How theory of evolution is useful: predicting food allergies!

Faith & Science Conversation
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Thanks, the article you referenced is definitely coherent and well articulated, but not convincing.

In the end they have two arguments (1):
“So, how well do phylogenetic trees from morphological studies match the trees made from independent molecular studies?”
See, morphology is not independent from molecular characteristics.
They counter with “many very different DNA sequences or biochemical structures can result in the same functions and the same morphologies” and “Heredity correlates sequences, even in the absence of functional necessity: There is one, and only one, observed mechanism which causes two different organisms to have ubiquitous proteins with similar sequences (aside from the extreme improbability of pure chance, of course). That mechanism is heredity.”
Just because the model doesn’t fall apart, doesn’t make it anything more than a model. And “one, and only one, observed mechanism”??? Funny considering that we have not observed said mechanism and no one is interested in even trying to test it: http://nonlin.org/evotest/ Saying “this is the only way” is equivalent to sticking one’s head in the sand.

…and (2): “Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent, unique nested hierarchy. The difference drawn here between “subjective” and “objective” is crucial and requires some elaboration, and it is best illustrated by example. Different models of cars certainly could be classified hierarchically—perhaps one could classify cars first by color, then within each color by number of wheels, then within each wheel number by manufacturer, etc. However, another individual may classify the same cars first by manufacturer, then by size, then by year, then by color, etc. The particular classification scheme chosen for the cars is subjective.”
Who classifies cars/beings by color, year and size? But if you do the proper classification, you will put the 2000 VW Beetle after the 1970 model, not before it. And in the end you end up with an objective grouping that matches the development history. Yet cars are all designed implements.

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OK, I’ll buy that. Apagakis derived benefit from an analysis based on evolutionary thinking and methodologies. However, her goal was not to show the superiority of evolution-based methods to similarity-based methods.

Exactly. When phylogenetic models consistently yield more accurate predictions than similarity-based models, it is strong evidence that phylogeny is more accurate description of the ground truth.

If I am not mistaken, NonlinOrg, parsimony refers to the notion that the cladistic structure that minimizes the number of branches is preferred. With a large number of taxa this could be very difficult to compute by brute force, which is why Markov Chain Monte Carlo Bayesian inference is used to derive the most parsimonious cladistic structure. Distance/similarity measurements are vastly easier to compute, so MCMC is not used for them.

Long story short, these approaches are calculating nested hierarchies, not distance/similarity measurements.

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Look at this @NonlinOrg ! @Chris_Falter is admitting his original point was wrong. The allergy study did not actually test evolution vs. other theories, and he recognizes this now. That is the sign of humble thinker, and make me trust him all the more.

I’ll look forward to you doing the same sometime.

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Google: “A clade is a grouping that includes a common ancestor and all the descendants (living and extinct) of that ancestor.” So Clades presuppose evolution.
I define Similarity more broadly to include all info available from morphology to DNA. I think you mean to narrowly include only morphology.

If so, what are the alternative hypotheses tested? Please do not include random distribution here.

I wrote something else. Please review.

Rest assured I do not fear the evidence. I already said many times that True, False or Revised, either way Evolution doesn’t affect my religious views.

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I am not trying to win points here. Just to learn something new and to test my hypotheses. The fact that I continue the discussion should be taken as an appreciation of your thoughts.

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This is not what I am referring to. I am referring, instead, to a specific pattern in sequences. In this case, it has nothing to do with morphology. Of course, morphology falls in nested clades too, but that is a different conversation. We are talking about sequences here.

Just read the papers I linked to and the original post. It is very clear.

As I have explained several times, the alternative hypothesis tested is that similarity predicts function better than phylogeny. This exactly your hypothesis.

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@NonlinOrg you would understand more by reading the whole thread, but this is a key post.

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I agree that classifying by color is a poor choice. However, it may be educational to look deeper at this analogy.

The main difference between a developmental ‘tree’ of cars and the tree of life is that we see characteristics get invented and, within a few years, spread to all cars, regardless of their line of ‘descent:’ anti-lock brakes, electric keys, etc. Multicellular creatures don’t operate this way; they only, if you will, descend according to kind or lineage. (Bacteria play by different rules for gene transfer.)

Human design messes up the tree. It is still possible to do a car tree, but you have to take into account and ignore ‘common design’ elements like the spread of new technology or new regulations.

The tree of life does not have these kinds of elements. The closest you could come would be convergent evolution cases, but it is quite obvious when we look closely at these instances that the underlying mechanisms and processes are entirely different even if the phenotypic results are similar. Instead, the pattern of descent, nested hierarchy, is quite stark and mathematically clear.

I’ve said before, if people want to accept that the pattern looks like descent while actually being just the way God created, I have no further argument with them. My problem is when people deny reality to say that the pattern of the tree of life was invented and no better describes biology than a bunch of sticks in the ground.

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Of course there are differences between cars and beings, but that’s not the point. Instead, their argument is that the tree for cars is Subjective while the one for organisms is Objective. This is false.

The tree for cars is just as objective as the one for beings. We know this because the 2017 Toyota Camry (for instance) followed a known path from the prehistoric wheel and was influenced by all environmental factors along the way. There is no Space-X technology in the Camry, but if there were, a previously unknown link would be responsible, or else “convergent evolution” conveniently would take care of that. So you see, the tree of life can never fail because this game is rigged.

Once again, the only information is the similarity between organisms (including morphology, genetics and all else we know). Everything else including the imaginary lines in the tree of life are human constructs. This is like looking at clouds - I see a camel, you see a weasel.

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I read that and think it’s the same argument they make at talkorigins: “many very different DNA sequences or biochemical structures can result in the same functions and the same morphologies” and “Heredity correlates sequences, even in the absence of functional necessity: There is one, and only one, observed mechanism which causes two different organisms to have ubiquitous proteins with similar sequences (aside from the extreme improbability of pure chance, of course). That mechanism is heredity.”
If so, I disagree with their claims as the third observed mechanism resulting in “similar sequences” is design. Of course they would not even mention that.

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You’re missing the point. If we found Space-X tech in a Toyota, it would mean a ‘link’ between separate branches, totally unlike the way real trees grow, and unlike anything we find in the tree of life. All tigers come solely from felines, all felines fit entirely within Carnivora, all of Carnivora are mammals, all mammals are vertebrates, all vertebrates are in the animal kingdom. It’s not that the tree of life can never fail; a centuar, a mermaid, or a manticore would upend it in a moment. But for nearly three hundred years now, it’s been added to again and again, with each species we find, without violating the basic pattern.

You want to call them imaginary lines, fine, but they are statistically verified, mathematically solid constructs. Your camel just isn’t there.

Why do you fight so hard for something the Bible doesn’t even say? Nowhere does it say, ‘a kind has fixed and unchanging borders beyond which it may not evolve into other kinds of animals.’ No, it says God created the animals in all their kinds, and they reproduced according to kind. This is perfectly compatible with evolution. It even describes abiogenesis; “God said, let the earth bring forth…”

In the Middle Ages, they used to think that animals literally were born out of non-living material all the time. Only after Pasteur demonstrated that they had to come from other living animals did the Biblical understanding change to God creating all the animals that modern animals were descended from.

Is common descent really that much of a leap?

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That’s a good point. This would indicate that there is no Biblical reason not to accept abiogenesis, or evolution over time in a population.

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Remember, the tree of life is not a given. You are trying to establish its validity.

Once again, transportation implements fit similar patterns, yet we know they are 100% designed by humans. You can verify something only with additional independent data, not by using the conclusion as an assumption.

The irony is that everything about evolution is a magical story of emergence and arising -
http://nonlin.org/arising-of-everything/ :
"Too often it’s assumed that thing “arise”. As in:

a. “The universe arises in the Big Bang”
b. “Life arises from non life”
c. “Human intelligence arises from animals”
d. “Consciousness arises”
e. “AI machines will arise”

It’s better to say “we have no idea” than assume these – so far – insurmountable, qualitative jumps are trivial. The only experience we have with “arising” is the failed “spontaneous generation” theory."

I am not fighting anything, but merely trying to make sense of the world around us. And so far the explanations provided do not make any sense to me. Frankly, I am perplexed of how many otherwise intelligent people accept the evolution story as presented by Darwin and his followers.

The fact that we go on and on and on debating instead of looking at some simple experiment goes to show there are some major problems with the explanation.

Now, lets turn the tables: how do you reconcile your faith with something that gives so much strength to atheism? The Dawkins of this world think that evolution should absolutely eliminate all deistic beliefs. Where exactly does your story diverge from theirs?

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That’s something we can all agree on: Evolution is Creation – NonLin
“As an instrument of creation, a version of Evolution may be valid. One has to simply consider how a Creator would use the mechanics of Evolution and Abiogenesis as Creation tools. The automobile is clearly a Creation, yet it is shaped by the same Evolutionary principles observed by Darwin: each model could cover the Earth were it not for competing designs; a model is reproduced with variability; divergence of character helps models spread into all available environments; the better features are retained and passed to the next generation, while natural selection ensures the extinction of the uncompetitive designs; totally different “species” like the passenger car and the interstate truck display convergent evolution; etc. Unassisted growth and reproduction are of course missing because the automobile is only a human Creation. In turn, Abiogenesis is very much in line with Abrahamic Religions as mentioned in several faith writings.”

But this doesn’t absolve us from seeking that version of evolution that makes sense. The explanations I have seen so far do not.

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Do you just intentionally ignore everything this website publishes? It should be clear to anyone who is making an attempt to understand.

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The question was addressed to Lynn. Maybe she thinks differently than other people on this website.

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I do, actually, it’s come up in other discussions but not this one yet. I’m not Christian, though most on this site are; I’m a pantheist. To answer your question, I have no problem with evolution “giving so much strength to atheism.” If your faith in God depends on not being able to think up any reasonable explanation for the mechanical functionings of the world around you, tough. We are made of cells and chemical reactions and neuroelectrical impulses.

If you think that means life is boring and meaningless and pedestrian and without purpose, you’re incredibly wrong. Dawkins believes religion has outlived its purpose. I think science has barely scratched the surface of a lot of the most important discussions we have, about what it means to be human and how we should live and how to maintain communities and nurture morality.

It turns out, once you want to start talking about the most important, difficult concepts, you pretty much have to start using metaphor or parable or sentences that make no sense at all in a “literal” sense until you figure out the life lesson they’re talking about. Maybe someday, science will have developed far enough to be able to have these kinds of discussions; but it’s still pretty dang far from it now.

People like Ken Ham who insist on turning the Bible into a (really bad) dinosaur textbook aren’t just assaulting science, they’re perverting the role that religion should be playing in our society, too.

In sum, I’m glad you asked, and I’ll get to the rest of your reply to me tomorrow; I usually like to go in order, but this bit jumped the line.

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That’s an example of the popular combo of the Genetic Fallacy and the Negative Associations Fallacy.

I remember when a similar logical fallacy was used by some fundamentalist pastors in the 1970’s when Christian authors started publishing books meant to encourage healthy sexual expression among married couples. Some saw the sexual revolution of the late 1960’s and the 1970’s as a natural result of the “God is Dead” new-wave atheism of the early 1960’s. They ranted against “sex-obsession” as Satan’s follow-up after convincing people that “atheism was hip” and that “do-whatever-feels-good” was great because there was no God to judge you.

Yes, I remember IFCA pastors preaching sermons which were basically a rewording of your sentence quoted above:

“How do you reconcile your faith with something [“Christian sex books”] that gives so much strength to atheism?”

I remember one of those angry sermons being triggered by the pastor going ballistic when he discovered the women’s Bible study had been secretly passing around a shared copy of Tim & Beverly LaHaye’s The Act of Marriage! He said that they were helping Satan and atheism by “normalizing” in the Church the sins of a sex-saturated culture. (Of course, over the centuries there had been recurrent condemnations of good things God had created. Some theologians would call the good, evil, just as the Bible warns. So I’ve not been surprised that the evolutionary processes of God’s “very good” creation would be condemned by some.)

How do you reconcile your faith with Newton’s Law of Universal Gravitation and Laws of Motion when both make possible the deaths of millions by means of bullets, artillery shells, and bombs? Isn’t belief in that kind of physics endorsing Satan’s destruction of the Image of God in humankind?

Yes, logical fallacies don’t make for good arguments. They may work well in debates in front of uninformed audiences but in the long run they undermine credibility. I used to make all of those traditional anti-evolution arguments because I heard them at my church and from my favorite seminary professors. But when I eventually got more serious about the Hebrew scriptures and then began a study of the scientific evidence, I was shocked at the misrepresentations. I strongly resented those in the Church who had misled me. For a while, it made me terribly skeptical of virtually everything. Fortunately, that period of my life led me to a grasp of evolutionary processes and an even greater appreciation of the power and wisdom of God as the Creator of all. (A creator capable of creating the laws of physics and the evolutionary processes which resulted from them is an impressive Creator indeed!)

Nowadays I love to help my Christian brethren to reconcile their faith in Christ with the evolutionary processes which God created because it gives so much strength to theism and the Great Commission. By removing unnecessary stumbling blocks to the acceptance of the Gospel of Jesus Christ, I’m better able to make disciples as our Savior commanded!

If we can destroy the false dichotomy preaching of “You can’t believe in both the Bible and the Theory of Evolution!”, many millions of people would be more open to the Gospel. Sadly, many people believe him when Ken Ham says that Evolution=Atheism.

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It seems, Nonlin, that you did not understand Dr. Swamidass’ linked post (earlier in this thread). Numerous experiments have already been conducted to determine whether common ancestry is a better explanation of biological data than mere similarity.

Here’s the methodology: Scientists compare the predictions of two different models in order to determine which of the two models more closely reflects the data. Per the scientific method, the model which is more accurate in a statistically significant fashion is deemed to be a better representation of the ground truth.

There are plenty of examples of this kind of “shoot-out” between models. The Michelson-Morley experiment, for example, compared the predictions of the “ubiquitous ether” model with the “no ether” model. The data showed that the “no ether” model was far more accurate, and that was the day that the ubiquitous ether theory died.

The guitar you’ve been playing in this thread has one string and one fret. The tune you’ve been playing is “similarity predicts data just as well as phylogeny.” While the song may be comforting, is it accurate? Have there been any experiments that have compared the predictions of the similarity model vs. the similarities of the phylogeny model?

Yes, many such experiments have been performed and published in peer-reviewed journals. Given that Evolution News and Views has not reported these (that I’m aware of), you probably have not heard about them previously. But they exist. Let’s take a brief look at the ones reported in Dr. Swamidass’ linked post.

Here are the details of their method:

  1. Select a genetic sequence and a comparison set of similar sequences from other species.
  2. Make two arrangements of the relationship between the sequences (and thus the relationship between the species).
    a. Arrangement #1 = similarity arrangement. Species are arranged along an axis based on a set of distance scores using pairwise similarity (as measured by BLAST). This is the similarity model.
    b. Arrangement #2 = phylogeny/common ancestry. Place the sequences (and thus the species) in a phylogenetic hierarchy, based on SIFTER analysis of the sequences. This is the common ancestry model.
  3. Assign function labels to the sequences in the comparison set.
  4. Use the model + function labels to predict the function of the genetic sequence under study.

If phylogeny does not perform significantly better than similarity in predicting the function of the sequence, the experiment shows that it is not a better representation of the ground truth. Such a finding would be the triumphant coda to your song. If, on the other hand, the phylogeny predictions are significantly better than the similarity predictions, then we can say from a scientific perspective that phylogeny/common ancestry is a better representation of the ground truth–just as Michelson and Morley were able to say that the “no ether” model was a better representation of the ground truth than the “ubiquitous ether” model. And your song would sink to the bottom of the charts.

You indicate that you read Dr. Swamidass’ post. Thus you probably already know, then: which model (similarity vs. common ancestry) yielded more accurate predictions? Were the findings statistically significant?

Best regards,
Chris Falter

EDIT: Hat tip to Joshua @Swamidass, who very patiently helped me understand this body of research.

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Those are excellent explanations, Chris!

And the Michelson-Morley experiment was indeed such a great comparison of explanations. It was a wonderfully conclusive falsification test for the ether model.

Ya know, I can’t think of a single peer-reviewed published paper authored by an anti-evolution creationist which thoroughly compared two models in a similar manner (to the Michelson-Morley experiment) or which described and conducted falsification testing for their own preferred theory. I mostly see cherry-picking of evidence and arguments based on logic fallacies like guilt-by-association. (Example: “The Theory of Evolution can’t be valid because Darwin was an evil racist and both Hitler and Stalin loved evolution.”)

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