Is evolution a fact or theory?

[dcalling]

Actually, algorithms are much older than software. A recipe, for example, is an algorithm. As you just learned, a genetic algorithm is a means of applying evolutionary processes to solving engineering problems.



It uses random variation and natural selection to optimize fitness.
A genetic algorithm (GA) is a search and optimization method which works by mimicking the evolutionary principles and chromosomal processing in natural genetics. A GA begins its search with a random set of solutions usually coded in binary string structures. Every solution is assigned a fitness which is directly related to the objective function of the search and optimization problem. Thereafter, the population of solutions is modified to a new population by applying three operators similar to natural genetic operators-reproduction, crossover, and mutation. A GA works iteratively by successively applying these three operators in each generation till a termination criterion is satisfied.



Evolution just works better than design for complicated problems. That's why engineers use it.

Barb, @2tim_215 is correct on that one. the so called genetic algorithm is basically a simplified path finding, where the base algrithm finds the most optimized solution, and this one to save computational time finds a solution that may or (most likely) may not the best solution, but uses shorter time.

 

[The Barbarian]

This is the issue. Right now we classify things based on how things look.

No. That is the fallacy creationists use to suppose lizards are more like dinosaurs than dinosaurs are like birds. What matters is not "how things look", but homologies, which often look quite different, but show common descent. Hence, birds and dinosaurs, which have scutes (specialized scales which can be induced to form feathers) specialized shoulder joints and pneumatized bones, are closely related, while bats and pterosaurs which "look alike", are not closely related to birds.

What we really should do is do more research, check their DNA,

Turns out, birds are genetically more closely related to archosaurs than archosaurs (group including diosaurs, thecodonts, and crocodiles) are to other reptiles.

When it comes to DNA, crocodiles and birds flock together
Down near the roots of that avian tree lies a mysterious ancestor that was decidedly more terrestrial and terrifying than the finch or the wren.


The archosaur, or so-called "ruling reptile," roamed Earth about 250 million years ago, and "was something that was very reptilian, very early-dinosaur-ish, and then it evolved into modern-day crocodiles and birds," said David Haussler, Scientific Director of the UC Santa Cruz Genomics Institute, a coauthor of several studies that came out of the avian genomics effort.


"So it really is the proper dinosaur ancestor," Haussler said. "And birds and crocodiles are the proper descendants of this ancestor."


Haussler isn't a fossil-digging researcher. He digs through genetic code. So does John McCormack, an Occidental College biologist who usually is plenty busy curating a collection of some 65,000 Mexican birds at Moore Lab of Zoology on the college's Los Angeles campus.


But both researchers are keenly interested in a kind of living molecular fossil -- small strands of DNA, the code of life, that are shared among a wide array of species.

"These markers are very nice for doing comparative genomics, because they're so conserved. They're easy to find among organisms that are very distantly related," said McCormack. "We can find them across all of these genomes, and use them to build a phylogeny -- an evolutionary history."
http://www.latimes.com/science/sciencenow/la-sci-sn-crocodile-bird-genome-20141212-story.html

It's not just DNA. Not long ago, scientists found a bit of heme in a T-Rex bone. Heme is a fragment of the hemoglobin molecule. When tested, it was found to be more like the heme of birds than like the heme of other reptiles.

and find out how they are related by DNA, from how similar they are, to if there is a natural mutation path to each other.

See above. DNA and conserved molecules are as good a means as homologies for finding common descent. Sometimes better. And DNA, as you see, shows that birds have a common descent with archosaurs.

It is like coding, where people who don't know what's going on asking for how things should look and feel, and the engineers decide what libraries to use, and the exact RGB colors to use.

Not surprisingly, when you find homologous traits, you find DNA relatedness as well.

"Looks alike" often won't do it, though. This is why the shoulder joint of raptoral dinosaurs, used for balance and grasping, is homologous to the avian shoulder joint, used for flight.

The motion is the same; it was just recruited for a new purpose. That is the way evolution works.

 

[dcalling]

No. That is the fallacy creationists use to suppose lizards are more like dinosaurs than dinosaurs are like birds. What matters is not "how things look", but homologies, which often look quite different, but show common descent. Hence, birds and dinosaurs, which have scutes (specialized scales which can be induced to form feathers) specialized shoulder joints and pneumatized bones, are closely related, while bats and pterosaurs which "look alike", are not closely related to birds.



Turns out, birds are genetically more closely related to archosaurs than archosaurs (group including diosaurs, thecodonts, and crocodiles) are to other reptiles.

When it comes to DNA, crocodiles and birds flock together
Down near the roots of that avian tree lies a mysterious ancestor that was decidedly more terrestrial and terrifying than the finch or the wren.


The archosaur, or so-called "ruling reptile," roamed Earth about 250 million years ago, and "was something that was very reptilian, very early-dinosaur-ish, and then it evolved into modern-day crocodiles and birds," said David Haussler, Scientific Director of the UC Santa Cruz Genomics Institute, a coauthor of several studies that came out of the avian genomics effort.


"So it really is the proper dinosaur ancestor," Haussler said. "And birds and crocodiles are the proper descendants of this ancestor."


Haussler isn't a fossil-digging researcher. He digs through genetic code. So does John McCormack, an Occidental College biologist who usually is plenty busy curating a collection of some 65,000 Mexican birds at Moore Lab of Zoology on the college's Los Angeles campus.


But both researchers are keenly interested in a kind of living molecular fossil -- small strands of DNA, the code of life, that are shared among a wide array of species.

"These markers are very nice for doing comparative genomics, because they're so conserved. They're easy to find among organisms that are very distantly related," said McCormack. "We can find them across all of these genomes, and use them to build a phylogeny -- an evolutionary history."
http://www.latimes.com/science/sciencenow/la-sci-sn-crocodile-bird-genome-20141212-story.html

It's not just DNA. Not long ago, scientists found a bit of heme in a T-Rex bone. Heme is a fragment of the hemoglobin molecule. When tested, it was found to be more like the heme of birds than like the heme of other reptiles.



See above. DNA and conserved molecules are as good a means as homologies for finding common descent. Sometimes better. And DNA, as you see, shows that birds have a common descent with archosaurs.



Not surprisingly, when you find homologous traits, you find DNA relatedness as well.

"Looks alike" often won't do it, though. This is why the shoulder joint of raptoral dinosaurs, used for balance and grasping, is homologous to the avian shoulder joint, used for flight.

The motion is the same; it was just recruited for a new purpose. That is the way evolution works.

So let me ask you, shoulder joins look-a-like is not look-a-like? Don't you think it is better to dig thing from the basic levels, i.e. DNA levels?

Do you not find it a little bit strange that without a clear path (i.e. how DNA mutate from one form to the other one step at a time), that we declared humans are evolved from some primates? If during the evolution process 2 genes fused together, do you not find it a little interesting to know how they fused before we delcalre they must have fused?

 

[The Barbarian]

So let me ask you, shoulder joins look-a-like is not look-a-like?

It's homlologous, not "look-alike." That is, the joint has been reconfigured for flying, not grappling. The same joint was modified to a new use.

Don't you think it is better to dig thing from the basic levels, i.e. DNA levels?

And as you see, DNA shows that archosaurs (birds and crocodiles) are more closely related than crocodiles are to other modern reptiles.

Likewise, conserved molecules like heme and collagen, show the same genetic relationship between birds and dinosaurs.

Do you not find it a little bit strange that without a clear path

The path is very clear. As you also learned, the DNA phylogenies of the primates show precisely how they evolved.

that we declared humans are evolved from some primates?

We can do much better than that. DNA analyses show that humans and chimpanzees have a common ancestor after that ancestor and other apes diverged.

And we know this shows common descent, since we can test the method on organisms of known descent.

If during the evolution process 2 genes fused together,

Chromosomes, not genes. And the predicted fusion was verified by finding remains of the telomeres prescisely where they should be if a fusion occurred.

do you not find it a little interesting to know how they fused

Geneticists know precisely how such fusions happen. Every now and then, we can observe one as it happens.

 

[pat34lee]

It is, by the definition above, observation of biological evolution.

So, what did the bacteria become by the end of the observations?

 

[pat34lee]

It is, by the definition above, observation of biological evolution.

Micro-evolution, or adaptation, but not Darwinian evolution.
Adaptation goes round and round, but leads nowhere new.

 

[The Barbarian]

Micro-evolution, or adaptation, but not Darwinian evolution.

Let's see if you know what you're talking about. What are the four basic points of Darwinian evolution?

 

[Job 33:6]

So, what did the bacteria become by the end of the observations?

They became bacteria with mutated physical features that allowed them to out-compete their ancestors. Were you expecting them to transform into dinosaurs and for these wild animals to come bursting out of the petri dish?

 

[The Barbarian]

pat34lee said: ↑
Micro-evolution, or adaptation, but not Darwinian evolution.

Barbarian suggests:
Let's see if you know what you're talking about. What are the four basic points of Darwinian evolution?

(no reply)

Guess not.

 

[JacksBratt]

No. That is the fallacy creationists use to suppose lizards are more like dinosaurs than dinosaurs are like birds. What matters is not "how things look", but homologies, which often look quite different, but show common descent. Hence, birds and dinosaurs, which have scutes (specialized scales which can be induced to form feathers) specialized shoulder joints and pneumatized bones, are closely related, while bats and pterosaurs which "look alike", are not closely related to birds.



Turns out, birds are genetically more closely related to archosaurs than archosaurs (group including diosaurs, thecodonts, and crocodiles) are to other reptiles.

When it comes to DNA, crocodiles and birds flock together
Down near the roots of that avian tree lies a mysterious ancestor that was decidedly more terrestrial and terrifying than the finch or the wren.


The archosaur, or so-called "ruling reptile," roamed Earth about 250 million years ago, and "was something that was very reptilian, very early-dinosaur-ish, and then it evolved into modern-day crocodiles and birds," said David Haussler, Scientific Director of the UC Santa Cruz Genomics Institute, a coauthor of several studies that came out of the avian genomics effort.


"So it really is the proper dinosaur ancestor," Haussler said. "And birds and crocodiles are the proper descendants of this ancestor."


Haussler isn't a fossil-digging researcher. He digs through genetic code. So does John McCormack, an Occidental College biologist who usually is plenty busy curating a collection of some 65,000 Mexican birds at Moore Lab of Zoology on the college's Los Angeles campus.


But both researchers are keenly interested in a kind of living molecular fossil -- small strands of DNA, the code of life, that are shared among a wide array of species.

"These markers are very nice for doing comparative genomics, because they're so conserved. They're easy to find among organisms that are very distantly related," said McCormack. "We can find them across all of these genomes, and use them to build a phylogeny -- an evolutionary history."
http://www.latimes.com/science/sciencenow/la-sci-sn-crocodile-bird-genome-20141212-story.html

It's not just DNA. Not long ago, scientists found a bit of heme in a T-Rex bone. Heme is a fragment of the hemoglobin molecule. When tested, it was found to be more like the heme of birds than like the heme of other reptiles.



See above. DNA and conserved molecules are as good a means as homologies for finding common descent. Sometimes better. And DNA, as you see, shows that birds have a common descent with archosaurs.



Not surprisingly, when you find homologous traits, you find DNA relatedness as well.

"Looks alike" often won't do it, though. This is why the shoulder joint of raptoral dinosaurs, used for balance and grasping, is homologous to the avian shoulder joint, used for flight.

The motion is the same; it was just recruited for a new purpose. That is the way evolution works.

DNA is a complex molecule. It is the building block of every organism.

Thing is, just because the DNA of one organism is similar to another... is mute.

Ethanol and vinegar are very similar in chemical make up. So close that fruit flies in your wind during fermentation will result in vinegar... two very different compound with different properties, taste, and the effect when ingested by humans.... Yet, similar chemical structure.

DNA is instructions and blue prints..

Tell two people to do the exact same thing, in the instructions... except for one little change... say... telling one to turn left and the other to turn right..... And.. one ends up in the ocean, off of a steep cliff while the other ends up in a village.

The complexity of DNA shouts that there is a creator and none of this was left to chance... The fact that some organisms are close in DNA is mute as that small difference creates incredibly different products. Which just leads to the understanding of how detailed DNA is and how small changes can cause chaos or harmony. DNA is not something that mutates to create all different organisms... They must be planned.

 

[The Barbarian]

DNA is a complex molecule.

Ya think?

Thing is, just because the DNA of one organism is similar to another... is mute.

Moot? No, it's not. In fact, we can demonstrate this by showing DNA analyses of organisms of known descent. It's very clear that genetic data shows common descent. Would you like to learn how we know?

Ethanol and vinegar are very similar in chemical make up.

No. They are quite different. Ethanol has a hydroxyl group attached to a 2-carbon chain, while acetic acid has a methane molecule with one of the hydrogen atoms replaced by a COOH group. The change is structure is what makes them chemically different.

However, DNA molecules are all quite alike chemically. They are different in that they have different genes and different alleles of those genes. The information is group into base pairs, a number of which forms a gene. Genes and the associated control units are what makes DNA work.

So we can, by comparing DNA, find paternity, ancestry, and even relationships between species. As I said, we know this is a fact, because we can test it on organisms of known ancestry.

The complexity of DNA shouts that there is a creator and none of this was left to chance...

As you know, Darwin's great discovery was that it isn't determined by chance. It turns out that even DNA evolves over time. Not all organisms have the same functions for all codons.

The fact that some organisms are close in DNA is mute

Nope. Not moot. In fact, as you just learned, it's how we can determine paternity of a child, how we can learn about our ancestors, and how we can find evolutionary relationships.

as that small difference creates incredibly different products.

You have a dozen or so mutations that didn't exist in either of your parents. And yet, you aren't "incredibly different." How can that be? Because most mutations don't do much of anything. Since proteins are quite large, a single change in the genes coding for them, usually doesn't change them significantly. If it's in right place, however, it can cause all sorts of things to happen. But usually not.

 

[dcalling]

It's homlologous, not "look-alike." That is, the joint has been reconfigured for flying, not grappling. The same joint was modified to a new use.

I like your choice of word, "reconfigured".

And as you see, DNA shows that archosaurs (birds and crocodiles) are more closely related than crocodiles are to other modern reptiles.

And God might used bones from some dinosaurs created both of them. Shared libraries

Chromosomes, not genes. And the predicted fusion was verified by finding remains of the telomeres prescisely where they should be if a fusion occurred.

Geneticists know precisely how such fusions happen. Every now and then, we can observe one as it happens.

I have talked this with either you or Kom before, this 'fusion' is not as simple as you thought and it might hurt your case: http://www.icr.org/article/new-research-debunks-human-chromosome/ "In 2002, 614,000 bases of DNA surrounding the fusion site were fully sequenced, revealing that the alleged fusion sequence was in the middle of a gene originally classified as a pseudogene because there was not yet any known function for it.5,6 The research also showed that the genes surrounding the fusion site in the 614,000-base window did not exist on chimp chromosomes 2A or 2B—the supposed ape origins location. In genetics terminology, we call this discordant gene location a lack of synteny."

Do you have any repeatable, verifiable test that show in nature the same fusion can happen? In fact detailed study has shown this is not a fusion that we have seen, and it is in question if this can indeed happen in nature.

 

[The Barbarian]

The ICR article was debunked a long time ago. Look up "transposing" and learn. The telomere is no longer functional, and over time, random mutations have changed it.

No geneticist would be surprised by that. Here are some example:
http://www.indiana.edu/~ensiweb/chrom.surviv.html
http://homepage.usask.ca/~schmutz/chromosome.html

 

[pat34lee]

They became bacteria with mutated physical features that allowed them to out-compete their ancestors. Were you expecting them to transform into dinosaurs and for these wild animals to come bursting out of the petri dish?

Like every other experiment in history, you can do whatever you
like to animals and plants, and you will never get something other
than what you began with. One thing science should take as truth
by now is that any change to the form of an animal can not happen
in nature or by natural means, because they can't even force it to
happen in a lab, by the most knowledgeable people available.

Just think. Humans supposedly separated from apes in terms of
a few thousand generations. How many generations of fruit flies
have been tested in over 100 years? Tens of thousands? Scientists
have mutated every gene in the flies and have never come close
to anything resembling evolution. Why?

Because you can't add new features. Only new proteins. The
template just isn't there to change fins to legs or arms to wings.

 

[pat34lee]

The ICR article was debunked a long time ago. Look up "transposing" and learn. The telomere is no longer functional, and over time, random mutations have changed it.

No geneticist would be surprised by that. Here are some example:
http://www.indiana.edu/~ensiweb/chrom.surviv.html
http://homepage.usask.ca/~schmutz/chromosome.html

Those seem to show that some mutations are not deadly but
it doesn't show that cows are better off with the mutations
than without them, or that the mutations are passed on.

 

[dcalling]

The ICR article was debunked a long time ago. Look up "transposing" and learn. The telomere is no longer functional, and over time, random mutations have changed it.

No geneticist would be surprised by that. Here are some example:
http://www.indiana.edu/~ensiweb/chrom.surviv.html
http://homepage.usask.ca/~schmutz/chromosome.html

You have to do better than that, quoting from pages of 2 students? I have yet to find official sources that debunk the article (some don't like it, but they can't debunk it).

Not only that, What about my question "Do you have any repeatable, verifiable test that show in nature the same fusion can happen"? Do you claim something as fact when you can't provide repeatable, verifiable tests?

 

[dcalling]

Like every other experiment in history, you can do whatever you
like to animals and plants, and you will never get something other
than what you began with. One thing science should take as truth
by now is that any change to the form of an animal can not happen
in nature or by natural means, because they can't even force it to
happen in a lab, by the most knowledgeable people available.

Just think. Humans supposedly separated from apes in terms of
a few thousand generations. How many generations of fruit flies
have been tested in over 100 years? Tens of thousands? Scientists
have mutated every gene in the flies and have never come close
to anything resembling evolution. Why?

Because you can't add new features. Only new proteins. The
template just isn't there to change fins to legs or arms to wings.

Somehow most people can't see that, they just take what ever they learned from books or told by so called authorities without doubt.

 

[The Barbarian]

You have to do better than that, quoting from pages of 2 students?

Let's take a look at one of the citations I left you:
One of the anomalies that affects fertility in cattle is called a Robertsonian translocation. This type of translocation was named after a person called Robertson from Scotland. Because cattle autosomes always have their centromere at the end, two chromosomes can fuse at the centromere and result in 1 larger bi-armed chromosome with a Robertsonian translocation. This also changes the chromosome number in cattle with this to 59 instead of 60. This fusion or Robertsonian translocation does not alter any genes, just alters the position of such genes. Therefore carriers of such translocations look perfectly normal.


The most common type of Robertsonian translocation in cattle is the t(1;29) which is a fusion of a chromosome 1 (the largest of the autosomes) with a chromosome 29 (the smallest of the chromosomes). This translocation has been shown to occur in most beef breeds which came from the European continent. It therefore is either very old or arose many times or most likely, both.


The second most common Robertsonian translocation in cattle is the t(14;20) which has primarily been seen only in Simmental cattle. It is very rare, occuring in less than 1% of Simmentals.

It's just a fact. There are more examples in the literature, but these are sufficient to debunk the ICR claims.

Not only that, What about my question "Do you have any repeatable, verifiable test that show in nature the same fusion can happen"?

Read the links. I cut and pasted one here for you.

 

[The Barbarian]

Those seem to show that some mutations are not deadly

You, for example, have a dozen or so, that are not present in either of your parents. Most mutations don't do much of anything. If this puzzles you, we can talk about why this is so.

(sound of goalposts being frantically repositioned)

it doesn't show that cows are better off with the mutations

The challenge was to show that chromosome fusions are an observed fact. Turns out that they are.

or that the mutations are passed on.

Of course, they are passed on. How would reproduction undo a chromosome fusion?

 

[The Barbarian]

Like every other experiment in history, you can do whatever you
like to animals and plants, and you will never get something other
than what you began with.

No, that's wrong. For example, maize (corn) is vastly different than it's ancestor of just a few thousand years ago. A series of mutations made it much more desirable as a crop. Humans merely kept each mutation that happened to be useful at making it more desirable as a crop. They are no longer the same species:

Just think. Humans supposedly separated from apes in terms of
a few thousand generations.

About 200,000 generations, assuming generations are 16 years (which is longer than normal for all other apes than humans).

How many generations of fruit flies
have been tested in over 100 years? Tens of thousands? Scientists
have mutated every gene in the flies and have never come close
to anything resembling evolution.

In fact, the first documented evolution of a fly into a new species was a long time ago...

Genetics. 1935 Jul;20(4):377-91.
Drosophila Miranda, a New Species.
Dobzhansky T

It's not all that hard to evolve a new species.

Why?

Because all you need is reproductive isolation. Once you do that, the two populations continue to evolve apart.

Because you can't add new features.

No, that's wrong. For example, a population of lizards introduced to a new environment on an island in the Adriatic, evolved a new digestive organ.

Lizards Undergo Rapid Evolution After Introduction To A New Home

Date:
April 18, 2008
Source:
University Of Massachusetts, Amherst
Summary:
In 1971, biologists moved five adult pairs of Italian wall lizards from their home island of Pod Kopiste, in the South Adriatic Sea, to the neighboring island of Pod Mrcaru. Now researchers have shown that introducing these small, green-backed lizards, Podarcis sicula, to a new environment caused them to undergo rapid and large-scale evolutionary changes.

“Striking differences in head size and shape, increased bite strength and the development of new structures in the lizard’s digestive tracts were noted after only 36 years, which is an extremely short time scale,” says Duncan Irschick, a professor of biology at the University of Massachusetts Amherst. “These physical changes have occurred side-by-side with dramatic changes in population density and social structure.”

Only new proteins.

Demonstrably false.

The template just isn't there to change fins to legs or arms to wings.

No, that's wrong, too. The same HOX genes that form arms in humans form fins in boney fish, front legs in reptiles, and wings in birds and bats. Just modified a bit.

To help his readers fathom evolution, Charles Darwin asked them to consider their own hands.

“What can be more curious,” he asked, “than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include similar bones, in the same relative positions?”

Darwin had a straightforward explanation: People, moles, horses, porpoises and bats all shared a common ancestor that grew limbs with digits. Its descendants evolved different kinds of limbs adapted for different tasks. But they never lost the anatomical similarities that revealed their kinship.
...
On Wednesday, a team of researchers at the University of Chicago reported that our hands share a deep evolutionary connection not only to bat wings or horse hooves, but also to fish fins.

The unexpected discovery will help researchers understand how our own ancestors left the water, transforming fins into limbs that they could use to move around on land.
...
Mr. Gehrke observed that a cluster of cells started making the Hox proteins early in the development of fish fins. When the fins were fully developed, Mr. Gehrke found that the fin rays were glowing. In a similar experiment on mice, the digits and wrist bones lit up.

“Here we’re finding that the digits and the fin rays have some sort of equivalence at the level of the cells that make them,” Dr. Shubin said. “Honestly, you could have knocked me over with a feather — it ran counter to everything that I was expecting after working on this problem for decades.”

The new study was important because it revealed that the development of fins and limbs follows some of the same rules, said Matthew P. Harris, a geneticist at Harvard Medical School. In both cases, the Hox genes tell a clump of embryonic cells that they need to end up at the far end of an appendage. “The molecular address is the same,” said Dr. Harris, who was not involved in the study.

In zebrafish, the cells that get that molecular address end up making dermal bone for fin rays. In tetrapods like us, the research indicates, the same cells produce endochondral bone in our hands and feet.

The new discovery could help make sense of the intermediate fish with limb-like fins that Dr. Shubin and his colleagues have unearthed. These animals still used the molecular addresses their ancestors used. But when their cells reached their addresses, some of them became endochondral bone instead of fin rays. It may have been a simple matter to shift from one kind of tissue to another.
https://www.nytimes.com/2016/08/18/...ntists-discover-a-deep-evolutionary-link.html

Geneticists have inadvertently confirmed Darwin's findings in the developmental genes of vertebrates.