Category Archives: Kingdoms & Cultures

New Speciation Model Challenges Evolution, Supports Creation

Which model, naturalistic evolution or supernatural creation, best explains the pattern of life’s history on Earth? If a test produces “strikingly divergent results” for the expectations of a model, what does that tell us? A new study on speciation and extinction rates provides persuasive evidence.

Model Tenets

A fundamental tenet of all naturalistic models for the history of Earth’s life is that natural changes in the genomes of life will be responsible for the observed changes in the physical body structures (morphology) of life. Consequently, evolutionary trees (phylogenies, see figure 1) developed from the observed patterns in present-day genomes and the presumed natural rates of change of those genomes (molecular clocks). Assuming that strictly natural processes are responsible for the changes occurring throughout the history of life, the phylogenetic trees should match the morphological changes and the timing of those changes observed in the fossil record (or paleontological trees—see figure 2).

The same kind of match between the paleontology and phylogenetics can be realized if God intervened throughout life’s history. However, apparently only supernatural interventions can explain significant mismatches between phylogenetic and paleontological trees.

 

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Figure 1: Phylogenetic Tree of Life Derived from Completely Sequenced Genomes. The center represents the presumed first life-form on Earth. The genomes denoted on the outer circle are based on actual genetic data. The branching patterns in the inner circle presume that all species are entirely related to one another through strictly natural processes. Image credit: Ivica Letunic

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Figure 2: Spindle Diagram of the Presumed Evolution of Vertebrates. Width of the spindles indicates the number of extant families or the number of families represented in the fossil record. The curved (presumed) connecting lines are not supported by any physical remains. Image credit: Peter Bockman

In an open-access paper published in Nature Communications1, four computational biologists and biochemists led equally by Daniele Silvestro and Rachel Warnock concede:

“The fossil record and molecular phylogenies of living species can provide independent estimates of speciation and extinction rates, but often produce strikingly divergent results.”2

Silvestro, Warnock, and their two colleagues do not concede, however, that supernatural interventions explain the “strikingly divergent results.” They attempt to offer a possible naturalistic explanation.

Divergence Is Real and Striking

Biologists use over a dozen different definitions of a species. In their paper, the Silvestro-Warnock team defines a species as “an identifiable taxonomic unit (a lineage) that can persist through time, give rise to other species, and become extinct.”3

The team first recognizes that since “extant and fossil species are samples of the same underlying diversification process,”if the diversification process is by strictly natural means, researchers expect that in all cases the phylogenetic (presumed evolutionary) trees will match the paleontological (fossil record) trees. To put it another way, a match is expected since “methods used to estimate rates [of change] from fossils and phylogenies are based on the same underlying mathematical birth-death theory.”The team then documents that evolutionary biologists can no longer deny the frequent and striking divergences between phylogenetic and paleontological trees.

The Silvestro-Warnock team cited a recent study of extant terrestrial Carnivora.There, the estimated mean species longevity based on fossil evidence was 2.0 million years, contrasted with 9.8 million years derived from phylogenetics. They also cited a study demonstrating incongruence between phylogenies and fossils for primates.They noted that, at least for mammals, the occurrences of congruence are few.8

Speciation rates derived from phylogenetics consistently supersede those derived from the fossil record, while derived extinction rates are consistently lower than speciation rates. Perhaps the best studied example (see featured image) is for cetaceans (whales, dolphins, and porpoises). The Silvestro-Warnock team cited research showing:

“Phylogenetic estimates of diversification rates among cetaceans suggest speciation has exceeded extinction over the past 12 Myrimplying diversity has increased towards the recent. In contrast, analyses of the cetacean fossil record indicate extinction has exceeded speciation over this same interval, and that the diversity of cetaceans was in fact much higher than it is today.”10

In other words, the naturalistic biological evolution model based on phylogenetics predicts that introduction of new species has exceeded extinctions, but the fossil record shows that the reverse is true. The research team did not address the fact that the discrepancies between phylogenetics and the fossil record appear to increase with the complexity and the adult body size of the genus. By contrast, such a correlation is predicted from a biblical creation model perspective for life.11

Silvestro, Warnock and collaborators do point out that several other researchers have attempted to explain the discrepancies by underestimates of the statistical and systematic errors in the two methods. However, the discrepancies in fact are much too large to be attributed to these errors.12

Attempted Reconciliation

The Silvestro-Warnock team suggests that many of the discrepancies between phylogenetics and the fossil record are due to sensitivities to different speciation modes. They identify three distinct modes of speciation that can leave behind fossil evidence without impacting the calculated phylogenetic trees:

  1. Cladogenesis via budding: a speciation event that gives rise to one new species. The ancestral species persists and no extinction occurs.
  2. Cladogenesis via bifurcation: a speciation event that gives rise to two new species, replacing the ancestral species, which becomes extinct.
  3. Anagenetic speciation: evolutionary changes along a lineage that result in the origination of one new species and the extinction of the ancestral species.

They also point out that extinction without replacement is a frequent occurrence, where a species becomes extinct without leaving any descendants. More simply put, the fossil record includes extinct and extant (living) species; whereas phylogenetic data typically include extant species only.

Silvestro, Warnock, and their colleagues developed a model in which they unify budding, bifurcation, anagenesis, and extinction in a single “birth−death chronospecies” (BDC) process. Their BDC model shows that phylogenetic and paleontological speciation and extinction rate estimates will only be equal if all speciation has occurred through budding. Furthermore, they demonstrate that “even in an ideal scenario with fully sampled and errorless data sets, speciation and extinction rates can only be equal across phylogenetic and stratigraphic inferences if all speciation events have occurred through budding and no speciation has occurred through bifurcation or anagenesis”13 (emphasis added). Their BDC model also reveals that phylogenetic analysis indicating extinction equal to zero does not imply that no extinction occurred.

Actual Reconciliation

The team’s BDC model establishes that relative to the fossil record, phylogenetics always underestimates extinction rates. The fossil record, which is largely incomplete, underestimates the true extinction rates. Much higher extinction rates pose a serious challenge to all strictly naturalistic models for Earth’s life because higher extinction rates require higher speciation rates to explain the increasing diversity of life observed in the fossil record throughout life’s history.

This requirement of higher speciation rates is all the more problematic for Earth’s most advanced species. For mammals, birds, and advanced plants, the observed extinction rates far exceed the observed speciation rates during the era of human existence (God’s seventh day when, according to Genesis 2, God ceased from his creation work and allowed natural processes operate).

The Silvestro-Warnock BDC model also exposes a fundamental limitation in naturalistic explanations for the history of Earth’s life. Since all naturalistic models require more than one speciation mode, and since the only way to reconcile phylogenetics and paleontology is to posit just one speciation mode, something other than strictly natural processes must operate.

Some evolutionary biologists will insist on the caveat that perhaps some unknown natural process might salvage a reconciliation between phylogenetics and paleontology. However, it is difficult to conceive how a natural process of sufficient magnitude to reconcile phylogenetics and paleontology could remain undiscovered. It appears to me that a creation model positing that the supernatural Creator intervened at several times throughout life’s history to replace life-forms driven to extinction fully reconciles this “discrepancy.” I am reminded of a verse (Psalm 104:24) from the longest of the creation psalms:

How many are your works, Lord! In wisdom you made them all; the earth is full of your creatures.

Original article: New Speciation Model Challenges Evolution, Supports Creation

In Old English…

No one ever hindered the wicked by putting chains on the righteous.

Does Information Come from a Mind?

Imagine you’re flying over the desert, and you notice a pile of rocks down below. Most likely, you would think little of it. But suppose the rocks were arranged to spell out a message. I bet you would conclude that someone had arranged those rocks to communicate something to you and others who might happen to fly over the desert.

You reach that conclusion because experience has taught you that messages come from persons/people—or, rather, that information comes from a mind. And, toward that end, information serves as a marker for the work of intelligent agency.

Recently, a skeptic challenged me on this point, arguing that we can identify numerous examples of natural systems that harbor information, but that the information in these systems arose through natural processes—not a mind.

So, does information truly come from a mind? And can this claim be used to make a case for a Creator’s existence and role in life’s origin and design?

I think it can. And my reasons are outlined below.

Information and the Case for a Creator

In light of the (presumed) relationship between information and minds, I find it provocative that biochemical systems are information systems.

Two of the most important classes of information-harboring molecules are nucleic acids (DNA and RNA) and proteins. In both cases, the information content of these molecules arises from the nucleotide and amino acid sequences, respectively, that make up these two types of biomolecules.

The information harbored in nucleotide sequences of nucleic acids and amino acid sequences of proteins is digital information. Digital information is represented by a succession of discrete units, just like the ones and zeroes that encode the information manipulated by electronic devices. In this respect, sequences of nucleotides and amino acids for discrete informational units that encode the information in DNA and RNA and proteins, respectively.

But the information in nucleic acids and proteins also has analog characteristics. Analog information varies in an uninterrupted continuous manner, like radio waves used for broadcasting purposes. Analog information in nucleic acids and proteins are expressed through the three-dimensional structures adopted by both classes of biomolecules. (For more on the nature of biochemical information, see Resources.)

If our experience teaches us that information comes from minds, then the fact that key classes of biomolecules are comprised of both digital and analog information makes it reasonable to conclude that life itself stems from the work of a Mind.

Is Biochemical Information Really Information?

Skeptics, such as philosopher Massimo Pigliucci, often dismiss this particular design argument, maintaining that biochemical information is not genuine information. Instead, they maintain that when scientists refer to biomolecules as harboring information, they are employing an illustrative analogy—a scientific metaphor—and nothing more. They accuse creationists and intelligent design proponents of misconstruing scientists’ use of analogical language to make the case for a Creator.1

In light of this criticism, it is worth noting that the case for a Creator doesn’t merely rest on the presence of digital and analog information in biomolecules, but gains added support from work in information theory and bioinformatics.

For example, information theorist Bernd-Olaf Küppers points out in his classic work Information and the Origin of Life that the structure of the information housed in nucleic acids and proteins closely resembles the hierarchical organization of human language.2 This is what Küppers writes:

The analogy between human language and the molecular genetic language is quite strict. . . . Thus, central problems of the origin of biological information can adequately be illustrated by examples from human language without the sacrifice of exactitude.3

Added to this insight is the work by a team from NIH who discovered that the information content of proteins bears the same mathematical structure as human language. To this end, they discovered that a universal grammar exists that defines the structure of the biochemical information in proteins. (For more details on the NIH team’s work, see Resources.)

In other words, the discovery that the biochemical information shares the same features as human language deepens the analogy between biochemical information and the type of information we create as human designers. And, in doing so, it strengthens the case for a Creator.

Further Studies that Strengthen the Case for a Creator

So, too, does other work, such as studies in DNA barcoding. Biologists have been able to identify, catalog, and monitor animal and plant species using relatively short, standardized segments of DNA within genomes. They refer to these sequences as DNA barcodes that are analogous to the barcodes merchants use to price products and monitor inventory.

Typically, barcodes harbor information in the form of parallel dark lines on a white background, creating areas of high and low reflectance that can be read by a scanner and interpreted as binary numbers. Barcoding with DNA is possible because this biomolecule, at its essence, is an information-based system. To put it another way, this work demonstrates that the information in DNA is not metaphorical, but is in fact informational. (For more details on DNA barcoding, see “DNA Barcodes Used to Inventory Plant Biodiversity” in Resources.)

Work in nanotechnology also strengthens the analogy between biochemical information and the information we create as human designers. For example, a number of researchers are exploring DNA as a data storage medium. Again, this work demonstrates that biochemical information is information. (For details on DNA as a data storage medium, see Resources.)

Finally, researchers have learned that the protein machines that operate on DNA during processes such as transcription, replication, and repair literally operate like a computer system. In fact, the similarity is so strong that this insight has spawned a new area of nanotechnology called DNA computing. In other words, the cell’s machinery manipulates information in the same way human designers manipulate digital information. For more details, take a look at the article “Biochemical Turing Machines ‘Reboot’ the Watchmaker Argument” in Resources.)

The bottom line is this: The more we learn about the architecture and manipulation of biochemical information, the stronger the analogy becomes.

Does Information Come from a Mind?

Other skeptics challenge this argument in a different way. They assert that information can originate without a mind. For example, a skeptic recently challenged me this way:

“A volcano can generate information in the rocks it produces. From [the] information we observe, we can work out what it means. Namely, in this example, that the rock came from the volcano. There was no Mind in information generation, but rather minds at work, generating meaning.

Likewise, a growing tree can generate information through its rings. Humans can also generate information by producing sound waves.

However, I don’t think that volcanoes have minds, nor do trees—at least not the way we have minds.”

Roland W. via Facebook

I find this to be an interesting point. But, I don’t think this objection undermines the case for a Creator. Ironically, I think it makes the case stronger. Before I explain why, though, I need to bring up an important clarification.

In Roland’s examples, he conflates two different types of information. When I refer to the analogy between human languages and biochemical information, I am specifically referring to semantic information, which consists of combinations of symbols that communicate meaning. In fact, Roland’s point about humans generating information with sound waves is an example of semantic information, with the sounds serving as combinations of ephemeral symbols.

The type of information found in volcanic rocks and tree rings is different from the semantic information found in human languages. It is actually algorithmic information, meaning that it consists of a set of instructions. And technically, the rocks and tree rings don’t contain this information—they result from it.

The reason why we can extract meaning and insight from rocks and tree rings is because of the laws of nature, which correspond to algorithmic information. We can think of these laws as instructions that determine the way the world works. Because we have discovered these laws, and because we have also discovered nature’s algorithms, we can extract insight and meaning from studying rocks and tree rings.

In fact, Küppers points out that biochemical systems also consist of sets of instructions instantiated within the biomolecules themselves. These instructions direct activities of the biomolecular systems and, hence, the cell’s operations. To put it another way, biochemical information is also algorithmic information.

From an algorithmic standpoint, the information content relates to the complexity of the instructions. The more complex the instructions, the greater the information content. To illustrate, consider a DNA sequence that consists of alternating nucleotides, AGAGAGAG . . . and so on. The instructions needed to generate this sequence are:

  1. Add an A
  2. Add a G
  3. Repeat steps 1 and 2, x number of times, where x corresponds to the length of the DNA sequence divided by 2

But what about a DNA sequence that corresponds to a typical gene? In effect, because there is no pattern to that sequence, the set of instructions needed to create that sequence is the sequence itself. In other words, a much greater amount of algorithmic information resides in a gene than in a repetitive DNA sequence.

And, of course, our common experience teaches us that information—whether it’s found in a gene, a rock pile, or a tree ring—comes from a Mind.

Resources

Original article: Does Information Come from a Mind?

Elsuon – Amazon Review (★★★★★)

Elsuon Offer

This is an epic fantasy with a different, fresh prose. Unapologetic in his exercise of the English language (another reason to be thankful for the Kindle Dictionary) the author educates as he entertains. Regular readers will appreciate the sentence structure and word choices enhancing the story and a deeper immersion into this world. Unique and artistic would be a fair summary.

I thoroughly enjoyed the first book though the end is unexpectedly abrupt — understanding the story is multiple volumes helps to both forgive, and generate anticipation for the next book!

Full disclosure: the author is an old, close friend who has honed his gift, weaving tales and illustrations both verbal and visual, since we were youngsters. I’m relieved David has finally “formalized his gifts” so to speak… we’ve begged him for years.

Discovering D&D, creating worlds and wonder (this book being a small fraction thereof) – the nostalgia of reading our adventures is heavy and sweet.

I’m giddy with anticipation for the unraveling tales of our youth and we are definitely out of the gate at a spirited pace! One request – we need a map of this world in a future book!

From Amazon buyer PraeValien


A great review from an old friend.

Killing Words

I came across this tagline on Instagram by an artist who is clearly still in darkness.

Pet the snake, enjoy the darkness, ignore the faith.

This person has chosen killing words and doesn’t even know it.

Death and life are in the power of the tongue, and they that love it shall eat the fruit thereof.

Proverbs 18:21

Jeffrey Epstein Commits Suicide

The millionaire convicted of operating a profane underage sex-ring for the political powerful of the world was allowed to commit suicide today.

Right on schedule.

Don’t worry, noble citizens! Our completely effective and reliable Federal Bureau of Investigation and our equally impartial Department of Justice is on the case!