Tag Archives: Evolution

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

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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

News

New study: another biological Big Bang, this time for bird development

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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.

Polemics

New study: enzymes cannot easily evolve to perform other functions

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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.