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Author Topic:   How novel features evolve #2
kofh2u
Member (Idle past 2157 days)
Posts: 1162
From: phila., PA
Joined: 04-05-2004


Message 346 of 402 (677161)
10-27-2012 2:12 PM
Reply to: Message 341 by mindspawn
10-26-2012 6:28 PM


Re: adding an extra functional gene
The question about evidence for supernatural causes seems unfair when as soon as evidence is supplied the effect is no longer called supernatural.

For instance, when Genesis says God created the Plant kingdom through Spontaneous Generation of life on Earth, the science person will simply define that as Biogenesis and supply the information that explains the theory along the lines og Urey/Miller.

I see Supernatural as anything we can not yet demoinstrate to have a Cause and Effect relationship, like a Quantum Jump, Quantum Entanglement, or the collapse of the wave function by mere observation, etc.


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 Message 341 by mindspawn, posted 10-26-2012 6:28 PM mindspawn has not yet responded

  
Meddle
Member
Posts: 174
From: Scotland
Joined: 05-08-2006


(1)
Message 347 of 402 (677174)
10-27-2012 6:21 PM
Reply to: Message 304 by herebedragons
10-23-2012 9:31 AM


Re: On topic news
Is citrate utilization an identifying characteristic of e-coli? I looked at an older version of the Enterotube and cit - is one of the identifying characteristics of e-coli, with 0% showing cit +. However, a newer version appears to have some more leeway as to the citrate test in identification of e-coli.

With you doing this on a daily bases, is cit - a characteristic you would use to identify e-coli? Do you use Enterotube for diagnostic purposes?

I've not used Enterotube but looks like the same principle as Biomerieux's API system we've used, which also lists E.coli as 0% citrate positive. With these methods it is the pattern of reactions to many biochemical tests which identify the bacteria. For API, there are usually 20 tests which generate a profile number which you enter into a web-based server which calculates the accuracy of the identification and highlights any contraindicated tests. So for something like citrate a positive citrate for E.coli would push the percentage probability of the ID down. Can't think I've seen this happen, but then I've not been paying particular interest in citrate. Now we use cards in the automated Vitek system which contain even more biochemical tests but again the same principles apply, with any inconsistent results being highlighted. However, couldn't find their criteria for different biochemical tests in this method, but then it is being constantly updated.

I would say that I've found that biochemical tests are fairly consistent. For example we use MacConkey agar which causes lactose fermenting bacterial colonies to appear pink. There is a number of bacterial species are never found to be lactose-fermenters, such as Salmonella, so this is a good presumptive diagnostic test. So I would say it is consistent to describe cit- as an identifying characteristic of E.coli. An earlier paper by Blount mentions previous examples of cit+ E.coli. The majority of these were the result of acquiring plasmids from other species that contained the relevant genes for citrate uptake, but only a single documented example of the ability resulting from changes in an E.coli chromosome. This is probably why Enterotube is open towards the possibility of cit+ E.coli, even if it may be transitionary depending on other bacteria present.


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herebedragons
Member (Idle past 69 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 348 of 402 (677222)
10-28-2012 2:30 AM
Reply to: Message 347 by Meddle
10-27-2012 6:21 PM


Re: On topic news
I've not used Enterotube but looks like the same principle as Biomerieux's API system we've used, which also lists E.coli as 0% citrate positive.

Thanks Malcolm. I wanted to point this out to zaius but couldn't confirm the specifics. If citrate utilization is a diagnostic feature of E coli, then a positive result is unusual to say the least. But hey, its still a bacteria huh? It didn't evolve into a puppy ... so not novel.

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.


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mindspawn
Member (Idle past 997 days)
Posts: 1015
Joined: 10-22-2012


Message 349 of 402 (677300)
10-29-2012 2:32 AM
Reply to: Message 344 by Percy
10-27-2012 10:24 AM


Re: adding an extra functional gene
Percy, that is funny. All I need to do is start more threads? I cannot keep up with the current ones, so that just is not going to happen. I would love to discuss the proof for the bible being a supernatural book, I would love to discuss radiometric dating, but its just impossible time wise.

In this thread we are discussing proof for evolution, can organisms evolve complexity, and develop additional genes with new functions (that add fitness)? This is the question I have been asking. when I look at chromosomal organizations of modern organisms it speaks to me of a perfect design with a few mutations. When an evolutionist looks at the same DNA sequence they will see an organism in a state of evolving, with many mutations.

Both of us haven't got evidence for the process involved, evolutionists use the assumption of evolution as proof of evolution. ie they use the assumption that many areas of the genome are in a mutated state and there are a lot of mutations occurring. and then in many cases assume the less complex precedes the more complex. Under ID assumptions the more complex precedes the less complex in most cases, with increased fitness sometimes occurring when a problematic gene is disabled (eg Duffy gene)


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mindspawn
Member (Idle past 997 days)
Posts: 1015
Joined: 10-22-2012


Message 350 of 402 (677301)
10-29-2012 2:37 AM
Reply to: Message 343 by Theodoric
10-27-2012 9:42 AM


Re: adding an extra functional gene
Theodoric, you are missing the point of this thread, where is the proof for essential evolutionary processes? without added genes with new functions we would all be bacteria, where's your proof of this process? Is it a myth? At least I have a religious book to back up my beliefs, you have a few unproven ideas. You can't use evolution to prove evolution, that lacks science.

even the lack in evolutionary circles to assume both ID and evolution are valid hypotheses and then to look at DNA sequences with both view equally in mind, is showing non-scientific bias.


This message is a reply to:
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mindspawn
Member (Idle past 997 days)
Posts: 1015
Joined: 10-22-2012


Message 351 of 402 (677302)
10-29-2012 2:46 AM
Reply to: Message 345 by Tangle
10-27-2012 11:30 AM


Re: adding an extra functional gene
Tangle, Religious belief is not always on an intellectual level. I enjoy the intellect and value the intellect, but understand the inability for humans to be perfectly unbiased. There is a deeper and more accurate determination of right and wrong called our spirit. When our spirit is in line with the truth we have peace in our hearts, its a communication far more accurate than the intellect because we are in touch with a higher being, Jesus. So I know in my heart that God reveals himself through the bible, and it does help that on an intellectual level the bible is increasingly proved to be accurate from a historical point of view, and does also have prophecies recorded before historical events that unfold exactly as predicted. This is all off-topic but it just may mean something to any reader seeking for peace in their hearts.

So to answer your question clearly, I have confirmation on a deeper level than intellect regarding the truth of the bible, and so have not examined the bible from an intellectual level, I've accepted its truth and this has been confirmed throughout my life. With answered prayer, healings, history confirming the bible, peace in my heart, principles of the bible working accurately. In every sphere, including intellect, the bible continues to be confirmed truth to me.

Edited by mindspawn, : Answering the question put to me

Edited by mindspawn, : No reason given.


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mindspawn
Member (Idle past 997 days)
Posts: 1015
Joined: 10-22-2012


Message 352 of 402 (677305)
10-29-2012 3:09 AM
Reply to: Message 342 by NoNukes
10-27-2012 12:12 AM


Re: adding an extra functional gene
Having a specific function alone would not make a section of DNA resistant to change. It might mean that such changes would not be selected and would not propagate but only if the mutation does not affect your ability to sire or mother offspring. As has been already presented, you possess mutations that are not a part of your parent's genetic makeup. Everyone does.

You also seem to be confusing junk DNA with functioning DNA being able to operate despite modification.

I understand we get mutations, but not as often as the theory of evolution believes in. Evolutionists have assumed a lot of DNA has no function, and yet these sections have been found to have a function, which believers in Intelligent Design have been saying all along.

http://www.nytimes.com/...tter-proves-crucial-to-health.html


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Replies to this message:
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PaulK
Member
Posts: 15629
Joined: 01-10-2003
Member Rating: 2.8


Message 353 of 402 (677306)
10-29-2012 3:21 AM
Reply to: Message 352 by mindspawn
10-29-2012 3:09 AM


Re: adding an extra functional gene
To be more accurate, evolutionists have known that some parts of non-coding DNA have a function for a long time. And we can find these through an understanding of evolution. ID has just been dogmatically declaring that all DNA has a function, and refusing to accept the evidence that a lot of it doesn't (the huge variations in the length of DNA, that don't seem to correlate with anything else, for one - see "the onion test" for an example).

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Tangle
Member
Posts: 7189
From: UK
Joined: 10-07-2011
Member Rating: 3.6


(1)
Message 354 of 402 (677308)
10-29-2012 4:24 AM
Reply to: Message 352 by mindspawn
10-29-2012 3:09 AM


Re: adding an extra functional gene
mindspawn writes:

I understand we get mutations, but not as often as the theory of evolution believes in. Evolutionists have assumed a lot of DNA has no function, and yet these sections have been found to have a function, which believers in Intelligent Design have been saying all along.

Geneticists [not evolutionists, whatever they are] established that a large part of our DNA did not code for proteins. It was labelled 'junk' to differentiate it from the parts that did seem useful. Geneticists then spent a lot of time and effort trying to understand what it was for.

Geneticists have now found that those regions are involved in switching protein making genes on and off in response to environmental factors.

At no point in this scientific process, was an ID believer involved and at no time has any ID believer shown that junk DNA was involved in gene switching.


Life, don't talk to me about life - Marvin the Paranoid Android

This message is a reply to:
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Percy
Member
Posts: 19069
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.2


(1)
Message 355 of 402 (677324)
10-29-2012 8:18 AM
Reply to: Message 349 by mindspawn
10-29-2012 2:32 AM


Re: adding an extra functional gene
mindspawn writes:

Percy, that is funny. All I need to do is start more threads? I cannot keep up with the current ones, so that just is not going to happen. I would love to discuss the proof for the bible being a supernatural book, I would love to discuss radiometric dating, but its just impossible time wise.

I was suggesting that you suspend participation in this thread while discussing the Bible's qualifications as a science book in a new thread, not that you participate in both threads simultaneously. Also, there's no time limit on replies. Take as much time as you need. Make your goal to post x messages per week, not to reply to everyone every week.

It's interesting that you said, "I would love to discuss the proof for the bible being a supernatural book," because that's not what you originally said back in Message 341. What you said there was that, "I haven't got evidence, except that the bible is a proven and accurate book..." A thread where you tried to present evidence that the Bible has supernatural origins would be very interesting, but concerning your original claim, if the Bible really is "proven and accurate" then you need only seek recourse to evidence relevant to this thread that proved the Bible accurate.

Except that there isn't any Biblical evidence relevant to this thread. The Bible doesn't declare that the development of novel features is impossible. It says that creatures reproduce according to their kind, and so does evolution. The Bible says that cows beget cows and crows beget crows, and so does evolution.

But evolution says something additional, which is that what we know as cows and what we know as crows changes over time. Cows have begat cows since the beginning of time, but what is a cow has changed. The Bible makes no comment on this, and there can be no Biblically based objection.

Both of us haven't got evidence for the process involved...

You're only half right. You haven't got evidence, we have, we win. Evolution is a very widely accepted theory because of evidence, not assumptions. You're ignoring the evidence that mutations occur (indeed, they must occur since the DNA copying of reproduction is imperfect and we even know the mutation rates for many organisms), and then you're ignoring the implications. We have evidence of mutations and selection, while you only have assumptions you mistakenly think are Biblically based.

And then in many cases assume the less complex precedes the more complex.

I thought it was already mentioned in this thread, but maybe not, so I'll say it again. Evolution definitely does not say that the less complex precedes the more complex. It says that whatever traits are favored by the environment have increased probability of making it to the next generation. Whether those traits are simpler or more complex is not a factor.

It's a common mistake to think that evolution believes the simpler precedes the more complex because that is a dominant feature in the fossil record. One reason for this is known as the evolutionary arms race. The gazelle becomes faster and more evasive, so the cheetah becomes faster and more agile in order to catch it, and so the gazelle becomes even faster and more evasive, and so on. But if the environmental situation changed so as to somehow favor being slower and less agile, then that's what would happen. There are many examples of organisms becoming simpler, for example, blind cave fish which once had sight and now do not.

--Percy


This message is a reply to:
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mindspawn
Member (Idle past 997 days)
Posts: 1015
Joined: 10-22-2012


Message 356 of 402 (677332)
10-29-2012 9:31 AM
Reply to: Message 353 by PaulK
10-29-2012 3:21 AM


Re: adding an extra functional gene
yes PaulK I agree they shouldn't be quite as dogmatic, mutations are quite common. But I don't see any proof that they are common enough to assume every gene would reflect them.

The duplications can't be proven as such unless you have an initial population that is devoid of that mutation, and then they are subsequently observed with mutations. This can be observed in humans, because our defects are the most studied. You can get a new mutation appearing in offspring that obviously neither parent had. This is a genuine mutation. To contribute as an explanation for how complex organisms exist today, the mutation would have to improve fitness, and add a gene with a function. To find proof of this is near impossible because its difficult to reproduce evolutionary time frames in the laboratory.


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mindspawn
Member (Idle past 997 days)
Posts: 1015
Joined: 10-22-2012


Message 357 of 402 (677336)
10-29-2012 9:49 AM
Reply to: Message 354 by Tangle
10-29-2012 4:24 AM


Re: adding an extra functional gene
Geneticists [not evolutionists, whatever they are] established that a large part of our DNA did not code for proteins. It was labelled 'junk' to differentiate it from the parts that did seem useful. Geneticists then spent a lot of time and effort trying to understand what it was for.

Geneticists have now found that those regions are involved in switching protein making genes on and off in response to environmental factors.

At no point in this scientific process, was an ID believer involved and at no time has any ID believer shown that junk DNA was involved in gene switching.

that's the problem. ID's , using the biblical concept of creation ~6000 years ago, assumed that most of the genome was created like that. So when the term "junk DNA" was introduced 40 years ago, the predictive quality of the ID assumption is that these areas of the genome would be found to be useful. And they (I say that because I have only recently become involved) were right. Without looking at the alternative ID explanations for anything seen in the genome, the entire science of molecular biology is being unnecessarily slowed down and it is very frustrating to observe. True science should now interpret each genome sequenced under both ID and evolutionist assumptions and see which one fits reality of current observed genomes better. There just are not enough scientists who take ID as a serious possibility this is why the evidence is slow to establish.

Do we have to wait another 40 years before science discovers that genetic entropy is more observed than evolution? With evolutionists kicking against it every step of the way? (rhetorical question)


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NoNukes
Inactive Member


(1)
Message 358 of 402 (677370)
10-29-2012 12:46 PM
Reply to: Message 352 by mindspawn
10-29-2012 3:09 AM


Re: adding an extra functional gene
I understand we get mutations, but not as often as the theory of evolution believes in.

Evolution "believes in"? What rate is that and what are you claiming is the real rate?

Evolutionists have assumed a lot of DNA has no function, and yet these sections have been found to have a function, which believers in Intelligent Design have been saying all along.

As I have explained, this is not related to whether mutations occur in existing DNA.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

The apathy of the people is enough to make every statue leap from its pedestal and hasten the resurrection of the dead. William Lloyd Garrison.

If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass


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Taq
Member
Posts: 8207
Joined: 03-06-2009
Member Rating: 3.9


(1)
Message 359 of 402 (677379)
10-29-2012 1:13 PM
Reply to: Message 341 by mindspawn
10-26-2012 6:28 PM


Re: adding an extra functional gene
I haven't got evidence , except that the bible is a proven and accurate book, which is of topic for this thread.

You are contradicting yourself. If the Bible is proven and accurate then you should be able to provide the evidence that species were created by a supernatural deity. You should be able to evidence your claims independent of what the Bible says.

In a court of law, do we find people guilty because the District Attorney says so? Or does the DA have to provide evidence?

Neither have you got evidence for your evolutionary process because you are using the assumption of evolution to prove evolution.

Not at all. We are making predictions of what we should and should not see in the field of biology if evolution is true. For example, if the carboxylesterase gene went through a recent duplication then we should see a lack of divergence between the two genes. This is a testable prediction. It is a scientific prediction.

So what predictions does creationism/ID make, and why? How do we test for these mechanisms as it relates to the emergence of novel features?

To what extent are these neutral mutations truly neutral, when some so-called "junk-DNA" has recently been found to have a function.

They set the bar really low for what they consider "function". Using an analogy, they would consider the trash in your kitchen to be functional since it adds odor molecules to the air which changes the biochemistry of your kitchen. Using their definition of functional they would classify real junk as having function.

The fact of the matter is that there is a lot of junk DNA, and a lot of changes within genes that are selectively neutral (e.g. third base wobble and conservative changes to amino acids). As I cited earlier, there is a 40% difference between human and yeast cytochrome C and yet the human gene can replace the yeast gene without a change in fitness.


This message is a reply to:
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Taq
Member
Posts: 8207
Joined: 03-06-2009
Member Rating: 3.9


Message 360 of 402 (677385)
10-29-2012 1:25 PM
Reply to: Message 350 by mindspawn
10-29-2012 2:37 AM


Re: adding an extra functional gene
Theodoric, you are missing the point of this thread, where is the proof for essential evolutionary processes?

I have cited both the Luria-Delbruck fluctuation experiment and the Lederberg's plate replica experiment as examples of beneficial mutations arising through random mutation. These experiments looked at bacteriophage and antibiotic resistance, and it involved the modification of genes into new genes that changed the fitness of the organism.

Lenski's experiments demonstrating the evolution of citrate utilization involved DNA duplication and substitution mutations that resulted in a novel phenotype and a new gene.

I have also cited the evolution of dark fur in pocket mice that was due to substitution mutations in the MC1R gene. This novel phenotype was strongly beneficial in the darker lava fields.

So how many evidenced examples have we been given of this supposed designer doing anything? Zero.

At least I have a religious book to back up my beliefs, . . .

That's what they said when they put Galileo under house arrest.

You can't use evolution to prove evolution, that lacks science.

We can use testable hypotheses to test the theory. That is scientific.

even the lack in evolutionary circles to assume both ID and evolution are valid hypotheses and then to look at DNA sequences with both view equally in mind, is showing non-scientific bias.

Even ID supporters are incapable of creating testable hypotheses that can be used to test ID. The Discovery Institute is full of people who claim that ID is scientific, so where is the science? Why aren't they doing the research? I can only conclude that ID is not scientific but it is purely religious.


This message is a reply to:
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