Wintery Knight

…integrating Christian faith and knowledge in the public square

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.

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What should you study to prepare yourself for a career?

Here’s an interesting post from the Chapman Kids blog. The father is a software engineer like me, and he’s serious and intentional about how he is leading his children.

In a recent post, he talks about one of the adventures that the two kids are having with a community college professor of English writing. The post is entitled “Continued conversation with the kid’s commie teacher”.

He writes:

As many already know, Kelly and Christian take a “writing” class at the community college where the dear leader of the class lectures on the evils of all things Christian, the beauty of communism and atheism, and the righteousness of drug legalization and abortion.  Today’s topic was Christianity.

[...]At the point when he made the claim that Adam and Eve could not have existed because of the scientific evidence for evolution, Christian raised his hand and said, “There is just as much scientific evidence against macroevolution as there is for it.”

“You don’t believe in evolution!” exclaimed the professor incredulously with a look of disdain and horror.

“We DO believe in microevolution.  It is grossly arrogant for you NOT to question your own beliefs when it comes to evolution” said Kelly.  “That is what you are demanding from us.”

The professor said, “Evolution is established scientific fact” and used several of the standard canards (fossil record, etc.) to establish his point.

Then they were off to the races.  Fortunately, during homeschool, Christian and Kelly had read books like The Victory of Reason:  How Christianity Led to Freedom, Capitalism, and Western Success by Rodney Stark, Understanding Intelligent Design:  Everything You Need to Know in Plain Language by William Dembski and Sean McDowell, Tactics: A Game Plan for Discussing Your Christian Convictions by Greg Koukl, and Intellectuals by Paul Johnson.  The professor was armed with shibboleths about the truth of macroevolution and quotes from John Shelby Spong about the virgin birth.  John Shelby Spong!?!!  You have to be WILDLY out of touch with both current scholarship and reality if you quote John Shelby Spong about virtually anything.  He quotes the likes of losers like Noam Chomsky and Bertrand Russell, too.

I tweeted Kelly a link to the William Lane Craig vs John Shelby Spong. Here is part 1 and part 2 of that debate on Youtube. It’s worth watching if you haven’t seen it before.

Mr. Chapman continues his post:

It is frustrating.  Here is a writing a professor who fervently believes he is making students question their beliefs through these profoundly silly arguments.  The subject matter is objectionable, but this guy’s incompetence is even more objectionable.  He does not appear to understand the difference between scientific method and historic method (very important in discussion of the resurrection).  Neither does he understand that it is impossible to argue for the primacy of scientific method without consideration of its philosophical underpinings.  I guess I should be grateful he is incompetent with respect to his arguments–he does nothing to get the kids to question their faith or worldview.  Still, a lot of taxpayer money is wasted on professors like this throughout the land.

Well, the kids have to learn how to write, but I think it is important to note English classes are especially politicized. There is an awful lot of ideology in English classes, because that’s the easiest place for people who want to teach to go if they want to avoid being corrected by real life. In English, and other similar areas, it’s easier for a teacher to go on and on about their ideas without have to test them against the real world. It’s the easiest subject for teachers to force students to agree with your ideology without allowing them to be able to bring in facts to disagree. Basically, a secular lefty teacher can always find literature (usually modern literature, blech!) that casts Christians as brutes, Christian moral standards as outdated and harmful, and non-Christian behavior as praiseworthy. Because literature is necessarily made-up – it’s just opinion.

Even someone like me who gets courting and chivalry guidance from Shakespeare and Austen is cautious about taking courses in literature. Plus, you can can get into a lot of trouble for disagreeing with the teacher. I took English electives during my undergraduate degree and they do grade you on your viewpoint, something which is much harder for them to do in math, science, physics, chemistry, etc.

Another post from Mr. Chapman discusses how children should study STEM (science, technology, engineering and math) topics, even if those children intend to work in a non-STEM field.

He writes:

I found a great article in the Wall Street Journal this morning titled Generation Jobless:  Students Pick Easier Majors Despite Less Pay.  It had some startling statistics:

Workers who majored in psychology have median earnings that are $38,000 below those of computer engineering majors, according to an analysis of U.S. Census data by Georgetown University.

Wow.  The article tells a story about a student who switched from Electrical and Computer Engineering because her team stayed up past midnight in a lab to write a soda machine program.  They could not get it to work, so to keep from getting a bad grade, she withdrew from the course.  Then she switched from engineering to a double major in psychology and policy management.  Her grades went from B’s and C’s to A’s.  She said her high school did not prepare her for the rigor of an engineering degree.

So the upshot is that she is willing to work in a low-paying career for the rest of her life because she was unwilling to do what was necessary to pass a few hard classes.  I have had this discussion with people before.  If you cannot handle a specifc course, you can do a TON of things to make it happen. You can get a tutor.  You can take the class two or even three times if needed.  You can take a more remedial course, then try the tough one again.  Is it worth it to go to school for a year or two more to do something you like and that pays well for the next forty or fifty year?  It seems like a no brainer.

The crazy part is that even for those who want to do less technical jobs, it is best to prepare for that non-technical job with a hard degree.

Research has shown that graduating with these majors provides a good foundation not just for so-called STEM jobs, or those in the science, technology, engineering, and math fields, but a whole range of industries where earnings expectations are high. Business, finance and consulting firms, as well as most health-care professions, are keen to hire those who bring quantitative skills and can help them stay competitive.

We joked about this quite a bit, but I wanted to get it into the kids head that, if they went to college (not necessarily a given–preparation for many careers–pilot, electrician, writer, and small business owner are monumentally better served through some type of preparation other than college), they could study their passion, but they needed to start with a rigorous degree.  We defined rigorous as anything that involves hard math.  The use of hard math and statistics is creating new breakthroughs in a lot of fields right now:  medicine, agriculture, sociology, etc., etc. etc.

I agree with Mr. Chapman. And I think that he is definitely going to raise successful, influential Christians, because he and the children are well prepared and engaged. He has a great relationship with his kids. They are definitely more advanced than I was when I was their age. It’s encouraging to me to see a Christian Dad who is focused and purposeful about having solid relationships with his kids, and preparing them for the dangerous world they are entering as adults. I think it’s important to admire the people who are getting it right (the parents and the kids together) and learn from their successes. I like that he is still involved with what his children are learning even after they are finished with high school.

I really do think that engineers make the best husbands and fathers. Engineers learn how to gather requirements, evaluate alternative solutions, and then implement. Engineers care about designing to support expandability, maintenance, security and unexpected emergencies. They are easy to argue with, because they believe in logic and evidence. They are pragmatic – they make decisions based on what works, not what sounds good or feels good. Good engineers also have training in project management, budgeting, leadership and resource management, too. The best engineers are the entrepreneurs, who understand business, economics, business law and politics. It really is an ideal skill set for marriage and parenting. Engineers try to build things, and those building skills can be re-used to build a family.

Filed under: Mentoring, , , , , , , , , , , , , , , , , , , , , , , ,

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.

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How religious faith drives the delusion of Darwinism

Commenter ECM alerted me to Cornelius Hunter’s new blog “Darwin’s God”. Cornelius is a software engineer like me who rose up the ranks of the firm through “sweat equity”, and was able to eventually pursue a PhD in Biophysics from the University of Illinois. I have his first book “Darwin’s God” and I read it. His thesis is basically that theological beliefs about what God would and would not do are the driving force behind evolution.

Evolution and the problem of evil

Here is his latest post about a debate that occured at Westminster Abbey between an atheistic evolutionist and a theistic evolutionist.

Here’s what the theistic evolutionist said:

Alexander is a theist and Jones an atheist. But they both agree that God would not have created what we find in this world. Everything from programmed cell death to the extinction of so many species and the food chain points to a massive economy of death in nature. With this sort of evidence, “What kind of a designer,” asks Alexander, “are you going to end up believing in?

…According to Alexander, this problem of death and evil does not leave much room for a divine creator. Alexander concludes that God did not create the details of the world. He is thus absolved of the world’s many evils. He implemented a framework of sorts, but let unguided processes do the rest.

And here’s what the atheist evolutionist said:

As with Alexander, Jones also finds that biology does not meet with his expectations of divine creation. “The feeblest of designer,” Jones has written, could improve the design of the human eye. This and other examples, says Jones, shows that complex organs are “not the work of some great composer but of an insensible drudge: an instrument, like all others, built by a tinkerer [i.e., the evolutionary process] rather than by a trained engineer.” As with Alexander, Jones’ religious sentiment mandates some sort of evolution to be true.

So let’s think about what causes people to become evolutionists, beyond the normal answers of peer-pressure, career preservation, wanting to be thought of as smart, wanting to rebel against parents, wanting to have sex and drink alcohol, etc. Is it about science? No. It’s about knowing what God would do and observing that the world does not correspond to these ideas of what atheists think God would do.

Remember that post I wrote a while back about Christopher Hitchens’ case against God. None of his arguments against God were based on evidence, but only on his personal preferences. God wouldn’t have done it that way. God should have done it this way. I don’t like this theology. I don’t like that feature of the universe. It’s just a long-running temper tantrum against any kind of authority, regardless of the evidence.

Here’s Dawkins explaining how unobservable aliens must ave evolved, even if Dawkins doesn’t have any evidence:

He doesn’t even need to see the evidence that we evolved. He knows that God wouldn’t have created the life this way, and so the evidence is irrelevant.

Evolution and the problem of sub-optimal design

Another way that assume that evolution is true, other than childhood trauma and the desire to be morally evil, is by assuming that if material forces did not do the creating, then the design must be optimal. Now I am a software engineer, with undergraduate and graduate degrees, a published paper that I presented at the IEEE and a patent in wireless technology. My specialty is architecture. So I will tell you.

There is no such thing as an optimal design.

As part of my graduate course work, I had to study the work done at the Software Engineering Institute at the Carnegie-Mellon University. They have invented an entire methodology for designing software based on analyzing trade-offs between alternative architectural candidates. They use use case scenarios, disaster scenarios, maintenance scenarios and other scenarios in order to evaluate how well each architecture performs.

All of the architectures can satisfy the so-called “functional requirements”. But the architectures differ in their ability to satisfy non-functional requirements, the “-ilities”. These can include performance, maintainability, security, extensibility, testability, simplicity, re-usability. This is the bread and butter that software engineers like me have to deal with every day.

Here’s an excerpt from a related post from Uncommon Descent:

It is simply impossible for one architecture to have all the “ilities” because many conflict. For instance, if I want high “security” I am going to have to give up a good deal of “interoperability”. A large part of architecture is actually deciding what you are going to give up, which incidentally affects how the architecture can change in the future (i.e. usually it cannot “evolve” to conform to different “ilities”). This is all still fairly new, but we are now able to judge architectures in terms of the “ilities” they match and the “ilities” they do not match. A better understanding of the conflicts between certain “ilities” is gradually developing.

When I worked in the embedded space on operating systems like VxWorks, we regularly traded-off memory against speed. It’s the nature of the engineering business. And make no mistake – God is a software engineer. He writes code.

Conclusion

Hunter’s article concludes with this:

Have the theists sold out? Have the theists been duped? Are they afraid to stand up for themselves? Are the atheists taking over? No, no, no, and no. The theists and atheists are united in their religious beliefs about God and how he would interact with the world. They may have their differences, but regarding evolution those differences are irrelevant. Their shared religious convictions mandate evolution. Religion drives science and it matters.

I have an idea. Let’s keep religion out of science and decide how we really got here, no holds barred. Instead of blocking debates and persecuting dissent, let’s actually have a debate about origins, and not rule intelligent causes out before we look at the evidence.

Further study

Atheist responses to scientific arguments for theism are fun to understand. Atheists attribute the beginning of the universe to untestable theories and the fine-tuning to an unobservable multiverse. (And don’t forget their lame responses to galactic, stellar and planetary habitability arguments)

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