and D are not in the actual lineage leading to E, which remains unknown.

It turns out that no series of fossils can provide evidence for Darwinian descent with modification. Even in the case of living species, buried remains cannot generally be used to establish ancestor-descendant relationships. Imagine finding two human skeletons in the same grave, one about thirty years older than the other. Was the older individual the parent of the younger? Without written genealogical records and identifying marks (or in some cases DNA), it is impossible to answer the question. And in this case we would be dealing with two skeletons from the same species that are only a generation apart and from the same location. With fossils from different species that are now extinct, and widely separated in time and space, there is no way to establish that one is the ancestor of another--no matter how many transitional fossils we find.

In 1978, Gareth Nelson of the American Museum of Natural History wrote: "The idea that one can go to the fossil record and expect to empirically recover an ancestor-descendant sequence, be it of species, genera, families, or whatever, has been, and continues to be, a pernicious illusion."¹³ Naturescience writer Henry Gee wrote in 1999 that "no fossil is buried with its birth certificate." When we call new fossil discoveries "missing links," it is "as if the chain of ancestry and descent were a real object for our contemplation, and not what it really is: a completely human invention created after the fact, shaped to accord with human prejudices." Gee concluded: "To take a line of fossils and claim that they represent a lineage is not a scientific hypothesis that can be tested, but an assertion that carries the same validity as a bedtime story--amusing, perhaps even instructive, but not scientific."¹⁴

Next time, I'll address Coyne's mistakes on embryos.

Notes
⁹ Coyne, Why Evolution Is True, p. 48.
¹⁰ Coyne, Why Evolution Is True, pp. 49-51.
¹¹ Kevin Padian & Luis M. Chiappe, "The origin and early evolution of birds,"Biological Reviews 73 (1998): 1-42. Available online (2009) here.
Wells, Icons of Evolution, pp. 119-122. 
¹² Coyne, Why Evolution Is True, pp. 25, 53.
Chico Marx in Duck Soup (Paramount Pictures, 1933). This and other Marx Brothers quotations are available online (2009) here.
¹³ Gareth Nelson, "Presentation to the American Museum of Natural History (1969)," in David M. Williams & Malte C. Ebach, "The reform of palaeontology and the rise of biogeography--25 years after 'ontogeny, phylogeny, palaeontology and the biogenetic law' (Nelson, 1978)," Journal of Biogeography 31 (2004): 685-712.
¹⁴ Henry Gee, In Search of Deep Time. New York: Free Press, 1999, pp. 5, 32, 113-117.
Jonathan Wells, The Politically Incorrect Guide to Darwinism and Intelligent Design (Washington, DC: Regnery Publishing, 2006). More information available online (2009) here.