Tag Archives: Software

Convergence detected in the genetic structure of bats and dolphins

Apologetics and the progress of science
Apologetics and the progress of science

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.

Jonathan Wells explains the problem that convergence poses for naturalistic evolution:

Human designers reuse designs that work well. Life forms also reuse certain structures (the camera eye, for example, appears in humans and octopuses). How well does this evidence support Darwinian evolution? Does it support intelligent design more strongly?

Evolutionary biologists attribute similar biological structures to either common descent or convergence. Structures are said to result from convergence if they evolved independently from distinct lines of organisms. Darwinian explanations of convergence strain credulity because they must account for how trial-and-error tinkering (natural selection acting on random variations) could produce strikingly similar structures in widely different organisms and environments. It’s one thing for evolution to explain similarity by common descent—the same structure is then just carried along in different lineages. It’s another to explain it as the result of blind tinkering that happened to hit on the same structure multiple times. Design proponents attribute such similar structures to common design (just as an engineer may use the same parts in different machines). If human designers frequently reuse successful designs, the designer of nature can surely do the same.

I’m a software engineer, and we re-use components all the time for different programs that have no “common ancestor”. E.g. – I can develop my String function library and use it in my web application and my Eclipse IDE plug-in, and those two Java programs have nothing in common. So you find the same bits in two different programs because I am the developer of both programs. But the two programs don’t extend from a common program that was used for some other purpose – they have no “common ancestor” program.

Now with that in mind, take a look at this recent article from Science Daily, which Mysterious Micah sent me.

Excerpt:

The evolution of similar traits in different species, a process known as convergent evolution, is widespread not only at the physical level, but also at the genetic level, according to new research led by scientists at Queen Mary University of London and published in Nature this week.

The scientists investigated the genomic basis for echolocation, one of the most well-known examples of convergent evolution to examine the frequency of the process at a genomic level.

Echolocation is a complex physical trait that involves the production, reception and auditory processing of ultrasonic pulses for detecting unseen obstacles or tracking down prey, and has evolved separately in different groups of bats and cetaceans (including dolphins).

The scientists carried out one of the largest genome-wide surveys of its type to discover the extent to which convergent evolution of a physical feature involves the same genes.

They compared genomic sequences of 22 mammals, including the genomes of bats and dolphins, which independently evolved echolocation, and found genetic signatures consistent with convergence in nearly 200 different genomic regions concentrated in several ‘hearing genes’.

[…]Consistent with an involvement in echolocation, signs of convergence among bats and the bottlenose dolphin were seen in many genes previously implicated in hearing or deafness.

“We had expected to find identical changes in maybe a dozen or so genes but to see nearly 200 is incredible,” explains Dr Joe Parker, from Queen Mary’s School of Biological and Chemical Sciences and first author on the paper.

“We know natural selection is a potent driver of gene sequence evolution, but identifying so many examples where it produces nearly identical results in the genetic sequences of totally unrelated animals is astonishing.”

Nature is the most prestigious peer-reviewed science journal. This is solid material.

There is an earlier article from 2010 in New Scientist that talked about one of the previous genes that matched for hearing capability.

Excerpt:

Bats and dolphins trod an identical genetic path to evolve a vital component of the complex sonar systems they use to pursue and catch prey.

The finding is unusual, because although many creatures have independently evolved characteristics such as eyes, tusks or wings, they usually took diverse genetic routes to get there.

Analysis of a specific gene has now demonstrated that although bats live in air and dolphins in water, where sound travels five times faster, they independently evolved a near-identical gene that allows them to accept high-frequency sound in the ear – vital for sonar.

The gene makes prestin, a protein in hair cells of the cochlea, which is the organ in the inner ear where sonar signals are accepted and amplified. Prestin changes shape when exposed to high-frequency sound, and this in turn deforms the fine hair cells, setting off an electrical impulse to the brain. So the protein has the important jobs of detecting and selecting high-frequency sounds for amplification.

When researchers examined the molecular structure of the prestin gene from a range of animals, they found that the variants in echolocating bats and dolphins were virtually indistinguishable.

Indistinguishable genes in animals that don’t share a common ancestor? Maybe a better explanation for the evidence we have is – common designer.

How to subscribe to and download the Wintery Knight’s favorite podcasts

I thought it might be a good idea to explain podcasts and RSS feeds to my readers and then list out the podcasts I like best.

So here is a quick introduction to RSS feeds:

RSS stands for “Really Simple Syndication”. It is a way to easily distribute a list of headlines, update notices, and sometimes content to a wide number of people. It is used by computer programs that organize those headlines and notices for easy reading.

Most people are interested in many websites whose content changes on an unpredictable schedule. Examples of such websites are news sites, community and religious organization information pages, product information pages, medical websites, and weblogs. Repeatedly checking each website to see if there is any new content can be very tedious.

Email notification of changes was an early solution to this problem. Unfortunately, when you receive email notifications from multiple websites they are usually disorganized and can get overwhelming, and are often mistaken for spam.

RSS is a better way to be notified of new and changed content. Notifications of changes to multiple websites are handled easily, and the results are presented to you well organized and distinct from email.
RSS works by having the website author maintain a list of notifications on their website in a standard way. This list of notifications is called an “RSS Feed”. People who are interested in finding out the latest headlines or changes can check this list. Special computer programs called “RSS aggregators” have been developed that automatically access the RSS feeds of websites you care about on your behalf and organize the results for you.

(RSS feeds and aggregators are also sometimes called “RSS Channels” and “RSS Readers”.)

For the more technical people, RSS is an implementation of the Observer design pattern. When used in a distributed or enterprise environment, it is called Publish/Subscribe design pattern. You can implement it with technologies like message queues, and that’s one of the things I do at work (sometimes).

So, if you look at the front page of my blog right now, you can see some little item lists from sources like Reasonable Faith and Investors Business Daily. Those are RSS feeds supplied by those people. My blog is subscribing to those feeds and display the last 5 items from each feed. And whenever those sources publish something new, then the content of what is displayed on my blog’s front page changes to show the new item.

On my home computer, I subscribe to lots of RSS news feeds, which is one way of finding news stories for my blog. The software I use for this at home is my Chrome browser pointed to the Feedly RSS aggregator web site. You have to have a gMail account to use Feedly. You can read about how to add RSS feeds to Feedly here. If you don’t want to have a gMail account, then you can use a desktop application like RSS Owl and add feeds to that. On my Android phone, I use a application called gReader and add feeds to that.

I also have RSS feeds for podcasts so that I can see the new ones that people make and then download them and listen to them. I use an Android application called Podkicker for subscribing to podcasts. It also downloads them and plays them. Usually, I download them when I am at home and listen to them on the road.

Anyway, without further ado, here is my list of favorite podcasts:

NEWS

Name: Weekly Standard Podcast
URL: http://dailystandardpodcast.weeklystandard.libsynpro.com/rss

Name: FRC – Washington Watch Weekly – Tony Perkins
URL: http://www.frc.org/rss/pod_WR.xml

Name: FRC – Daily Commentary – Tony Perkins
URL: http://www.frc.org/rss/pod_CM.xml

POLICY

Name: Banter: American Enterprise Institute
URL: http://media.aei.org/category/banter-podcast/feed/rss/

Name: Uncommon Knowledge – Hoover Institute – Peter Robinson
URL: http://feeds.podtrac.com/raBAhhrHEQY$

Name: Ruth Institute Podcast – Jennifer Roback Morse
URL: http://ruthinstitute.libsyn.com/rss

SCIENCE

Name: Intelligent Design: The Future – Various
URL: http://intelligentdesign.podomatic.com/rss2.xml

Name: Reasons to Believe – Science News Flash
URL: http://c450913.r13.cf2.rackcdn.com/podcast.xml

APOLOGETICS

Name: Reasonable Faith Podcast – Kevin Harris and WLC
URL: http://feeds.feedburner.com/ReasonableFaithPodcast

Name: Apologetics 315 Interviews – Brian Auten
URL: http://feeds.feedburner.com/apologetics315interviews

Name: Please Convince Me Podcast – J. Warner Wallace
URL: http://thepleaseconvincemeradioshowpodcast.libsyn.com/rss

Name: Stand to Reason Please Convince Me Podcast – J. Warner Wallace
URL: http://pleaseconvinceme.libsyn.com/rss

So, if you’re looking from some good podcasts, those are the ones I recommend. Please don’t feel badly if your favorite podcast is not listed here. You can leave a comment and tell us all what it is.

Convergence detected in the genetic structure of bats and dolphins

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.

Jonathan Wells explains the problem that convergence poses for naturalistic evolution:

Human designers reuse designs that work well. Life forms also reuse certain structures (the camera eye, for example, appears in humans and octopuses). How well does this evidence support Darwinian evolution? Does it support intelligent design more strongly?

Evolutionary biologists attribute similar biological structures to either common descent or convergence. Structures are said to result from convergence if they evolved independently from distinct lines of organisms. Darwinian explanations of convergence strain credulity because they must account for how trial-and-error tinkering (natural selection acting on random variations) could produce strikingly similar structures in widely different organisms and environments. It’s one thing for evolution to explain similarity by common descent—the same structure is then just carried along in different lineages. It’s another to explain it as the result of blind tinkering that happened to hit on the same structure multiple times. Design proponents attribute such similar structures to common design (just as an engineer may use the same parts in different machines). If human designers frequently reuse successful designs, the designer of nature can surely do the same.

I’m a software engineer, and we re-use components all the time for different programs that have no “common ancestor”. E.g. – I can develop my String function library and use it in my web application and my Eclipse IDE plug-in, and those two Java programs have nothing in common. So you find the same bits in two different programs because I am the developer of both programs. But the two programs don’t extend from a common program that was used for some other purpose – they have no “common ancestor” program.

Now with that in mind, take a look at this recent article from Science Daily, which Mysterious Micah sent me.

Excerpt:

The evolution of similar traits in different species, a process known as convergent evolution, is widespread not only at the physical level, but also at the genetic level, according to new research led by scientists at Queen Mary University of London and published in Nature this week.

The scientists investigated the genomic basis for echolocation, one of the most well-known examples of convergent evolution to examine the frequency of the process at a genomic level.

Echolocation is a complex physical trait that involves the production, reception and auditory processing of ultrasonic pulses for detecting unseen obstacles or tracking down prey, and has evolved separately in different groups of bats and cetaceans (including dolphins).

The scientists carried out one of the largest genome-wide surveys of its type to discover the extent to which convergent evolution of a physical feature involves the same genes.

They compared genomic sequences of 22 mammals, including the genomes of bats and dolphins, which independently evolved echolocation, and found genetic signatures consistent with convergence in nearly 200 different genomic regions concentrated in several ‘hearing genes’.

[…]Consistent with an involvement in echolocation, signs of convergence among bats and the bottlenose dolphin were seen in many genes previously implicated in hearing or deafness.

“We had expected to find identical changes in maybe a dozen or so genes but to see nearly 200 is incredible,” explains Dr Joe Parker, from Queen Mary’s School of Biological and Chemical Sciences and first author on the paper.

“We know natural selection is a potent driver of gene sequence evolution, but identifying so many examples where it produces nearly identical results in the genetic sequences of totally unrelated animals is astonishing.”

Nature is the most prestigious peer-reviewed science journal. This is solid material.

There is an earlier article from 2010 in New Scientist that talked about one of the previous genes that matched for hearing capability.

Excerpt:

Bats and dolphins trod an identical genetic path to evolve a vital component of the complex sonar systems they use to pursue and catch prey.

The finding is unusual, because although many creatures have independently evolved characteristics such as eyes, tusks or wings, they usually took diverse genetic routes to get there.

Analysis of a specific gene has now demonstrated that although bats live in air and dolphins in water, where sound travels five times faster, they independently evolved a near-identical gene that allows them to accept high-frequency sound in the ear – vital for sonar.

The gene makes prestin, a protein in hair cells of the cochlea, which is the organ in the inner ear where sonar signals are accepted and amplified. Prestin changes shape when exposed to high-frequency sound, and this in turn deforms the fine hair cells, setting off an electrical impulse to the brain. So the protein has the important jobs of detecting and selecting high-frequency sounds for amplification.

When researchers examined the molecular structure of the prestin gene from a range of animals, they found that the variants in echolocating bats and dolphins were virtually indistinguishable.

Indistinguishable genes in animals that don’t share a common ancestor? Maybe a better explanation for the evidence we have is – common designer.

Science Daily reports on genetic convergence in bats and whales

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.

Jonathan Wells explains the problem that convergence poses for naturalistic evolution:

Human designers reuse designs that work well. Life forms also reuse certain structures (the camera eye, for example, appears in humans and octopuses). How well does this evidence support Darwinian evolution? Does it support intelligent design more strongly?

Evolutionary biologists attribute similar biological structures to either common descent or convergence. Structures are said to result from convergence if they evolved independently from distinct lines of organisms. Darwinian explanations of convergence strain credulity because they must account for how trial-and-error tinkering (natural selection acting on random variations) could produce strikingly similar structures in widely different organisms and environments. It’s one thing for evolution to explain similarity by common descent—the same structure is then just carried along in different lineages. It’s another to explain it as the result of blind tinkering that happened to hit on the same structure multiple times. Design proponents attribute such similar structures to common design (just as an engineer may use the same parts in different machines). If human designers frequently reuse successful designs, the designer of nature can surely do the same.

I’m a software engineer, and we re-use components all the time for different programs that have no “common ancestor”. E.g. – I can dump develop my String function library and use it in my web application and my Eclipse IDE plug-in, and those two Java programs have nothing in common. So you find the same bits in two different programs because I am the developer of both programs. But the two programs don’t extend from a common program that was used for some other purpose – they have no “common ancestor” program.

Now with that in mind, take a look at this post from Evolution News.

Excerpt:

Earlier this year I wrote about how convergent genetic evolution is highly unlikely under neo-Darwinism, but makes perfect sense if you allow common design. An article in ScienceDaily titled “In Bats and Whales, Convergence in Echolocation Ability Runs Deep,” points to evidence that, in my opinion, might be best explained by common design.

According to the standard mammalian phylogeny, the common ancestor of bats and whales was not capable of echolocation. Thus, the ability to echolocate must have evolved independently, and bat and whale echolocation is often cited by evolutionists as a textbook example of convergent evolution. However, the ScienceDaily article reports that these similarities are not just phenotypic but extend down into the level of the gene sequences:

two new studies in the January 26th issue of Current Biology, a Cell Press publication, show that bats’ and whales’ remarkable ability and the high-frequency hearing it depends on are shared at a much deeper level than anyone would have anticipated — all the way down to the molecular level

Just as I noted that convergent genetic evolution was said to be “surprising” under neo-Darwinian thinking, this article reports, “The discovery represents an unprecedented example of adaptive sequence convergence between two highly divergent groups and suggests that such convergence at the sequence level might be more common than scientists had suspected.”

The typical Darwinist tack is to call similar structures “superficially similar”. I.e. – the appearance (phenotypes) are similar, but at the genotype (code) level, there is nothing in common. They have to say that because there is no common ancestor who shares the structure, so the biological information CANNOT be similar. A naturalistic theory can’t accommodate similarities at the genetic level unless there is a shared common ancestor who has those instructions. But guess what? When you actually take a closer look at the evidence… the biological information IS similar between bats and whales – AND THEY DON’T SHARE A COMMON ANCESTOR. So it exactly like the software design scenario, where the designer has put the same bits into two programs that were developed independently and don’t extend from a common program.

The Science Daily article explains more:

“The natural world is full of examples of species that have evolved similar characteristics independently, such as the tusks of elephants and walruses,” said Stephen Rossiter of the University of London, an author on one of the studies. “However, it is generally assumed that most of these so-called convergent traits have arisen by different genes or different mutations. Our study shows that a complex trait — echolocation — has in fact evolved by identical genetic changes in bats and dolphins.”

[…]”We were surprised by the strength of support for convergence between these two groups of mammals and, related to this, by the sheer number of convergent changes in the coding DNA that we found,” Rossiter said.

Read the whole thing at Evolution News. This is quality work by Casey Luskin.

Watch two great intelligent design documentaries online for free!

Here’s the first one, all about biological information in DNA and the origin of life.

Part 1 of 12:

The full playlist is here.

Here’s the second one, all about what it takes to have a habitable planet.

Part 1 of 12:

The full playlist here.

These are each about an hour long. The third one in the series is called “Darwin’s Dilemma”, and it covers the origin of new body plans and organ types in the Cambrian explosion. It’s the best of the series.

(H/T Apologetics 315)