Wintery Knight

…integrating Christian faith and knowledge in the public square

New study: bird origins poses a convergence challenge to common ancestry

Male normal gray cockatiel preens his wife's crest

Male cockatiel preens his wife’s crest

We have to start this post with the definition of convergence in biology.

In evolutionary biology, convergent evolution is the process whereby organisms not closely related (not monophyletic), independently evolve similar traits as a result of having to adapt to similar environments or ecological niches.

It is the opposite of divergent evolution, where related species evolve different traits.

On a molecular level, this can happen due to random mutation unrelated to adaptive changes; see long branch attraction. In cultural evolution, convergent evolution is the development of similar cultural adaptations to similar environmental conditions by different peoples with different ancestral cultures. An example of convergent evolution is the similar nature of the flight/wings of insects, birds, pterosaurs, and bats.

All four serve the same function and are similar in structure, but each evolved independently.

And now, this new article on convergence in birds and humans, from Evolution News.

They write:

Everyone is familiar with the striking ability of certain birds (such as parrots) to vocalize speech, much as humans do. Well, according to the new papers published in Science that I wrote about earlier, confirming that birds arose explosively, those vocalization abilities are the result of “convergent evolution” at both the morphological and genetic levels.

Nature News reports, “The authors also conclude that vocal learning may have evolved independently in the ancestors of parrots, hummingbirds and songbirds.” But this is about more than just birds. According to a Science Daily article about the technical papers, the genetic “convergent evolution” extends to birds and humans:

“We’ve known for many years that the singing behavior of birds is similar to speech in humans — not identical, but similar — and that the brain circuitry is similar, too,” said Jarvis, an associate professor of neurobiology at the Duke University Medical School and an investigator at the Howard Hughes Medical Institute. “But we didn’t know whether or not those features were the same because the genes were also the same.”Now scientists do know, and the answer is yes — birds and humans use essentially the same genes to speak.

After a massive international effort to sequence and compare the entire genomes of 48 species of birds representing every major order of the bird family tree, Jarvis and his colleagues found that vocal learning evolved twice or maybe three times among songbirds, parrots and hummingbirds.

Even more striking is that the set of genes involved in each of those song innovations is remarkably similar to the genes involved in human speaking ability.

If you’re already thinking “This isn’t ‘convergent evolution,’ it’s common design,” you haven’t seen the best part yet. Science Daily goes on:

One of the Dec. 12 papers in Science found there is a consistent set of just over 50 genes that show higher or lower activity in the brains of vocal learning birds and humans. These changes were not found in the brains of birds that do not have vocal learning and of non-human primates that do not speak, according to this Duke team, which was led by Jarvis; Andreas Pfenning, a graduate of the PhD program in computational biology and bioinformatics (CBB); and Alexander Hartemink, professor of computer science, statistical science and biology.”This means that vocal learning birds and humans are more similar to each other for these genes in song and speech brain areas than other birds and primates are to them,” Jarvis said.

These genes are involved in forming new connections between neurons of the motor cortex and neurons that control the muscles that produce sound.

The Science paper puts it this way:

More than 50 genes contributed to their convergent specialization and were enriched in motor control and neural connectivity functions. These patterns were not found in vocal nonlearners, but songbird RA was similar to layer 5 of primate motor cortex for another set of genes, supporting previous hypotheses about the similarity of these cell types between bird and mammal brains.(Pfenning et al., “Convergent transcriptional specializations in the brains of humans and song-learning birds,” Science, Vol. 346: 1256846-1 – 1256846-13 (December 12, 2014). )

So certain birds and humans use the same genes for vocalization — but those genetic abilities are absent in non-human primates and birds without vocal learning? If not derived from a common ancestor, as they clearly were not, how did the genes get there? This kind of extreme convergent genetic evolution points strongly to intelligent design.

The rest of the article talks about the conclusions of the study authors – they think it’s a huge problem – and it is.

I hope you’re all beginning to see why I love birds so much. I just adore them. In fact, I am excited about them right now, and will probably appear silly by gushing about how great they are. Fortunately, my editorette is not hear to stop me!

Birds are not just a living disproof of naturalistic evolution. They are also loveable and adorable. (Especially parrots, of course) If you guys are considering a pet, go out and get yourself a cockatiel, if it’s your first bird, or a green-cheek conure, if you’ve had birds before. Just remember that they live 20-25 years, so you have to be ready to face responsibilities, expectations and obligations if you make a commitment like that. And you know what? That is totally awesome, to have someone to care about. It’s good stewardship to care for animals. And if you can’t commit to a parrot of your own over the long haul, then put out an additional bird feeder this winter, and vote against wind power. Wind power kills birds, and I hate it.

Also, that bird in the Evolution News post is an Indian ringneck parrot. And they are awesome!!!!

More posts on convergence

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New study: enzymes cannot easily evolve to perform other functions

Can atheism explain the origin of life?

Can atheism explain the origin of life?

This is from Evolution News.


I am pleased to announce the publication of a new paper from Biologic Institute, a research organization devoted to investigating the limits of unguided evolution and advancing the development of a new paradigm for biology based on intelligent design. This paper, “Enzyme Families — Shared Evolutionary History or Shared Design? A Study of the GABA-Aminotransferase Family,” is the closing chapter of our long-term study of bacterial enzymes to determine if they can be coopted to new functions. The answer to this question is important for the evolution debate. If enzymes can’t be recruited to genuinely new functions by unguided means, no matter how similar they are, the evolutionary story is false.

Published in the journal BIO-Complexity, the work was done by Marci Reeves, Doug Axe, and myself [Ann Gauger].

In a previous paper we described the difficulty of coopting the enzyme Kbl to perform the function of BioF. The two enzymes are very similar in structure (see below) but have different reaction chemistries and different functions in the cell. We wanted to know if a mutated Kbl could replace missing BioF function. After changing nearly every amino acid in Kbl’s active site (where its chemistry is carried out) to look like BioF, Kbl never was able to make the switch to BioF’s function.

In this paper we expanded the story to include nine of the most closely related enzymes to BioF, including one that is supposed to be able to carry out both BioF’s and Kbl’s chemistry. Using random mutagenesis we tested every single-base mutation in those nine genes. None of them was within one mutation of cooption. We went on to test for cooption the two most likely enzymes by generating two-base combinations of mutations. After testing 70 percent of all possible two-base mutations for each enzyme, or about 40 million cells each, that also failed.

What does this mean? In an evolutionary scenario, to get an enzyme to switch functions the first step is to make a spare copy that can be mutated without destroying a function the cell needs. Second, the cell has to overproduce the mutating enzyme, because any newly emerging enzyme will be very bad at the job at first. To compensate there will need to be lots of enzyme around. Third, there is the problem of finding the right combination of mutations by random search.

Taken together, since we found no enzyme that was within one mutation of cooption, the total number of mutations needed is at least four: one for duplication, one for over-production, and two or more single base changes. The waiting time required to achieve four mutations is 1015 years. That’s longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations.

Read the rest of the post, they deal with criticisms to the paper.

Here is one Darwinist’s view of this enzyme proble, which they mention in a follow-up post.

Look: (links removed)

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’ scenarios 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.

That’s insufferable badness.

It’s not enough for Darwinists to take the age of the universe and then assert that anything can happen in that time. The time from the cooling of the Earth to the appearance of first life is on the order of millions of years. There just isn’t time to generate these organic components by chance.

Filed under: Polemics, , , , , ,

Stephen C. Meyer and Keith Fox debate intelligent design and evolution

From Justin Brierley’s “Unbelievable” podcast.


Stephen Meyer is a leading proponent of Intelligent Design who directs the Centre for Science and Culture at the Discovery Institute in Seattle. His [first] book “Signature in the Cell” claims to show that the DNA code is the product of intelligent mind, not naturalistic processes. Keith Fox is Professor of Biochemistry at Southampton University. He chairs the UK Christians in Science network but disagrees strongly with ID. They debate how life could have originated and whether design is allowed as an explanation in science.

Summary: (stuff in italics is my snarky paraphrase)


  • background and how he got interested in intelligent design
  • his research focus is on the origin of life – the first replicator
  • summarizes the history of origin of life studies
  • authored the book “Signature in the Cell”
  • the DNA enigma: where did the information in DNA come from?
  • naturalistic explanations of the DNA information have failed
  • but intelligent agents are known to be able to produce information
  • the best explanation of the information in DNA is that an intelligent agent authored it
  • Meyer’s book was named by atheist philosopher of science Thomas Nagel as a Times Literary Supplement Book of the Year in 2010
  • why is design so controversial? Many people think that Darwin explained why nature appears design
  • the Darwinian view is that nature can create the appearance of design using mutation and selection
  • however, Darwinian mechanisms cannot explain the origin of the first living cell, it assumes replication, and the origin of life is about where the first replicator comes from


  • Meyer’s argument is not about the evolution of life after the first cell
  • Meyer’s case for design is about the origin of life
  • naturalists do not know a naturalistic explanation for the origin of life
  • there are a number of naturalistic hypotheses for the origin of life, like the RNA-first hypothesis
  • maybe in a few years one of them will turn out to be correct
  • what intelligent design is arguing from a gap in our current naturalistic knowledge to infer that God intervened in nature


  • that’s not what intelligent design is at all
  • the approach ID theorists use is the inference to best explanation
  • you evaluate all explanations, non-intelligent causes and intelligent causes
  • you prefer the best possible explanation
  • we know that minds are capable of producing information just like the information we find in DNA


  • living cells replicate, so they have the ability to introduce mutations as they replicate and then some of those mutations can be selected
  • so maybe the process of replicating that living cells do created the first living cell
  • maybe the first living cell created itself, X brought X into being, self-creation, what’s irrational about that?


  • the issue is the origin of life – where did the first living cell come from?
  • you cannot appeal to the operations that a living cell can perform to explain the origin of the first living cell
  • there was no first living cell operating before the first living cell
  • there was no replication, mutation or selection before the first living cell
  • in fact, in my book I show that there is no known naturalistic mechanism that is able to produce the information needed for the first living cell
  • nothing can create itself, that is self-contradictory
  • Well, you are just saying that because something is complex that God did it
  • Sadly, no. What I actually said needed to be explained was the information, not complexity
  • And we know from software engineering that the process of adding information to code is performed by programmers
  • in the absence of any adequate naturalistic explanation for information, we are justified in taking the explanation that we are familiar with – namely, intelligent agency – based on our uniform, universal experience of what causes information
  • well, maybe we can appeal to the mutation and selection in existing living cells to explain the origin of the first living cell
  • maybe there were living cells before the first living cell, and then these other living cells created the first living cell
  • we can’t keep invoking mutation and selection when those processes are not operating prior to the origin of the first living cell
  • well maybe some bare-bones self-replication molecule was a precursor to the first living cell
  • even to generate very limited replicator would require a large amount of information
  • the argument I am making is – where does the evolution come from?
  • well, maybe we will think of an explanation for information that is naturalistic in 20 years
  • we’ve thought of explanations to things that were NOT information before
  • so maybe we will be able to think of something to explain information based on our ability to explain NOT information before

Moderator: Change topics: the Dover decision


  • the Discovery Institute opposed the policy that causes the trial
  • the wording of the statute was poor
  • the judge was completely wrong in his decision
  • young earth creationists used the phrase “intelligent design” to cover their agenda
  • intelligent design is an inference using the normal methods of science
  • intelligent design is a science stopper because it stops looking for a naturalistic explanation
  • everything in nature must have a naturalistic explanation
  • everything has to be explained using matter and time and chance
  • it just has to be that way!!!!
  • well, what luck would you have explaining an effect like Mt. Rushmore?
  • can you explain that using matter,time and chance?
  • Mt. Rushmore was the product of intelligence, not wind and erosion
  • similarly, there is information in the cell, and we know that intelligence causes information
  • So you are saying that we don’t understand and therefore an intelligence is necessary?


  • no I am saying we DO understand and we are making an inference based on that understanding
  • you are the one who is insisting on a material explanation because you pre-suppose materialism
  • we know that minds have causal powers, and we can infer mind as an explanation from information
  • well nature is a seamless chain of material causes and effects
  • agents can act without violating the laws of nature
  • even humans can act as intelligent agents to create information in books, and they don’t violate the laws of nature
  • intelligent causes are real, and they explain effects in nature
  • you’re trying to impose on science something to do with meaning and purpose
  • no that’s not what we’re doing, we’re inferring from from the fact that we ourselves are known causes of information to the fact that an intelligence cause is the best explanation for information in the cell
  • but I am a materialist, I need a materialist explanation
  • mind IS an answer to the how question
  • we infer to mind in many other scientific disciplines, like cryptography, archaeology, etc.
  • a materialist might accuse an archaeologist of engaging in a “scribe-of-the-gaps” argument, but the best explanation of an artifact with information is a scribe
  • we are inferring that mind is the cause from the nature of the effect: information
Moderator: is it appropriate to call DNA “information”


  • well DNA is just a molecular polymer, any reference to information is just by analogy
  • DNA is a molecular polymer, but it also exhibits the property of specified complexity
  • the arrangement of bases, which function as machine instructions in a software program, for performings task in the cell
  • we have observed that the property of specified complexity always comes from an intelligence
  • well, maybe there are other sequences that would work, so maybe it’s really not uncommon to develop functioning sequences by chance alone, without an intelligence
  • you can measure how precise the functional specificity is in DNA and proteins

Moderator: is Shannon information the same as functional information


  • Shannon information refers to the sequences of digits or symbols that do not necessarily have any function, i.e. – a four character string QSZX has as much Shannon information as WORD. However, only the latter is functional against the pattern of the English language. There are arrangements of DNA bases and amino acids that have the same number of symbols/characters as a functional sequence would have, but they have no biological function – they do not exhibit specified complexity
  • Well, maybe there are lots and lots of sequences of DNA and proteins so that it is fairly easy to get a functional one by chance


  • DNA sequences that are functional are extremely rare, protein sequences are even more rare
  • this is not my opinion, this is what the research shows – functional protein sequences are rare
  • well maybe there are other functional sequences that are occur before the first functional sequence that are precursors to the first functional sequence
  • maybe there are billions of years of replication, mutation and selection before the first replication, mutation and selection


  • you can’t get to the first selectable functional sequence by appealing to precursor selectable functional sequences – there are no selectable functional sequences before the FIRST one
  • you have to get the first selectable functional sequence by chance alone, because there is nothing to mutate or select before the first replicator
  • the chance hypothesis has been rejected because the minimal amount of information for the simplest replicator is too high to get by chance alone, given the resources, including time, that are available

Moderator: Keith are you confident that naturalism will be able to substantiate these naturalism-of-the-gap speculations that you offer in response to Meyer’s actual science that we have today? 


  • well, it is hard to know for sure because it was just a fluke event
  • but there’s nothing irrational or unscientific or miraculous about it – the fluke would have a material explanation
  • there is nothing that we can detect that would implicate God, my speculations about a fluke which I cannot observe or measure or test would all be compatible with an atheistic worldview that omits God as a causal entity


  • where are those material processes that could account for this fluke then?
  • the whole point of this argument is that the information in DNA transcends the material components in the sequence
  • it’s the arrangement of the material parts/letters/characters/symbols/instructions that needs to be explained
  • Well, I just have a different philosophy of science that rules out intelligent causation a priori


  • Yes, that’s the difference between us – you pre-suppose that all explanations of natural phenomena must exclude intelligent causes

There is a bit more where Meyer talks about how parts of the cell are implementations of various design patterns (Gang of Four design patterns) that are used by software architects who design software.

Find more posts on Stephen C. Meyer here.

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Blake Giunta and Justin Schieber debate Christian theism vs naturalism

Here is the video of the debate:

And Blake’s summary of the debate from his web site.

In Justin’s opening statement, he made four arguments:

  1. The existence of rational unbelief is more consistent with naturalism
  2. Darwinian evolution is more consistent with naturalism
  3. The hostility to life in most of the universe is is more consistent with naturalism
  4. The existence of suffering among sentient beings is more consistent with naturalism

These are all good arguments for naturalism. That’s what atheists argue if they are willing to bear the burden of proof – those are quality arguments.

In Blake’s opening statement, he made three arguments:

  1. The existence of “the moral arena” is more consistent with theism
  2. The intelligibility and discoverability of the universe is more consistent with theism
  3. The historicity of the resurrection of Jesus is more consistent with theism

These arguments are also good arguments for theism and the last one is good for Christian theism. Again, quality arguments.

Here’s part of his summary of his first argument, which I think is different from anyone else:

The Moral Arena is very unexpected if Naturalism is true

By contrast, on naturalism, a Moral Arena could not be more unexpected.

Getting brains

(a) A Universe is entirely unexpected,
(b) and even if there were one, the naturalist has no reason to expect that the Universe would be life-permitting (because of our “fine-tuning of physics for life” discoveries),
(c) and even if it were life-permitting, the naturalist has no reason to expected that there would be an origin of life event in it.
(d) and even if one (or more happened), the naturalist has no reason to expect that it would culminate in the existence of brains or anything that functions like a brain.

The alleged problem with this is that, it means that the likelihood of brains existing, on naturalism, are unfathomably low. Blake noted that the improbabilities of (a)-(d) could be multiplied together, and the likelihood of this chain of events assuming the truth of naturalism was well below .0000000001, just for the fine-tuning problem alone.

From there, getting consciousness

But getting such brains is not enough to get a Moral Arena. The next improbability was the brains being conscious. Once again, this could not be more unexpected on naturalism. Blake argued that consciousness is not adaptive on naturalism, because the brain is basically the machine, and consciousness was like smoke–the machine would evolve and operate the same with or without the smoke. Moreover, as a naturalist looks at the object of a brain, nothing “in it” would lead him to expect it has conscious experience, any more than looking at a star or electron would. Finally, Blake noted that many of the most prestigious naturalists argue that consciousness is not only entirely unexpected, but actually incompatible with naturalism–it has to be an illusion.

From there, getting beliefs

Blake then said, “Ok, but lets say you do get conscious brains. What is the likelihood, on naturalism, that they would also have these very particular things called beliefs?” He made the same moves: it could not be more unexpected on naturalism, and moreover some of the most prominent naturalists argue that beliefs are incompatible with naturalism. The reason is because beliefs are “about” things, but material objects (like rocks and brains) can’t be “about” anything. So beliefs are non-physical, which naturalism cannot accommodate.

From there, getting moral beliefs (for a Moral Arena)

Finally, Blake noted one more requirement: “Ok, so lets say you evolve conscious brains with beliefs, what is the likelihood that they would have moral beliefs in particular.” There is no reason to think moral beliefs, beliefs about good and evil, or right and wrong, would ever evolve twice in the entire Universe. But then why anticipate that they would have evolved even once? Again, Naturalism has no such reason. In each of these cases, all I can do is helplessly look at what has occurred, and say “oh, interesting.”

All together now

Calculating the final improbability involves multiplying the unlikelihood of brains evolving (.0000000001) with the unlikelihood of evolved brains being conscious (e.g. .01), with the unlikelihood of evolved conscious brains having beliefs (e.g. 01) with the unlikelihood of such brains having moral beliefs in particular (e.g. .5). The final probability is extraordinarily low, and insofar as moral beliefs are required for a moral arena, the likelihood of a moral arena existing on naturalism is unfathomably low (e.g. it seems like on naturalism, the likelihood of a moral arena would be far less than  .000001%), while on theism it is not nearly so low (e.g. well over a 1% likelihood, and certainly no less). By definition then, the Moral Arena is evidence for theism, and it turns out to be phenomenally strong evidence given the difference in expectations. Originally, the plan was to give Justin a sheet of paper to fill these in, so we could talk specifically about any particularly unreasonable values he assigned to these probabilities.

If you are looking for a classy, civil debate, this is the debate you are looking for. Justin is a great speaker and presented four real arguments, but I think Blake had him beat on on substance, because Justin did not respond adequately to Blake’s arguments.

One point that came up in the debate was the distinction between coarse-tuning and fine-tuning, and whether the range of possible values for the numbers in question could be infinite. Allen Hainline saw the debate live, and he wrote this blog post on that topic. is a web site for training Christians on how to map the flow of debates. If you haven’t already done so, check it out. Use the tree menu on the left to navigate the site by expanding topics that interest you.

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Darwinists thought whale hips were accidents of evolution, then science happened

Another win for reason in the long war between science and naturalistic philosophy.

Science Daily reports.


Both whales and dolphins have pelvic (hip) bones, evolutionary remnants from when their ancestors walked on land more than 40 million years ago. Common wisdom has long held that those bones are simply vestigial, slowly withering away like tailbones on humans.

New research from USC and the Natural History Museum of Los Angeles County (NHM) flies directly in the face of that assumption, finding that not only do those pelvic bones serve a purpose — but their size and possibly shape are influenced by the forces of sexual selection.

“Everyone’s always assumed that if you gave whales and dolphins a few more million years of evolution, the pelvic bones would disappear. But it appears that’s not the case,” said Matthew Dean, assistant professor at the USC Dornsife College of Letters, Arts and Sciences, and co-corresponding author of a paper on the research that was published online by Evolution on Sept. 3.

[…]”Our research really changes the way we think about the evolution of whale pelvic bones in particular, but more generally about structures we call ‘vestigial.’ As a parallel, we are now learning that our appendix is actually quite important in several immune processes, not a functionally useless structure,” Dean said.

This is not the first time this has happened – as they said, the appendix now has known functionality.

Flashback: ENCODE study falsifies Darwinian prediction that most of the genome is “Junk” DNA.

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