Applied Evolution: Phylogenomics And Comparative Genomics

[jason777 1]

So is genetic information simply about the number of genes an organism has? If an organism loses a gene, is that decrease of 1 unit measure of genetic information? If an organism gains a gene, is than an increase of 1 unit measure of genetic information?

You know that you cant quantify information,thats why you and all other evolutionists deny it exist.Theres no way you can reduce an encyclopedia to just one letter,all you would have is gibberish.

 

Information is the specific organization of genes that code for a specific function(i.e. eyes,legs,etc.)Theres no way you can end up with a code by chance.

 

Heres a challenge put forth by Fred Williams in one of his debates.

 

The genetic code in the DNA proves that life on earth originated from intelligence, since information requires an intelligent sender. There are no known examples in the universe where a code originated by chance. In the movie “Contact”, as soon as Jodie Foster’s character recognized a “code” within the signal received from space, she immediately and correctly attributed the signal to an intelligent sender. The code both falsified the notion that the signal was naturalistic, and affirmed the fact the signal originated from intelligence. Applying this standard to our debate, the genetic code thereby falsifies NeoDarwinian evolution (naturalistic origin of all life), while concurrently proving life must have originated via an intelligent sender.

 

Thanks.

[scott 3]

You still have not quantified things.  You need to provide a singular unit measure.  If something is decreasing (according to you) how much is it decreasing by?

 

For example, if I want to measure temperature, I can measure it in degrees of Celsius or Fahrenheit.  These are defined unit measures of temperature.  Therefore if I measure temperature, I can say "the temperature decreased by 5 degrees Celcius" for example.

 

If you want to talk about information content of the genome decreasing, you need a unit measure to tell me exactly what that decrease is.  You need to be able to say, "the information content of the genome is decreased by some number of some unit measurement".

 

So go on, define a unit measurement.  Put it in numbers.

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You can't either. Both sides is pure speculation, because humans in general have not figured the entire genome out.

[scott 3]

Perfectly.  You made a claim.  I'm calling you on it.  Can you back it up or do you want to retract it?

So is genetic information simply about the number of genes an organism has?  If an organism loses a gene, is that decrease of 1 unit measure of genetic information?  If an organism gains a gene, is than an increase of 1 unit measure of genetic information?

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Who knows, but that doesn't mean we can't continue to seek the answer. I do not believe the genetic unit decreases or increases, but then again as far as biology is concerned, humans don't know enough about the genome to know exactly how the genome works. Yes, you can speculate, and do test, but that is how we figure it out anyways.

 

But I could argue that finding similarities in the genes does not have anything to do with a common ancestor at all. Why would plants and animals have similarities in the genes. The answer is simple, yet very complex. You have to go down to the cell, and see what it has to break down to process and use energy. If the food source in no way connected with the cell genetically, how then could it be considered food.

[Guest shpongle]

You know that you cant quantify information,thats why you and all other evolutionists deny it exist.

Actually, information can be quantified and there are various ways of doing it depending on how you define it. There's an entire branch of mathematics called Information Theory in fact. But you made the claim that "genetic information" can only decrease, so I want to see if *you* can define it.

 

Information is the specific organization of genes that code for a specific function(i.e. eyes,legs,etc.)Theres no way you can end up with a code by chance.

We're not talking about where the "code" came from. We are talking about measuring information in the genome. I'm still waiting for a proper quantifiable definition.

[Guest shpongle]

But I could argue that finding similarities in the genes does not have anything to do with a common ancestor at all.

And in the case of paralogs, you'd be right. But this is why scientists work to distinguish paralogs from orthologs, because it's the orthologs that improve functional prediction of genes with unknown functions due to their evolutionary relationships.

[Guest shpongle]

I appreciate your level of knowledge on this topic, I really do. This subject is very new to me so hang in there with me. You sound like you have this great secret but I still don’t see why pockets of similarities goes against creation. Does this go along with the Cytochrome C discussion? I want to know if this is basically the same thing or is there more to it.

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I'm assuming you're talking about the phylogenetic tree stuff I was referring to?

 

If so, it's along the same lines as the Cytochrome C discussion. What it has to do with is constructing these genetic relationships between species. We want to see what the relative relationships based on different genetic sequences.

 

From a design perspective, I would expect phylogenetic tree constructions to be more or less random. This is because a designer would not be constrained by which genes or DNA sequences they inserted in different species. And this is because the genetic code is universal. A gene that codes for a protein in a fish is going to do the same thing if you transplant that gene into a tomato plant.

 

In fact, a great example of this is this transgenic rabbit. This rabbit was genetically engineered to have a gene from a jellyfish causing the rabbit to glow fluorescent green. This is the type of thing a designer could do by mixing and matching whatever genes they wanted. If something like this was found in nature (rabbits with jellyfish genes), this would falsify evolution on the spot.

 

Furthermore, if a designer did use the same proteins in different species (like Cytochrome C), you'd again expect a phylogentic reconstruction to show roughly the same divergence between each and every species you are comparing. There should in general be no nesting of species with this gene (outside of statistical error). In constrast, as I showed in the Cytochrome C thread, the phylogenetic tree you get it more in line with what you'd expect if the gene evolved via common ancestry. It's not perfect obviously based on the limitations of my approach and the dataset given, but pretty darned close.

[jason777 1]

Actually, information can be quantified and there are various ways of doing it depending on how you define it. There's an entire branch of mathematics called Information Theory in fact. But you made the claim that "genetic information" can only decrease, so I want to see if *you* can define it.

Like I said,you would have to know the amount of genes before a function is lost,something I cant do with my magnifying glass.I'm sure different functions require different amounts of information"Specified gene organization".

 

We're not talking about where the "code" came from. We are talking about measuring information in the genome. I'm still waiting for a proper quantifiable definition.

Start reducing or mutating genes until you loose a specified function.In a sense all genetic information is irreducibily complex,you can only reduce or mutate so much of it before you loose the function.

 

You know alot more about genetics than I do,you should'nt have any problem identifying the section of the genome that controls a specific function and then counting the amount of genes and identifying the order that their in.

 

Thanks.

[Adam Nagy 50]

I'm assuming you're talking about the phylogenetic tree stuff I was referring to?

 

If so, it's along the same lines as the Cytochrome C discussion. What it has to do with is constructing these genetic relationships between species. We want to see what the relative relationships based on different genetic sequences.

 

From a design perspective, I would expect phylogenetic tree constructions to be more or less random. This is because a designer would not be constrained by which genes or DNA sequences they inserted in different species. And this is because the genetic code is universal. A gene that codes for a protein in a fish is going to do the same thing if you transplant that gene into a tomato plant.

 

In fact, a great example of this is this transgenic rabbit. This rabbit was genetically engineered to have a gene from a jellyfish causing the rabbit to glow fluorescent green. This is the type of thing a designer could do by mixing and matching whatever genes they wanted. If something like this was found in nature (rabbits with jellyfish genes), this would falsify evolution on the spot.

 

Furthermore, if a designer did use the same proteins in different species (like Cytochrome C), you'd again expect a phylogentic reconstruction to show roughly the same divergence between each and every species you are comparing. There should in general be no nesting of species with this gene (outside of statistical error). In constrast, as I showed in the Cytochrome C thread, the phylogenetic tree you get it more in line with what you'd expect if the gene evolved via common ancestry. It's not perfect obviously based on the limitations of my approach and the dataset given, but pretty darned close.

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That's one funny bunny.

 

 

I can't find any pictures of it against a background. Can you show me what it looks like in perspective? I just want to see if the actual effect is as extreme as it looks in this photo with no perspective.

 

Shpongle, I think you're so focused on this concept that you aren't seeing the bigger picture. Doing genetic parlor tricks doesn't prove evolution. It shows that we can learn and study and understand the attributes of already living organisms.

 

Don't you see that this isn't a universal theory of everything? Yeah we can do strange things with critters that are already alive. We can make glow-in-the-dark bunnies. Would the bunny survive in the wild? The only benefit that it would have would be for the wolf.

 

Your trick would be selected out. For all that natural selection actually is, don’t you see how it works against the evolutionist? Natural selection actually disproves Darwin.

 

We breed all kinds of dog breeds. Nature would eliminate 99.999% of what we have manipulated into all the various dogs. Even with our efforts to pick out and nurture the strangest of the bunch we still only have dogs.

 

Your genetic mapping, from your perspective, looks so convincing because you have already approached it believing in Darwin.

 

Watch this:

 

If you had to be critical of yourself and admit the one or two best arguments against Neo-Darwinian Evolution what would you say?

Edited November 3, 2013 by Bonedigger
Fixed Youtube Link

[Guest shpongle]

That's one funny bunny.

 

I can't find any pictures of it against a background. Can you show me what it looks like in perspective? I just want to see if the actual effect is as extreme as it looks in this photo with no perspective.

I think it just looks like a regular bunny. The glow-in-dark effect occurs under ultra-violet light (i.e. from a black light).

 

Shpongle, I think you're so focused on this concept that you aren't seeing the bigger picture. Doing genetic parlor tricks doesn't prove evolution. It shows that we can learn and study and understand the attributes of already living organisms.

But I wasn't talking about proving evolution. I was actually talking about proving design.

 

A designer would not be constrained in which genes they used in which organisms. They could literally mix-n-match all they wanted. So I would expect that if I was to do phylogenetic tree constructions on a bunch of designed organims, I would not expect the trees to follow any consistent patterns.

 

Your trick would be selected out. For all that natural selection actually is, don’t you see how it works against the evolutionist? Natural selection actually disproves Darwin.

Well, no it doesn't. If the genes were engineered into the original ancestral organisms, even if that gene mutated and became disabled at some point, you could still find it in the current species' genome. Sort of like how we have a gene to make Vitamin C, but that gene doesn't function in humans.

 

Natural selection doesn't change this.

 

Watch this:

<snip>

 

If you had to be critical of yourself and admit the one or two best arguments against Neo-Darwinian Evolution what would you say?

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I watched the video and I've been spending the last 5 minutes really trying to give you a good answer here. I mean, it's easy for me to come up with a list of things that I would expect to find if evolution were false. I already mentioned random phylogenetic trees and genetic chimeric organisms (like our glowing bunny).

 

In terms of actualy criticism of Evolutionary Theory, I would say there probably too much emphasis on particular mechanisms of change (i.e. gene mutations and natural selection) and not enough emphasis on other things like developmental biology or horizontal gene transfer. Although, admittedly in recent times perspectives on these topics is starting to shift.

 

I also think that perhaps there needs to be more study of rates and patterns of evolutionary change, and a better understanding of discordance between genotypes and phenotypes. This would shed more light on things like apparent statis in the fossil record. Although I admit I haven't kept up with current literature on these topics, so perhaps they are being addressed.

 

That's about all that comes directly to mind, even after taking a few minutes to really think about this question.

[JudyV 0]

Watch this:

U6JJO4Tc4D8

 

 

 

I watched that video as well, and these are the thoughts that came to my mind:

 

 

While it's most likely true that scientists aren't eager to be criticized (who is?), or to try to disprove their own theories, what mechanism is in place in the modern world of science that would keep scientists from criticizing each other? Why would a scientist who could disprove another scientist's pet theory, whatever it may be, restrain himself for doing so?

[Adam Nagy 50]

But I wasn't talking about proving evolution. I was actually talking about proving design.

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Okay, let me get this straight. I feel like you’re all over the map now. What do you believe? Do you believe that banana's and the Chimpanzees eating them, ultimately have a common ancestor? Do you believe that Darwinian Evolution has been proven or don’t you?

 

One second you’re telling me about this great evidence for evolution and then you’re telling me it works against evolution. If you're on the fence, that's okay and I totally respect that, I'm just curious what you believe.

 

Give me a summary of what you believe about the Darwinian Evolution that high school students are going to get taught all over the world tomorrow like we had taught to us over a decade ago. Keep it simple. Boil it down to a paragraph or two.

 

Do you think Darwinian Evolution is good to teach as fact to kids?

[Adam Nagy 50]

I watched that video as well, and these are the thoughts that came to my mind:

While it's most likely true that scientists aren't eager to be criticized (who is?), or to try to disprove their own theories, what mechanism is in place in the modern world of science that would keep scientists from criticizing each other?  Why would a scientist who could disprove another scientist's pet theory, whatever it may be, restrain himself for doing so?

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Hi Sis,

 

You've seen 'Expelled'. There is a good starting point to see that evolutionists aren't above making power plays when considering how they do in an open debate. Get the DVD ‘Icons of Evolution’, and then convince me there isn’t selective pressure regarding the topic of Darwinian Evolution.

 

Ask Eugenie Scott and Richard Dawkins to answer your question. They and others think creation talk should be banned as some kind of poison. (or more directly Dawkins called it 'Creation Lunacy')

 

The bottom line is this. Scientists just like any group of people; yacht clubs, church denominations, political groups, radical activists, become cliquish. In certain ways this doesn’t really matter but when we start seeing legal power plays to distort the education process and peer-groups firing people for even mentioning anti-Darwinian concepts then the problem has taken on a life of its own. Darwinists are on the march to suppress the controversy, fortunately, they’re starting fail. I just hope the ball keeps going. The scopes/monkey trial has flipped 180 degrees the other way.

 

I think the more important thing is; what are we protecting our kids from? This is a lively and interesting topic. If evolution is going to be taught in schools let’s teach as much as we can about it. Let’s teach the controversy. Our problem is that, people who go through school with a mild to moderate interest in the sciences walk away thinking that Darwin’s Theory is a sealed deal. At least this was the way it was when I was in school. I was almost duped into believing this myself and for many years I did. I think things are finally starting to shift in the direction that there is growing skepticism, to which I say, hallelujah!

[Guest shpongle]

Okay, let me get this straight. I feel like you’re all over the map now. What do you believe? Do you believe that banana's and the Chimpanzees eating them, ultimately have a common ancestor?

Yes.

 

Do you believe that Darwinian Evolution has been proven or don’t you?

Nothing in science is technically "proven" in the strictest sense of the word. I do believe, however, that the evidence strongly supports shared common ancestry for life on Earth.

 

One second you’re telling me about this great evidence for evolution and then you’re telling me it works against evolution. If you're on the fence, that's okay and I totally respect that, I'm just curious what you believe.

I'm not following you here. What are you refering to when you say "this great evidence for evolution".

 

Give me a summary of what you believe about the Darwinian Evolution that high school students are going to get taught all over the world tomorrow like we had taught to us over a decade ago. Keep it simple. Boil it down to a paragraph or two.

 

Do you think Darwinian Evolution is good to teach as fact to kids?

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First, I'd drop the term "Darwinian" since I think that's pretty misleading and just call it The Theory of Evolution. The science has come along way since Darwin's time.

 

Second, on what to teach:

 

A general overview of evolutionary mechanisms (heredity and variation, mutations, selection, drift, etc). This would include stuff about population genetics. Brief overview of the lines of evidence that support common descent (morphology, fossils, genetics). Maybe a little bit about phylogenetics here. Maybe some basic application of evolution. And perhaps a bit about current challenges or frontiers in evolutionary biology research.

 

I don't know if all that would be feasible to teach at a high school level, but that's the gist of it.

[Guest shpongle]

If evolution is going to be taught in schools let’s teach as much as we can about it. Let’s teach the controversy.

The problem with this is... what controversy? A lot of the so-called "controversy" over evolutionary biology is political, not scientific. Most of the objection is not coming from biologists, but from religious groups (i.e. creationists) and primarily in the United States. It's reached a point where the ID movement itself has been somewhat hijacked by creationists for their own ends. And then you wind up with stuff like what happened in Dover.

 

And even though there are biologists who reject evolution they are in the extreme minority; AIG lists about ~20 to 25 and there are about 90,000 biologists working in the US alone. And of those who reject evolution, it all seems to come back to religious belief (i.e. Christianity in the US), not strictly science. Otherwise, you'd expect to see scientists of other faiths (or non-faith) rejecting evolution if the theory was as problematic as some seem to think. And especially in other countries if the issues with evolution were not tied to specific religious beliefs like it seems it is in the US.

 

Certaintly there are real controversies about evolutionary biology within the scientific community. But those controversies aren't the ones that people seem to want to teach.

[JudyV 0]

Hi Sis,

 

You've seen 'Expelled'. There is a good starting point to see that evolutionists aren't above making power plays when considering how they do in an open debate. Get the DVD ‘Icons of Evolution’, and then convince me there isn’t selective pressure regarding the topic of Darwinian Evolution.

 

Ask Eugenie Scott and Richard Dawkins to answer your question. They and others think creation talk should be banned as some kind of poison. (or more directly Dawkins called it 'Creation Lunacy')

 

The bottom line is this. Scientists just like any group of people; yacht clubs, church denominations, political groups, radical activists, become cliquish. In certain ways this doesn’t really matter but when we start seeing legal power plays to distort the education process and peer-groups firing people for even mentioning anti-Darwinian concepts then the problem has taken on a life of its own. Darwinists are on the march to suppress the controversy, fortunately, they’re starting fail. I just hope the ball keeps going. The scopes/monkey trial has flipped 180 degrees the other way.

 

I think the more important thing is; what are we protecting our kids from? This is a lively and interesting topic. If evolution is going to be taught in schools let’s teach as much as we can about it. Let’s teach the controversy. Our problem is that, people who go through school with a mild to moderate interest in the sciences walk away thinking that Darwin’s Theory is a sealed deal. At least this was the way it was when I was in school. I was almost duped into believing this myself and for many years I did. I think things are finally starting to shift in the direction that there is growing skepticism, to which I say, hallelujah!

21155[/snapback]

I think you misunderstood my question. Let me rephrase it.

 

It seems the fundamentalist Christian community (if your post above is any indication), feels there is a concerted effort on the part of the mainstream scientific community to suppress any public discussion about the "controversy" surrounding evolution versus creationism or intelligent design.

 

1) What is it that motivates scientists to suppress legitimate challenges to the widely held conclusion that the way living creatures got here is through evolution?

 

2) What is the mechanism inherent in the scientific method that would enable a worldwide conspiracy of this sort to take root?

[Adam Nagy 50]

Hi Sis,

 

I think your questions deserved a new thread:

 

The Engine of the Fairytale

[Adam Nagy 50]

Why would a scientist who could disprove another scientist's pet theory, whatever it may be, restrain himself for doing so?

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I really think people have an odd misconception that the moment a person puts on the white lab coat they suddenly become superhuman and social pressures and biases are a thing left at the front door when they walk in.

 

I’m sure it’s safe to assume that a lab works socially like any office building.

 

The convenient thing about Evolution in general (Big-Bang through Darwin) is that it’s a belief that’s been transfigured into the orthodox paradigm for explaining origins. Public schools have been teaching evolution as the naturalistic alternative to special creation since the early 60’s when, freedom of religion was reinterpreted to freedom from religion and since special creation had a religious tag, evolution suddenly found itself artificially without a competitor. Well, when an idea has no alternative, isn’t it safe to assume that it’s fact?

 

Now here’s the rub. People in science labs today and especially talking about those in charge, have gotten to where they are by adhering to the orthodox paradigm of Evolution. If your boss is an evolutionist and you’re interested in raises, you hang your faith in God on the hat rack on the way in and you put on your naturalistic glasses because that’s how the boss wants you to look at things and talk about things, through the language of Evolution.

 

At the end of the day neither Evolution ideas nor Creation ideas would technically alter the way the applied science or the scientific method is used. The problem comes when someone says:

 

“Wow, look how God designed this…oops… I mean look how it evolved…” and gets fired for bringing his biases into the shop because we’ve been indoctrinated to believe that only Darwinian assumptions are acceptable and pure enough to do the research properly. In fact they’re such good assumptions that they aren’t to be recognized as assumptions at all.

 

The bottom line is this:

 

Darwinian orthodoxy and science don’t clash naturally because the prior is a religious belief and the latter is testable, repeatable, observational data. However, there are a minority of fields that make a lot of noise while semi-successfully hiding behind the banner of “The Scientific Community” when their religious paradigm of pure naturalism gets challenged with relevant evidence and critical abstract reasoning that sufficiently calls into question the assumed origins story from Darwin.

 

These are the people that make a living off of painting the evolution story. People like Richard Dawkins, Eugene Scott, and Peter Atkins are all very active at keeping the public and even scientists convinced that, when evolution is attacked the scientific method is attacked. Unfortunately, so many people have been duped into believing this lie.

 

...including you, Sis.

 

The reason applied evolution looks functional is because evolution is assumed.

[Guest shpongle]

Has anyone actually been fired for being in ID or creationism?

[Adam Nagy 50]

Has anyone actually been fired for being in ID or creationism?

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Go get 'Expelled' and ‘Icons of Evolution’ if you haven't seen them yet. Professors and teachers seem to be the most likely targets but scientists and researchers are fair game as well for the harassment. I’ll look into getting some well known names for you but ‘Expelled’ is the best starting point.

 

The reason 99% of scientists believe in evolution is because we all know that real scientists believe in evolution anyway.

[Guest shpongle]

Go get 'Expelled' and ‘Icons of Evolution’ if you haven't seen them yet. Professors and teachers seem to be the most likely targets but scientists and researchers are fair game as well for the harassment. I’ll look into getting some well known names for you but ‘Expelled’ is the best starting point.

 

The reason 99% of scientists believe in evolution is because we all know that real scientists believe in evolution anyway. 

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Do you have any specific names? FWIW, I haven't seen Expelled yet, but according to details given at Expelled Exposed, none of the people in the film were fired. Caroline Crocker's case might be the closest, but she wasn't actually fired, her contract wasn't renewed.

[jamesf 1]

Go get 'Expelled' and ‘Icons of Evolution’ if you haven't seen them yet. Professors and teachers seem to be the most likely targets but scientists and researchers are fair game as well for the harassment.

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It is probably worth looking at both sides to the stories mentioned in Expelled. The movie did not make much effort to discover the universities' positions. You can read that here which includes excerpts from Expelled and comments from the Universities and institutions involved. Looks very different to me when you have both sides

http://www.expelledexposed.com/index.php/the-truth

 

The movie was pretty sleazy in places. I think Roger Ebert's review is pretty good. Especially the end. I like the cartoon at the end of the review.

http://blogs.suntimes.com/ebert/2008/12/wi...teins_mind.html

 

 

To tie this to this thread.....

 

Does intelligent design provide an opposing scientific view to comparative genomics? It looks a rather like astrology to me. However, if someone wants to point out the creationist genomics papers, it would be fun to take a look.

[Adam Nagy 50]

It is probably worth looking at both sides to the stories mentioned in Expelled.

Yeah, I looked at that web-site quite a while ago. I saw lots of posturing and smoke.

 

I hope people look at ‘Expelled’ and the objections to it critically. The objections are mostly gnat straining and posturing. Like how the evolutionists felt deceived because the title of the movie they were told was different than the one that actually ended up on the cover. Wow, what a scandal!

 

If evolutionists talk differently about what they believe depending on the type of person they are talking to, that tells me a lot about their underlying nature. If their own candor made their position painfully obvious, is that Ben Stein's fault?

[Guest shpongle]

But has anyone actually been fired simply for voicing their opinion in favor of ID or creationism? So far I see no examples being given.

[Adam Nagy 50]

But has anyone actually been fired simply for voicing their opinion in favor of ID or creationism?  So far I see no examples being given.

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Seriously, I'm not asking you to read 900 pages worth of data and calculations. I offered two documentaries that are both very intriguing and you'll, at least, get an opportunity to get more inside the head of the creationist.

 

The best way to defeat your enemy is to get to know him.

 

“Icons of Evolution’ and ‘Expelled’ are both mainly concerned with simple data. They even explain the paradigm between said ID and YECs to show that they aren’t necessarily contradictory but use different worldviews to come to very similar information about; that which we can test and demonstrate.

 

YECs have no problem promoting ID information. Even though they don’t confess a Young Earth, there is still a convergence from their observations to our worldview.

 

Be patient here. I’m going to find you a list of people who have publically stated how they were harassed and/or fired. (In fact, a little help from other creationists here would be nice.) BTW, if you want to believe the data on that web-site that supposedly debunks ‘Expelled’ that’s your prerogative. I could see why a documentary like ‘Expelled’ would get people to rearrange their stories to try and discredit the discreditor.

 

If you’re diligent, I promise you’ll see beyond the smoke and mirrors. The question is; do you want to take the red pill or the blue pill?

[Adam Nagy 50]

Does intelligent design provide an opposing scientific view to comparative genomics? It looks a rather like astrology to me. However, if someone wants to point out the creationist genomics papers, it would be fun to take a look.

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I don't see any problems with comparative genomics the way it currently works. Discovering that Camels and Whales have similar code sequences is useful information. Discovering that Bats and Dogs have similar code sequences is useful information.

 

Is there any Creationist here interested in shutting the doors on labs that study comparative genomics?

 

When someone stops and say; "We have scientifically proven that Camels and Whales have a common ancestor." I take umbrage at that. It's simply baloney to convince someone that you have enough information through comparative genomics to extrapolate this religious belief. It’s deceptive.