Tag Archives: Software Development

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.

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.

Alliance Defense Fund’s strong opposition to divorce

This is timely, at a time where I am considering whether I would do more good supporting Christian/conservative groups on campus as an assistant professor or as a free speech lawyer defending campus groups from student governments.

No one is better at these kinds of issues than the ADF.

Here’s the article.

Excerpt:

The longer I live, and the more time I spend in the Christian conservative movement, the more keenly I’m aware of the extent to which divorce is devastating the Body of Christ.  It’s destroying children’s lives, destroying their parents, and destroying our cultural witness.  I’m 41 years old, and by this point I’ve seen friends’ marriages end because of adultery, because they felt “trapped,” because the other spouse was cruel, because they allegedly “fell in love” with someone else, because of addictions, or because they simply “wanted to be happy.”  Every single time — every time — one or both of the spouses made a series of deliberate decisions to place their own desires over those of their husband or wife, over the best interests of their children, and over the explicit admonitions of the God they allegedly serve.

I am increasingly of the opinion that the Christian community simply will not prevail in the cultural battle to preserve marriage — especially when the argument for marriage absolutely depends on the fact that marriage does not exist merely to fulfill adult desires and sustain adult happiness — if we treat our own marriage vows so shabbily.  How can we tell any population of Americans — whether inclined to homosexual behavior or even polygamy — that marriage is the earthly model of Christ’s relationship to his church if we treat it as an instrument of our own happiness?

[…]Frequently I hear talk of “divorce recovery” or someone saying they’re “going through” a divorce.  This passive language detaches individuals from the acts of will that cause the dissolution of their family.  You “recover” from the flu.  You decide to divorce.  Divorcing couples are capable of almost-epic feats of rationalization.  Divorce without adultery?  They rationalize it by saying that their spouse’s failings are the moral equivalent of adultery.  Fall in love with someone else?  They rationalize it through facile arguments that God loves them and wants them to be happy.  Children devastated?  They rationalize their actions as ultimately for the best because (despite all social science to the contrary) divorce is better for kids than living in conflict.  Couples float away on oceans of psychobabble — incapable of confronting the hard truth: They are making a deliberate choice to defy God.

A bit more from a follow-up post.

Excerpt:

Marriage is particularly fragile not just because of very real cultural changes in the Body of Christ, but because of a key (and catastrophic) legal change — the institution of no-fault divorce.

[…]And so we’re faced with an enabling church and an enabling legal system — two escape hatches that are all too tempting in times of distress.  The enabling church (including, sadly, many pastors and Christian peers) argue that various real or imagined spousal sins are the “equivalent” of adultery or the “equivalent” of abandonment.  The enabling church tells you that “God’s best” or “God’s plan” is not the cross but a happy life, a joyful life.  And the enabling legal system is all too ready to take your check, put you in the system and process your (sometimes) very fast, and (occasionally) very cheap divorce.

It then lists the well-known damage done to children, and continues:

How, you ask, can parents be so much happier when their children are so much worse off?  Wouldn’t the emotional and sexual collapse of their own children cripple the parents’ emotional well being?  Not if they long ago shifted their life priorities — away from the Biblical model of self-denial and to the world’s model of personal fulfillment.

Divorce is child abuse. Period. I’d like to see the church come out and preach sermons with the facts and statistics on what divorce does, and then provide people with practical advice and STRICT RULES about how to conduct courtships, marriages and parenting to the glory of God.

Marriage as an engineering problem

God is the customer of the marriage product, and he expects adults to love each other self-sacrificially, to honor moral obligations, and to raise the children to know him and serve him effectively.

There is no room in marriage for amusement and self-centeredness.

  • No emotions
  • No intuitions
  • No “chemistry”
  • No “fun”

We should be designing marriage as a solution to specific problems with the aim of serving God in our relationships.

If we can’t agree to do that, then we should all serve the Lord as singles. Marriage isn’t about YOU.

On women leaving marriages that don’t make them happy enough

Don’t blame me! I didn’t write it. Alisha wrote it. She’s the meany, not me!

Excerpt:

I have a certain friend, a great guy I’ve known since I was a gawky teen, and who continues to be my friend in  my fully grown yet still gawky state. He has always been strong- fights hard, works hard, but loves the hardest.

When he married a few years ago, I was a little worried. Now that he’s divorced, I’m very hurt. And taken aback that he is not the only guy I know in this situation. In fact, I know about 4.

Now, these men are far from perfect. No one except God is. Yet in all these collapsed marriages, the women openly and willingly admitted the men they promised to be with until death had never hit, pushed, sexually or emotionally accosted them. They quite simply, no longer wanted to be married.

Of course, there is nothing really simple about dissolving one’s marriage, except for my simple-minded incomprehension as I sat at a showing of “The Devil Wears Prada” with one of these ladies a few years back. We had gone to the mall to do a little window shopping, and for what seemed to be the entire trip, this young lady- I’ll call her Amber- complained non-stop about what her husband wasn’t doing. He wasn’t buying her new clothes or shoes or taking her on vacations. She worked hard, many days 10 hours. And well, he worked, too, but it wasn’t fair he didn’t buy her more.

“Can he afford to buy you all that stuff?” I asked. She looked at me as if I were stupid. “MY FATHER works two even three jobs to make sure Mama gets everything she wants and deserves! Sometimes, he is away for weeks, working at construction sites to ensure it!”

[…]Another girl I know got hitched- only to ditch her groom before a tan line started to develop on her ring finger. The very same things she loved about him while they were dating- his commitment to God, desire to go into the ministry, his “good guy” sweetness- were instantly repulsive in marriage. Their marriage annulled, she jumped into a long term dating relationship which turned into cohabitation and a child together. But fortunate for her, no wedding.

I actually blame the men for choosing these women. Men have to test women during the courtship to see if what they are interested in is making a commitment and then acting self-sacrificially to honor their obligations. I could tell you nightmare stories about Christian women I know who can do the most amazing acts of selfishness and then totally refuse to make amends or accept any responsibility. But then, I’m not married to those women – because that all came out before I ever got serious about them. Many women are judging men today based on how amusing they are and whether their girlfriends will be envious and approving based on secular criteria supplied by TV shows and music videos. This all has to be detected during the courtship by the man. Courting is when the man has to detect if the woman is thinking anything other than “if I don’t like this – if it doesn’t make me feel happy all the time and impose no obligations on me – then I can get out of it”. Is she ready for a commitment? That’s the man’s job to find out.

What courtship is really about for men is communicating your plan and the challenges you’re facing and then standing back to see if she wants to help. I once met a Christian woman who would not so much as sit down with me to see what I did for a living. She wanted to have fun! And understanding my job so that she could help was not fun. (Presumably, spending my money that I earned from that job would have been more fun). So if a man marries a woman like that, then it is the man’s fault. If men are too stupid to know how to detect lemons then they deserve to suffer. Learning how to court is more important than playing video games. Knowing what laws strengthen men in their roles as husbands and fathers is more important than watching X-treme sports. Men are responsible to understand marriage, understand what women do in a marriage, and understand policies that strengthen or weaken marriage. Many men who are divorced today voted for the party of no-fault divorce (with the custody battles and fake charges of child abuse) and domestic violence laws (which criminalize criticizing your wife’s spending or weight) yesterday. And those men are fools. And they must be punished.

Men are terrible at knowing what they want from women. What matters to the stupid men about women today is not whether they are chaste and self-sacrificial and organized and goal-oriented, but only their physical appearance, how much they are willing to drink, and how far they are willing to go physically. Even Christian men have no idea what Christian women are supposed to DO in a marriage. Many men think that marriage will be 50% playing video games, and 50% sex or something. It’s just totally unrealistic. Not to mention that women are not inanimate objects. They are more like employees. If you bring a woman into your home and do not know how to motivate them, then they will not fill the role that they are assigned. Surely a wife is as entitled to as much “management” as an employee. Having sex with someone is not effective management. One-on-one eye-to-eye communication about current concerns and future goals is effective management.

I think that men and women really need to sit down and think about marriage and parenting as an engineering problem. What are the use cases? What are the requirements? What is the design plan? What are the possible solutions? What are the tradeoffs? What is the schedule? How much of this can we build ourselves, and how much of it can we purchase or outsource? If the woman is not on board with the seriousness of marriage, because she resents obligations, saving money and structure, then drop her like a hot potato. If she does not want a man to fulfill his roles in the marriage – protecting, providing and leading on moral/spiritual issues – then kick her to the curb. Spontaneity is good for a Sunday afternoon or a Friday night. It is not the way to run a a marriage, especially when there are kids. Spontaneity is not the way to produce quality software – with garbage in, you get garbage out. Can you imagine hiring an engineer based solely on their physical appearance and amusement value? Yet this is what men are doing. Christian men are doing this.