"If ENCODE is right then Evolution is wrong"

Lily of Valleys · Jul 25, 2017

For those who are interested, here are the links to the 2012 and 2014 paper by ENCODE. I have also added them to the opening post:

An integrated encyclopedia of DNA elements in the human genome : Nature : Nature Research
http://www.pnas.org/content/111/17/6131.full

Subduction Zone · Jul 25, 2017

Lily of Valleys said:
You were only mentioned because Bugeyedcreepy mentioned you.

Then you are admitting that you had not clue?

People would be more likely to engage in a conversation with you if you address only the points but not the person.

And no, I am not interested in having an argument with you. ad hominem is boring.

You don't seem to realize what ad hominem is. I do not engage in such.

No one said you linked Tim Minchin. The post wasn't addressed to you, it was addressed to Bugeyedcreepy.

Then why did you even mention Tim Minchin? You are the one if anyone that seems to be involved in ad hominem.

xianghua · Jul 25, 2017

PsychoSarah said:
-_- viruses evolve, since they have genetic material subject to mutation. Hence how ENTIRELY NEW diseases appear from time to time. However, the variation in viral mutation frequency is quite extreme compared to living organisms, for reasons of differences in replication and chemical stability. The rabies virus is so stable that we can recognize records of it from thousands of years ago by symptom descriptions. In contrast, HIV changes so frequently that treatment has to be tailored from person to person.

However, thanks to the limited genes a virus has and the predictable selection pressures they are subject to, it's easy to make vaccines for viruses that don't change super fast, such as the chicken pox and flu viruses. The faster the virus changes, the more frequently vaccines are needed to keep up. For the most part, some of them change so slowly that our acquired immunity will give out before they mutate enough to actually get around it.

and yet- they are still viruses and doesnt evolve any new complex system. so its not evolution. only a variation.

Subduction Zone · Jul 25, 2017

xianghua said:
and yet- they are still viruses and doesnt evolve any new complex system. so its not evolution. only a variation.

Nope, but thanks for telling us that you do not understand even the basics of evolution.

PsychoSarah · Jul 25, 2017

xianghua said:
and yet- they are still viruses and doesnt evolve any new complex system. so its not evolution. only a variation.

-_- you say that as if variation and trends in variation within populations isn't evolution. Furthermore, they can develop new systems of getting around immune systems and infecting over time. Why do you think there was a huge scare about the possibility of HIV becoming airborne when a bunch of people that attended the same dentist caught it? Turned out he was violating them while they were knocked out, so it hadn't gone airborne, but sometimes viruses do change their mode of infection.

Due to their lack of being alive and short genomes, viral strains can repeat periodically via mutation. Hence why flu strains from 30 years ago can pop up again today.

xianghua · Jul 25, 2017

so if im undernstand you right, we can (for instance) predict that if a medicine is good for an ape, it will fit well with human more then say a mouse, because ape and human are more closely related. correct?

if so: we can predict it also under the design model. we know that those two shared more similar morphology- therefore there is more chance that the medicine will fit well with human more then with a mouse. so we dont need evolution to explain it. as i said: we can still make medicines even if evolution were wrong.

Subduction Zone · Jul 25, 2017

xianghua said:
so if im undernstand you right, we can (for instance) predict that if a medicine is good for an ape, it will fit well with human more then say a mouse, because ape and human are more closely related. correct?

if so: we can predict it also under the design model. we know that those two shared more similar morphology- therefore there is more chance that the medicine will fit well with human more then with a mouse. so we dont need evolution to explain it. as i said: we can still make medicines even if evolution were wrong.

First off since humans are by definition "apes" your post is poorly worded.

The problem with ID is that it is not predictive. That is largely due to the fact that ID supporters are afraid to make proper predictions using their beliefs. They will not make a testable hypothesis and as a result they have no scientific evidence for their claims. ID is reactive, it is not proactive in the way that the theory of evolution is. One of the ways that the theory of evolution is tested is by the predictions it makes.

Once those predictions are verified the IDists merely claim "Me too". But since they made no predictions their claims are worthless in the world of science, since they would have "Me too"ed regardless of what the prediction was.

pitabread · Jul 25, 2017

xianghua said:
so if im undernstand you right, we can (for instance) predict that if a medicine is good for an ape, it will fit well with human more then say a mouse, because ape and human are more closely related. correct?

I'm assuming this post is in response to my prior post about genomics?

Anyway, what you wrote isn't what I'm talking about at all.

What I was referring to is research into figuring out what different parts of the genome actually do, particularly in respect to human health. Part of the reason researchers use genomic comparisons with other species is to determine which parts of the genome may be important for the organism in question.

But simply lining up genomes and comparing them doesn't tell the whole story. The reason researches use phylogenetic data in the comparisons is because if they know when two species last diverged (say they are 10 million years apart), they can estimate the amount of neutral evolution which would have taken place in their respective genomes. From that, they can zero in one regions that are more or less diverged than one would expect from strictly neutral evolution. This allows researches, particularly when it comes to highly conserved sequences, to make better determination of which parts of the genome are functionally important. On top of that, they can even use this extra information, if they know what what sequence does in a specific organism, to predict gene function in other organisms, even if the sequences are not identical.

As an analogy, say you wanted to find my house. If I told you that my house was north of your position, you could start walking north and try to find it. You wouldn't know how far to walk, so you'd just have to keep going until you found it. But if I told you that my house was 2 kilometers to the north, you would have a much easier time of finding it. That extra information allows you to make a more informed search for my house.

It's similar to genomics. By incorporating data about the relative evolutionary divergence of species (e.g. phylogenetic trees), researchers can make more informed analyses of the genomes they are studying.

if so: we can predict it also under the design model. we know that those two shared more similar morphology- therefore there is more chance that the medicine will fit well with human more then with a mouse. so we dont need evolution to explain it.

Again, none of this was what I was talking about. Plus, there is no "design model" in terms of applied biology. We don't gain any extra information by assuming that organisms were designed as opposed to evolved.

as i said: we can still make medicines even if evolution were wrong.

That's not the point though. The point is that evolutionary biology is being directly incorporated into modern pharmacology specifically with respect to genomics and drug discovery. It is being used in the medicine making process.

Bugeyedcreepy · Jul 25, 2017

sfs said:
Are you familiar with this project:

Tree of Life Web Project

They are trying to build as inclusive of a Tree of Life as possible.

Oh, Wow! I knew of efforts out there & heard AronRa talking about a site like this that he was going to run up at one point but I never did find it... How up to date is it, has there ben any maintenance since 2011? Thank you!

Lily of Valleys said:
You have brought up a very important point. The disagreement is not with the evidence, but the interpretation of the evidence.

All these DNA matching exercises are based on the assumption that similarities mean common descent, which doesn't pose any problem with paternity test since it is an established fact that human does reproduce human, or forensic DNA matching, which is comparing DNA between humans. But it becomes circular reasoning to state that based on the assumption that similarities between different kinds mean common descent, therefore if they are similar it proves common descent.

Well, the evidence shows that we share a common ancestor, that's probably why it's accept we have a common ancestor - no assumptions. Genetically, there's nothing special about our DNA makeup that would wall this fact off from being true - so it's a rational evaluation. What IS out of place is your claim that the evidence should be ignored in favour of an unfounded assertion that we DON'T share all these common traits with the other great apes... do you have any evidence in support of this idea?

Lily of Valleys said:
This article lays out in details how ERV does not prove common descent any more than common design:

Do Endogenous Retroviruses (ERVs) Support Common Ancestry?

lol! You seriously quoted Answers in Genesis?? I refer you to their declared bias - Statement of Faith , Section 4, last point where it states, and I quote:

"By definition, no apparent, perceived or claimed evidence in any field, including history and chronology, can be valid if it contradicts the scriptural record. Of primary importance is the fact that evidence is always subject to interpretation by fallible people who do not possess all information."

Essentially it says: "We will ignore everything that disagrees with our presuppositions"... This is not how Science is done. Looking at the article anyway, this is another whole opinion piece that doesn't even address the evidence, it just ridicules the evidence and uses derogatory terms for the research and belittles the outcome of the research without really addressing that evidence. Seriously, how is anyone besides those who already believe, supposed to take this seriously? At one point (to their credit), this article does admit that it could look like common ancestry, but then goes right on to say that it just couldn't possibly be! Completely without scientific foundation! It distorts the scientific research that supports Evolution supposing any number of other & often untestable reasons for why it couldn't be so. I'm sorry, this is just insulting to people who actually do scientific research.

Lily of Valleys said:
Well, if you go back to check their posts before where you mentioned them, none of them cited any links.

Oh, Sorry! I worded my reply too hastily & didn't proof what I wanted to convey to you - I meant to say "They've pointed out that valid scientific research shows otherwise", and it does. Now, If you go back, you will see that original statement of mine, you will see that 'I' am stating, as have both @Subduction Zone & @sfs , that there are plenty of reasons to ignore laypeoples opinions that contradict legitimate peer-reviewed scientific research. Different story if these laypeople submit their own scientific peer reviewed rebuttals of course, but this isn't the case.

But now we might be onto something, Both @Subduction Zone and (especially) @sfs have cited a great many legitimate sources for their arguments. @sfs in particular has around two decades of in-the-trenches research in the field of biology - as much as he might not be writing a peer-reviewed critique of your references, I'll take his 'opinion' over any of your referred 'opinions' any day of the week! Even so, their time here is resplendent with quotes from, and citations to legitimate scientific research in support of their positions. Is it your contention that peer-reviewed Scientific Research is invalid, or that their (and my) citing of peer-reviewed scientific research it is invalid?

Lily of Valleys said:
My point is, as far as I am aware, none of the posts on this forum are peer reviewed paper, what everyone said are simply their opinions, in your word "opinion pieces", yet you still read them, right? Then what's wrong with reading other "opinion pieces" outside of this forum?

Peer-reviewed paper are not necessarily fool-proof, non-peer-reviewed opinions are not necessarily invalid. Whether peer-reviewed or non-peer-reviewed, what matters is whether their points are valid, not where they come from.

Peer-review and the scientific method aren't perfect, I agree. What I will say though is that peer review and the scientific method are hands down the best way we come about reliable points of fact. It has literally given us nearly all the technological progress we enjoy today. If I might plagarise Winston Churchill's famous quote on Democratic governance in support of the Scientific Method - The Scientific Method is the Worst form of coming about the truth except for all the other forms we've tried...

Bugeyedcreepy · Jul 25, 2017

xianghua said:
and yet- they are still viruses and doesnt evolve any new complex system. so its not evolution. only a variation.

heh! that's like saying - "and yet- they are still animals and doesnt evolve any new complex system. so its not evolution. only variation."

Subduction Zone · Jul 25, 2017

Bugeyedcreepy said:
Oh, Wow! I knew of efforts out there & heard AronRa talking about a site like this that he was going to run up at one point but I never did find it... How up to date is it, has there ben any maintenance since 2011? Thank you!

Well, the evidence shows that we share a common ancestor, that's probably why it's accept we have a common ancestor - no assumptions. Genetically, there's nothing special about our DNA makeup that would wall this fact off from being true - so it's a rational evaluation. What IS out of place is your claim that the evidence should be ignored in favour of an unfounded assertion that we DON'T share all these common traits with the other great apes... do you have any evidence in support of this idea?

lol! You seriously quoted Answers in Genesis?? I refer you to their declared bias - Statement of Faith , Section 4, last point where it states, and I quote:

"By definition, no apparent, perceived or claimed evidence in any field, including history and chronology, can be valid if it contradicts the scriptural record. Of primary importance is the fact that evidence is always subject to interpretation by fallible people who do not possess all information."

Essentially it says: "We will ignore everything that disagrees with our presuppositions"... This is not how Science is done. Looking at the article anyway, this is another whole opinion piece that doesn't even address the evidence, it just ridicules the evidence and uses derogatory terms for the research and belittles the outcome of the research without really addressing that evidence. Seriously, how is anyone besides those who already believe, supposed to take this seriously? At one point (to their credit), this article does admit that it could look like common ancestry, but then goes right on to say that it just couldn't possibly be! Completely without scientific foundation! It distorts the scientific research that supports Evolution supposing any number of other & often untestable reasons for why it couldn't be so. I'm sorry, this is just insulting to people who actually do scientific research.

Oh, Sorry! I worded my reply too hastily & didn't proof what I wanted to convey to you - I meant to say "They've pointed out that valid scientific research shows otherwise", and it does. Now, If you go back, you will see that original statement of mine, you will see that 'I' am stating, as have both @Subduction Zone & @sfs , that there are plenty of reasons to ignore laypeoples opinions that contradict legitimate peer-reviewed scientific research. Different story if these laypeople submit their own scientific peer reviewed rebuttals of course, but this isn't the case.

But now we might be onto something, Both @Subduction Zone and (especially) @sfs have cited a great many legitimate sources for their arguments. @sfs in particular has around two decades of in-the-trenches research in the field of biology - as much as he might not be writing a peer-reviewed critique of your references, I'll take his 'opinion' over any of your referred 'opinions' any day of the week! Even so, their time here is resplendent with quotes from, and citations to legitimate scientific research in support of their positions. Is it your contention that peer-reviewed Scientific Research is invalid, or that their (and my) citing of peer-reviewed scientific research it is invalid?

Peer-review and the scientific method aren't perfect, I agree. What I will say though is that peer review and the scientific method are hands down the best way we come about reliable points of fact. It has literally given us nearly all the technological progress we enjoy today. If I might plagarise Winston Churchill's famous quote on Democratic governance in support of the Scientific Method - The Scientific Method is the Worst form of coming about the truth except for all the other forms we've tried...

I thought that that Tree of Life Project was the one that Aron Ra spoke of too. That does not seem to be the case. His name is not among the contributors and the last news was from 2009.

I guess I need to search some more.

Tanj · Jul 26, 2017

Bugeyedcreepy said:
If I might plagarise Winston Churchill's famous quote on Democratic governance in support of the Scientific Method - The Scientific Method is the Worst form of coming about the truth except for all the other forms we've tried...

Paraphrase, not plagarise. It wold be plagarism if you said it was your quote and didn't mention Winston.

Lily of Valleys · Jul 26, 2017

Bugeyedcreepy said:
Well, the evidence shows that we share a common ancestor, that's probably why it's accept we have a common ancestor - no assumptions. Genetically, there's nothing special about our DNA makeup that would wall this fact off from being true - so it's a rational evaluation.

Here you are simply reiterating your claim without addressing my counterpoint.

Bugeyedcreepy said:
What IS out of place is your claim that the evidence should be ignored in favour of an unfounded assertion that we DON'T share all these common traits with the other great apes... do you have any evidence in support of this idea?

When and where did I make that claim?

Bugeyedcreepy said:
At one point (to their credit), this article does admit that it could look like common ancestry, but then goes right on to say that it just couldn't possibly be!

Again, where is it in the article?

Bugeyedcreepy said:
Is it your contention that peer-reviewed Scientific Research is invalid, or that their (and my) citing of peer-reviewed scientific research it is invalid?

You missed my point. Please go back and read my post again.
"If ENCODE is right then Evolution is wrong"

xianghua · Jul 26, 2017

PsychoSarah said:
-_- you say that as if variation and trends in variation within populations isn't evolution.

why not actually?

xianghua · Jul 26, 2017

pitabread said:
This allows researches, particularly when it comes to highly conserved sequences, to make better determination of which parts of the genome are functionally important. On top of that, they can even use this extra information, if they know what what sequence does in a specific organism, to predict gene function in other organisms, even if the sequences are not identical.

ok. but how it's have any connection to common descent? even if common descent is wrong we can still do that and make a medicine. so we dont need evolution to do that..

pitabread said:
Plus, there is no "design model" in terms of applied biology. We don't gain any extra information by assuming that organisms were designed as opposed to evolved.

not realy. id predict "junk DNA" to be functional. id predict that if we something that to us is looks like a bad design is actually a good design and so on. take the appendix for instance. in the past it was remove by doctors because they consider it to be useless. but now we figuring out that the appendix actually have several functions.

pitabread · Jul 26, 2017

xianghua said:
ok. but how it's have any connection to common descent?

Because they are using the respective evolutionary divergence between species as part of the analysis. Again, if two species last diverged 10 million years ago, there is going to be 10 million years worth of evolutionary change in each species' population. By estimating the average mutation rate, they can calculate the average amount of neutral divergence in the populations they would expect (i.e. where natural selection isn't playing a role). Then any genomic regions that show greater or less divergence compared to that neutral baseline, they can then estimate if those regions of the genome are undergoing different types of selection (conserved versus purifying selection). This informs researchers about which regions of the genome may be important to the respective organisms.

This is especially the case when doing multi-species comparisons where the relative divergence times will vary from species to species.

not realy. id predict "junk DNA" to be functional.

This isn't really a prediction of ID though. If you think about it, a designer could do whatever they wanted. They could try to make a genome as completely efficient as possible (i.e. no wasted genome space) or they could make it as large as they wanted. In fact, when we look at various genome sizes of organisms, they are all over the map: Genome - Wikipedia

By saying that the genome should be mostly or entirely functional, you're making an assumption about the intent of the designer who created the genome. But you have no basis for that assumption.

id predict that if we something that to us is looks like a bad design is actually a good design and so on.

Again, that's not really a prediction of ID. Especially since in both cases it's humans making the prediction; all that sounds like is a difference of opinion.

Bugeyedcreepy · Jul 26, 2017

Tanj said:
Paraphrase, not plagarise. It wold be plagarism if you said it was your quote and didn't mention Winston.

You're probably right, it was in the spirit of robbing his phrase to present my own thoughts to pass off as mine... I thought it a grey area, though I'm no expert!

xianghua · Jul 27, 2017

pitabread said:
Because they are using the respective evolutionary divergence between species as part of the analysis. Again, if two species last diverged 10 million years ago, there is going to be 10 million years worth of evolutionary change in each species' population. By estimating the average mutation rate, they can calculate the average amount of neutral divergence in the populations they would expect (i.e. where natural selection isn't playing a role). Then any genomic regions that show greater or less divergence compared to that neutral baseline, they can then estimate if those regions of the genome are undergoing different types of selection (conserved versus purifying selection). This informs researchers about which regions of the genome may be important to the respective organisms.

This is especially the case when doing multi-species comparisons where the relative divergence times will vary from species to species.

ok, it doesnt have any connection to a common descent. we can do it under the id model too. by the way, how it's help us to produce a medicine?

pitabread said:
This isn't really a prediction of ID though. If you think about it, a designer could do whatever they wanted. They could try to make a genome as completely efficient as possible (i.e. no wasted genome space) or they could make it as large as they wanted. In fact, when we look at various genome sizes of organisms, they are all over the map: Genome - Wikipedia

no. the chance that 2 junk regions in two different species will be the same is very low if we dealing with a neutral mutations. so id predict that most of the genome should be functional.

pitabread said:
Again, that's not really a prediction of ID. Especially since in both cases it's humans making the prediction; all that sounds like is a difference of opinion.

for instance: under the evolutionery model the eye retina is backward because an evolutionery flaw. id predict the opposite (that it isnt a flaw but a good design).

sfs · Jul 27, 2017

xianghua said:
who is talking now about id?

I assumed that's who you meant by "we". Otherwise, I have no idea who you're talking about. It can't be "people who think most of the genome is functional", since nothing I said suggested that most of the genome was functional.

pitabread · Jul 27, 2017

xianghua said:
ok, it doesnt have any connection to a common descent.

...

I literally just explained that they are using evolutionary distances based on phylogenetic trees which are by definition common descent relationships. How can you possibly turn around and say this has no connection to common descent?

Do you understand what phylogenetic trees are? I suggest reading the Wikipedia page for a refresher: Phylogenetic tree - Wikipedia

Phylogenetic trees are directly applied in modern genomics research as I've already outlined with multiple examples. It's a direct example of an application of the common descent relationships of modern species.

we can do it under the id model too.

Except there is no "ID model". It doesn't exist in any current application.

by the way, how it's help us to produce a medicine?

I already explained this. It has to do with phylogenetics (evolutionary relationships) being incorporated into the drug discovery process by pharmacological companies, specifically when it comes to analyzing genomic sequences for druggable 'targets'.

no. the chance that 2 junk regions in two different species will be the same is very low if we dealing with a neutral mutations. so id predict that most of the genome should be functional.

"Functional" is a relative term here. In the case of genomic comparison, they are looking for areas of the genome that have been acted on by selective pressures and thus appear to have importance to the host organism.

for instance: under the evolutionery model the eye retina is backward because an evolutionery flaw. id predict the opposite (that it isnt a flaw but a good design).

Except there is no real prediction here, at least not in an objective sense. Saying something is "good" or "bad" has no meaning unless you have an underlying criteria for determining that.

Furthermore, it appears to assume that a designer would only inherently create "good" design. But why assume that? Why couldn't a designer create something that is flawed or otherwise an example of poor design? After all, we humans do that all the time.

"If ENCODE is right then Evolution is wrong"

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