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

Filed under: News, , , , , , , ,

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.

Excerpt:

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, , , , , ,

J. P. Moreland explains the meaning of happiness in the Christian worldview

From happiness expert and Christian philosopher J.P. Moreland.

Excerpt:

According to ancient thought, happiness is a life well lived, a life that manifests wisdom, kindness and goodness. For the ancients, the happy life — the life we should dream about — is a life of virtue and character. Not only did Plato, Aristotle, the Church Fathers and medieval theologians embrace this definition, but Moses, Solomon and (most importantly) Jesus did, too. Sadly their understanding is widely displaced by the contemporary understanding of happiness defined as pleasure and satisfaction, a subjective emotional state associated with fleeting, egocentric feelings.

Consider the differences:

Contemporary Understanding Classical Understanding
Happiness is: Happiness is:
1. Pleasure and satisfaction 1. Virtue and character
2. An intense feeling 2. A settled tone
3. Dependent on external circumstances 3. Depends on internal state; springs from within
4. Transitory and fleeting 4. Fixed and stable
5. Addictive and enslaving 5. Empowering and liberating
6. Irrelevant to one’s identity, doesn’t color the rest of life and creates false/empty self 6. Integrated with one’s identity, colors rest of life and creates true/fulfilled self
7. Achieved by self-absorbed narcissism; success produces a celebrity 7. Achieved by self-denying apprenticeship to Jesus; success produces a hero

How can we be certain Jesus is inviting us to a classical understanding of happiness in Matthew 16:24-26? He isn’t talking about going to heaven rather than hell, nor is He telling his followers how to avoid premature death. Where Matthew writes, “what will a man be profited, if he gains the whole world, and forfeits his soul” (emphasis added), Luke clarifies Jesus’ teaching by replacing “his soul” with the word “himself” (Luke 9:25). The issue is finding one’s self vs. losing one’s self. More specifically, to find one’s self is to find out how life ought to look like and learn to live that way; it’s to become like Jesus, with character that manifests the fruit of the Spirit and the radical nature of Kingdom living; it’s to find out God’s purposes for one’s life and to fulfill those purposes in a Christ-honoring way.

I like that “success produces a hero”. Who doesn’t want to be a hero? I certainly do.

In one of his lectures, Dr. Moreland says, and I quote: “Happiness is the freedom to do what we ought to do”. That’s right. When a person is free to comply with God’s design for human flourishing, then he/she is happy. My biggest source of unhappiness is the feeling that I cannot be who I want to be as a Christian. It’s getting even worse when I think about how the government is now using force to prevent me from spending what I earn the way I want, and saying what I want about the issues of the day, regardless of who is offended. I am becoming increasingly thankful for the time I spend with other dedicated Christians. That’s when I can be myself and not worry about what anyone is going to think of me. This is no small source of happiness.

Filed under: Commentary, , , , , , , ,

New study: invisible shield above the Earth protects us from electron threat

Science Daily reports on a new paper published in the prestigious peer-reviewed journal Nature.

Excerpt:

A team led by the University of Colorado Boulder has discovered an invisible shield some 7,200 miles above Earth that blocks so-called “killer electrons,” which whip around the planet at near-light speed and have been known to threaten astronauts, fry satellites and degrade space systems during intense solar storms.

The barrier to the particle motion was discovered in the Van Allen radiation belts, two doughnut-shaped rings above Earth that are filled with high-energy electrons and protons, said Distinguished Professor Daniel Baker, director of CU-Boulder’s Laboratory for Atmospheric and Space Physics (LASP). Held in place by Earth’s magnetic field, the Van Allen radiation belts periodically swell and shrink in response to incoming energy disturbances from the sun.

As the first significant discovery of the space age, the Van Allen radiation belts were detected in 1958 by Professor James Van Allen and his team at the University of Iowa and were found to be composed of an inner and outer belt extending up to 25,000 miles above Earth’s surface. In 2013, Baker — who received his doctorate under Van Allen — led a team that used the twin Van Allen Probes launched by NASA in 2012 to discover a third, transient “storage ring” between the inner and outer Van Allen radiation belts that seems to come and go with the intensity of space weather.

The latest mystery revolves around an “extremely sharp” boundary at the inner edge of the outer belt at roughly 7,200 miles in altitude that appears to block the ultrafast electrons from breeching the shield and moving deeper towards Earth’s atmosphere.

“It’s almost like theses electrons are running into a glass wall in space,” said Baker, the study’s lead author. “Somewhat like the shields created by force fields on Star Trek that were used to repel alien weapons, we are seeing an invisible shield blocking these electrons. It’s an extremely puzzling phenomenon.”

A paper on the subject was published in the Nov. 27 issue of Nature.

Something for us to be thankful for on Thanksgiving Day.

Filed under: News, , , , , , , ,

New study: how the hummingbird performs stunning feats of aerobatics

Hummingbird in flight

Hummingbird in flight

New study reported by Science Daily.

Excerpt:

The sight of a tiny hummingbird hovering in front of a flower and then darting to another with lightning speed amazes and delights. But it also leaves watchers with a persistent question: How do they do it?

Now, the most detailed, three-dimensional aerodynamic simulation of hummingbird flight conducted to date has definitively demonstrated that the hummingbird achieves its nimble aerobatic abilities through a unique set of aerodynamic forces that are more closely aligned to those found in flying insects than to other birds.

The new supercomputer simulation was produced by a pair of mechanical engineers at Vanderbilt University who teamed up with a biologist at the University of North Carolina at Chapel Hill. It is described in the article “Three-dimensional flow and lift characteristics of a hovering ruby-throated hummingbird” published this fall in the Journal of the Royal Society Interface.

For some time researchers have been aware of the similarities between hummingbird and insect flight, but some experts have supported an alternate model which proposed that hummingbird’s wings have aerodynamic properties similar to helicopter blades. However, the new realistic simulation demonstrates that the tiny birds make use of unsteady airflow mechanisms, generating invisible vortices of air that produce the lift they need to hover and flit from flower to flower.

You might think that if the hummingbird simply beats its wings fast enough and hard enough it can push enough air downward to keep its small body afloat. But, according to the simulation, lift production is much trickier than that.

For example, as the bird pulls its wings forward and down, tiny vortices form over the leading and trailing edges and then merge into a single large vortex, forming a low-pressure area that provides lift. In addition, the tiny birds further enhance the amount of lift they produce by pitching up their wings (rotate them along the long axis) as they flap.

Hummingbirds perform another neat aerodynamic trick — one that sets them apart from their larger feathered relatives. They not only generate positive lift on the downstroke, but they also generate lift on the upstroke by inverting their wings. As the leading edge begins moving backwards, the wing beneath it rotates around so the top of the wing becomes the bottom and bottom becomes the top. This allows the wing to form a leading edge vortex as it moves backward generating positive lift.

According to the simulation, the downstroke produces most of the thrust but that is only because the hummingbird puts more energy into it. The upstroke produces only 30 percent as much lift but it takes only 30 percent as much energy, making the upstroke equally as aerodynamically efficient as the more powerful downstroke.

Large birds, by contrast, generate almost all of their lift on the downstroke. They pull in their wings toward their bodies to reduce the amount of negative lift they produce while flapping upward.

Awesome design in nature!

So the question I have from reading the article is this. Do birds and flying insects have a recent common ancestor? I don’t have too many friends who can answer this for me, but I asked one of them and they both said there is no recent common ancestor for hummingbirds and flying insects. So this looks like another example of convergence – common design in two animals that don’t share a recent common ancestor.

Filed under: News, , , , , , , ,

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