Tag Archives: Genome

News

Another example of convergence found in human and squid eye genes

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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.

With that being said, here is an article from Real Clear Science with me. (H/T Melissa from Science, Faith and Reason)

Excerpt:

Eyes and wings are among the most stunning innovations evolution has created. Remarkably these features have evolved multiple times in different lineages of animals. For instance, the avian ancestors of birds and the mammalian ancestors of bats both evolved wings independently, in an example of convergent evolution. The same happened for the eyes of squid and humans. Exactly how such convergent evolution arises is not always clear.

In a new study, published in Nature Scientific Reports, researchers have found that, despite belonging to completely different lineages, humans and squid evolved through tweaks to the same gene.

Like all organs, the eye is the product of many genes working together. The majority of those genes provide information about how to make part of the eye. For example, one gene provides information to construct a light-sensitive pigment. Another gene provides information to make a lens.

Most of the genes involved in making the eye read like a parts list – this gene makes this, and that gene makes that. But some genes orchestrate the construction of the eye. Rather than providing instructions to make an eye part, these genes provide information about where and when parts need to be constructed and assembled. In keeping with their role in controlling the process of eye formation, these genes are called “master control genes”.

The most important of master control genes implicated in making eyes is called Pax6. The ancestral Pax6 gene probably orchestrated the formation of a very simple eye – merely a collection of light-sensing cells working together to inform a primitive organism of when it was out in the open versus in the dark, or in the shade.

Today the legacy of that early Pax6 gene lives on in an incredible diversity of organisms, from birds and bees, to shellfish and whales, from squid to you and me. This means the Pax6 gene predates the evolutionary diversification of these lineages – during the Cambrian period, some 500m years ago.

I asked Melissa if this was another example of “convergence”, and she said it was. That’s because the gene is present in animals that DO NOT SHARE A COMMON ANCESTOR. In short, this is exactly identical to the case where a computer programmer reuses the same library of functions in two completely different programs. For example, using the Apache CXF web service library to create two completely different REST-like web services with two completely different clients. (Which is what I am doing at work right now!).

This example of convergence makes no sense on naturalistic evolution – you can evolve the same gene so many times in animals with no common ancestry. It screams out design. See the related posts below for more examples of convergence, and remember that the more we know about science, the more difficult the problem becomes for a naturalist.

Related posts

 

 

News

New study: fruit fly DNA reveals unexpected complexity

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From Evolution News.

Excerpt:

You know about ENCODE, the project that found 80 percent or more of the human genome is transcribed and appears functional. Now, along comes modENCODE: the ENCODE project for model organisms. Results from the fruit fly are in, and Indiana University shares the surprises (for evolutionary theory, that is): “Study of complete RNA collection of fruit fly uncovers unprecedented complexity.”

The paper shows that the Drosophila genome is far more complex than previously suspected and suggests that the same will be true of the genomes of other higher organisms. The paper also reports a number of novel, particular results: that a small set of genes used in the nervous system are responsible for a disproportionate level of complexity; that long regulatory and so-called “antisense” RNAs are especially prominent during gonadal development; that “splicing factors” (proteins that control the maturation of RNAs by splicing) are themselves spliced in complex ways; and that theDrosophila transcriptome undergoes large and interesting changes in response to environmental stresses. (Emphasis added.)

Ten of the 41 researchers from 11 universities working on modENCODE came from IU. They found many genes transcribed only under stress, such as exposure to heat, cold, and toxins. “In total, 5,249 transcript models for 811 genes were revealed only under perturbed conditions,” they said. As if the “junk DNA” myth needed any more pounding, the lead author testifies:

“As usual in science, we’ve answered a number of questions and raised even more. For example, we identified 1,468 new genes, of which 536 were found to reside in previously uncharacterized gene-free zones.“

The post on Evolution News also talks about another study from the University of Vienna on the genome of the sea anemone.  Their genome was way more complex than expected, too.

So what is the best explanation for all this specified complexity that enables biological function?

Evolution News explains:

Intelligent design… knows how to explain the observations. Whenever we see a complex, functioning system (like a rollout of a software system), we know intelligence played a role in its origin. We also know that intelligence can explain multiple, independent instantiations of similar systems. We never see, however, complex, networked systems arising de novo by unguided natural processes.

Yes. In the company I work for, we have a release of functional code every month (at least). These explanation for the increase in specified complexity in our applications is that busy little software engineers have been carefully sequencing characters into lines of Java code, for  purpose. No rational person believes that you can get huge increases in specified complexity by random chance. Code is code is code. It all requires a coder, just like the Big Bang requires a Big Bang. 

News

30% of gorilla genome contradicts Darwinian prediction of human and ape phylogeny

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The latest episode of ID the Future discusses a recent (March 2012) paper about the gorilla genome.

Details:

On this episode of ID The Future, Casey Luskin discusses how the recent complete sequencing of the gorilla genome has challenged conventional thinking about human ancestry and explains what neo-Darwinists are doing to try to minimize the impact of this new information. Says Luskin: “There is not a clear signal of ancestral relationships that is coming out of the gorilla genome once you add it into the mix.” Tune in to hear about this interesting development!

The MP3 file is here.

Rather than summarize this short 10-minute podcast, I wanted to excerpt a post of Evolution News about it.

Excerpt: (links removed)

A whopping 30% of the gorilla genome — amounting to hundreds of millions of base pairs of gorilla DNA — contradicts the standard supposed evolutionary phylogeny of great apes and humans. That’s the big news revealed last week with the publication of the sequence of the full gorilla genome. But there’s a lot more to this story.

Eugenie Scott once taught us that when some evolutionary scientist claims some discovery “sheds light” on some aspect of evolution, we might suspect that’s evolution-speak for ‘this find really messed up our evolutionary theory.’ That seems to be the case here. Aylwyn Scally, the lead author of the gorilla genome report, was quoted saying, “The gorilla genome is important because it sheds light on the time when our ancestors diverged from our closest evolutionary cousins around six to 10 million years ago.” NPR titled its story similarly: “Gorilla Genome Sheds Light On Human Evolution.” What evolutionary hypothesis did the gorilla genome mess up?

The standard evolutionary phylogeny of primates holds that humans and chimps are more closely related to one-another than to other great apes like gorillas. In practice, all that really means is that when we sequence human, chimp, and gorilla genes, human and chimp genes have a DNA sequence that is more similar to one-another’s genes than to the gorilla’s genes. But huge portions of the gorilla genome contradict that nice, neat tidy phylogeny. That’s because these gorilla genes are more similar to the human or chimp version than the human or chimp versions are to one-another. In fact, it seems that some 30% of the gorilla genome contradicts the standard primate phylogeny in this manner.

The Evolution News post then cites New Scientist and Nature’s comments on the study.

This isn’t the first time we’ve heard about a study like this – the last time was about the chimpanzee genome and the paper was published in Nature – the most prestigious peer-reviewed journal.