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: another biological Big Bang, this time for bird development

Hummingbird in flight

Hummingbird in flight

Story from Evolution News about a new study exploring the genomes of birds.

Excerpt:

The evidence for intelligent design just keeps getting stronger. It’s long been known that the Cambrian explosion isn’t the only explosion of organisms in the fossil record. There’s also something of a fish explosion, an angiosperm explosion, and a mammal explosion. Paleontologists have even cited a “bird explosion,” with major bird groups appearing in a short time period. Frank Gill’s 2007 textbook Ornithology observes the “explosive evolution” of major living bird groups, and a paper in Trends in Ecology and Evolutiontitled “Evolutionary Explosions and the Phylogenetic Fuse” explains:

A literal reading of the fossil record indicates that the early Cambrian (c. 545 million years ago) and early Tertiary (c. 65 million years ago) were characterized by enormously accelerated periods of morphological evolution marking the appearance of the animal phyla, and modern bird and placental mammal orders, respectively.

Now, a massive genetic study published in Science has confirmed the fossil evidence that birds arose explosively. According to an article titled, “Rapid bird evolution after the age of dinosaurs unprecedented”:

His research helped confirm that some of the first lineages of modern birds appeared about 100 million years ago but that almost all of the modern groups of birds diversified in a small window of less than 10 million years, just after the dinosaurs were wiped out by an asteroid.

Another news article calls it a “‘Big Bang’ of bird evolution” and one of the technical papers uses the same language:

Paleobiological and molecular evidence suggests that such “big bang” radiations occurred for neoavian birds (e.g., songbirds, parrots, pigeons, and others) and placental mammals, representing 95% of extant avian and mammalian species, after the Cretaceous to Paleogene (K-Pg) mass extinction event about 66 million years ago (Ma).

The article further cites “an explosive diversification within Neoaves.” So both fossil and genetic evidence suggests diverse organisms arose in an “explosion” or “big bang” that lasted “less than 10 million years.”

I am excited to hear about this! Birds are my most favorite creatures in the whole world!

One of the other papers they looked at in the post found large numbers of species appearing within a 1-3 million year window.

The data from these genome studies also conflicts with the phylogenies that are different from phylogenies built from body plans.

Look:

[T]his molecular study has separated many groups previously thought to be closely related by morphological studies, as is made very clear from Figure 1 of the paper. Bird relations are thus quickly becoming a classic case of conflict between molecule-based and morphology-based trees. As Nature notes, in this study “the tree of life for birds has been redrawn by geneticists.” They simply appeal to convergent evolution (or other mechanisms) to explain away these non-tree-like patterns.

It’s not a tree – it’s a lawn.

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, , , , , ,

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, , , , , , , ,

Why does God allow so much natural evil from earthquakes?

My friend Eric Chabot of Ratio Christi shared this video with me, which features chemist Fazale Rana.

The video runs under 4 minutes:

Basically, there was an atheist who challenged the idea that nature is designed because there are things in nature which cause suffering, like earthquakes and volcanoes.

Now the first thing to note is that atheists commonly think that God’s job is to make humans happy. If he doesn’t make humans feel happy – regardless of their knowledge of him and relationship with him – then he is a big failure. Many atheists think that, it is one of the most common reasons why people become atheists. But of course anyone who reads the Bible and reads the story of Jesus knows that the purpose of life on God’s view is for humans to know him and to be disciples of a suffering Messiah who sacrifices himself in order to obey God the Father.  So that’s the first thing to say – purpose of life not happiness, but knowledge of God and being a disciple of Jesus. This may involve all kinds of suffering, and that’s to be expected.

Second, there is a response to the problem of evil based on the necessity of natural laws. The argument goes that you can’t have genuine morality without a predictable, knowable system of natural laws.

But I want to talk about something different in this post. In the video, Dr. Rana thinks that many of the things that cause suffering in the natural world are actually necessary for life to exist at all. He provides the example of plate tectonics in his video above, and I want to take that one and add to it the example of heavy element production and the stellar lifecycle. These are both from a book called “Rare Earth”, which is written by two non-Christians – Peter Ward and Donald Brownlee, but I’ll link to web sites to make the case.

Plate tectonics.

Here’s an article from Reasons to Believe by Dr. David Rogstad, who has a PhD in physics from Caltech – the top school for experimental science. The article not only goes over the basic plate tectonics to carbonate-silicate cycle connection, but it adds a newer discovery to boot.

Excerpt:

Earthquakes are a byproduct of plate tectonics, a theory in geology developed in recent years for explaining motions near the surface of the Earth. One of the benefits from plate tectonics is that Earth maintains the right levels of carbon dioxide (CO2) in the atmosphere to compensate for the Sun’s increasing luminosity. This is accomplished by what is called the carbonate-silicate cycle. CO2 is removed from the atmosphere through weathering. The weathered products are eventually drawn into the Earth’s interior via plate tectonics. Processes inside the Earth’s interior release the CO2 back into the atmosphere via volcanoes. While all aspects of this mechanism are not yet fully understood, it has been instrumental in providing a stable environment for life on the Earth for billions of years.

New research provides yet another component that appears fine-tuned for life. In a letter in the September 27, 2007 issue of Nature together with a corresponding news release from the University of Bonn, Arno Rohrbach and his colleagues have discussed another mechanism similar to the carbonate-silicate cycle. It also depends on plate tectonics but, in this case, the mechanism controls the amount of oxygen on the surface of the Earth.

Oxygen becomes bound up in various oxides which are then drawn into the Earth’s interior, where various processes result in its being incorporated into an exotic mineral called majorite. The results reported in this letter established that majorite functions as a kind of “reservoir” for oxygen, and when the majorite ascends nearer to the surface of the Earth it breaks down and releases its oxygen. Some of this oxygen also binds with hydrogen released from the interior of the Earth to form water. The authors have referred to the whole process as an “oxygen elevator.”

They go on to say that “without the ‘oxygen elevator’ in its mantle the Earth would probably be a barren planet hostile to life. According to our findings, planets below a certain size hardly have any chance of forming a stable atmosphere with a high water content.”

This research confirms the existence of one more finely tuned mechanism that depends on plate tectonics and contributes to an environment that can support life. It also gives humans one more reason to be appreciative rather than dismayed when we experience an earthquake that breaks some precious possessions beyond repair.

Astronomer Dr. Hugh Ross who has a PhD in Astronomy from the University of Toronto and did a 5-year post-doctoral work at Caltech, adds to this with another discovery.

Excerpt:

In the December 2007 issue of Astrobiology Stanford University geophysicists Norman H. Sleep and Mark D. Zoback note that the higher tectonic activity during Earth’s early history could have played a key role in cycling critically important nutrients and energy sources for life. The production of numerous small faults in the brittle primordial crust released trapped nutrients. Such faults could also release pockets of methane gas and molecular hydrogen. The methane and hydrogen could then provide crucial energy sources for nonphotosynthetic life. Finally, the production of faults could bring water to otherwise arid habitats, such as rocks far below Earth’s surface.

Faulting, generated by active and widespread tectonics, allowed a youthful Earth to support diverse and abundant life. This enhanced diversity and abundance of life quickly transformed Earth’s surface into an environment safe for advanced life. Also, the buildup of biodeposits for the support of human civilization occurred more rapidly due to active tectonics.

The more rapid preparation of Earth for humanity is critical. Without such rapid preparation, humans could not come upon the terrestrial scene before the Sun’s increasing luminosity would make their presence impossible (due to excessive heat).

So that’s the science behind earthquakes. So that’s a brief look at why we need plate tectonics for life, and we just have to buck up and take the earthquakes with it. It’s not God’s job to give us happiness and health. That’s not his plan. People who complain about earthquakes have to show how God could get the life-permitting effects of earthquakes without wrecking his ability to succeed in his plan to make people know him and follow him. But how can an atheist do that? They can’t. I think that people just need to realize that humans are not in charge here and we have to live with that. We have to accept that we didn’t make the universe, and we don’t get to decide what purpose it has. God decides.

On to star formation.

Star formation

Atheists often complain that the universe is too big or too old (which is actually the same thing, since the more time passes, the more it expands). The fact of the matter is that life appeared the earliest it could appear – we needed the universe to be a certain age before it could support life.

Dr. Hugh Ross explains in this article.

Excerpt:

The second parameter of the universe to be measured was its age. For many decades astronomers and others have wondered why, given God exists, He would wait so many billions of years to make life. Why did He not do it right away? The answer is that, given the laws and constants of physics God chose to create, it takes about ten to twelve billion years just to fuse enough heavy elements in the nuclear furnaces of several generations of giant stars to make life chemistry possible.

Life could not happen any earlier in the universe than it did on Earth. Nor could it happen much later. As the universe ages, stars like the sun located in the right part of the galaxy for life (see chapter 15) and in a stable nuclear burning phase become increasingly rare. If the universe were just a few billion years older, such stars would no longer exist.

The Rare Earth book explains the details on p. 40-4:

The trick for getting from helium to the generation of planets, and ultimately to life, was the formation of carbon, the key element for the success of life and for the production of heavy elements in stars. Carbon could not form in the early moments following the Big Bang, because the density of the expanding mass was too low for the necessary collisions to occur. Carbon formation had to await the creation of giant red stars, whose dense interiors are massive enough to allow such collisions. Because stars become red giants only in the last 10% of their lifetimes (when they have used up much of the hydrogen in their cores), there was no carbon in the Universe for hundreds of millions to several billion years after the Big Bang—and hence no life as we know it for that interval of time.

[…]The sequence of element production in the Big Bang and in stars provided not only the elements necessary for the formation of Earth and the other terrestrial planets but also all of the elements critical for life—those actually needed to form living organisms and their habitats.

[…]The processes that occurred during the billions of years of Earth’s “prehistory” when its elements were produced are generally well understood. Elements are produced within stars; some are released back into space and are recycled into and out of generations of new stars. When the sun and its planets formed, they were just a random sampling of this generated and reprocessed material. Nevertheless, it is believed that the “cosmic abundance” mix of the chemical elements—the elemental composition of the sun—is representative of the building material of most stars and planets, with the major variation being the ratio of hydrogen to heavy elements.

[…]Many stars are similar in composition, but there is variation, mainly in the abundance of the heavier Earth-forming elements relative to hydrogen and helium. The sun is in fact somewhat peculiar in that it contains about 25% more heavy elements than typical nearby stars of similar mass. In extremely old stars, the abundance of heavy elements, may be as low as a thousandth of that in the sun. Abundance of heavy elements is roughly correlated with age. As time passed, the heavy-element content of the Universe as a whole increased, so newly formed stars are on the average more “enriched” in heavy elements than older ones.

[…]The matter produced in the Big Bang was enriched in heavier elements by cycling in and out of stars. Like biological entities, stars form, evolve, and die. In the process of their death, stars ultimately become compact objects such as white dwarfs, neutron stars, or even black holes. On their evolutionary paths to these ends, they eject matter back into space, where it is recycled and further enriched in heavy elements. New stars rise from the ashes of the old. This is why we say that each of the individual atoms in Earth and in all of its creatures—including us—has occupied the interior of at least a few different stars.

What he’s saying is that heavy elements are created gradually because of the star formation lifecycle. The first generation of stars are metal-poor. The next generation of stars is better. And so on until we get to stars that can support life by providing a steady, stable amount of energy – as well as other benefits like planets with an atmosphere.  Our planet is 4.5 billion years old, and the universe is about 14 billion years old. Simple life appears about 4 billion years ago on Earth. That means we got life practically immediately, given that we had to develop the heavy elements needed to make a life-supporting star, a life-supporting planet and our physical bodies

Filed under: Polemics, , , , , , , , , , , , , , ,

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