Answering any questions on Evolution

Huram Abi · Apr 8, 2012

thompsonb24 said:
Does he actually think that bacteria are a form of plant life? Hearing things like this really troubles me.

No. He just wants others to believe this.

He claims that "the plant kingdom DID establish itself before the animal kingdom" and says that this is science that supports the genesis account.

Because it has been demonstrated that animals came before plants, he now has pulled bacteria into the conversation so that he can still say that plants came before animals and that science supports Genesis.

He says that bacteria qualify as plants because they have cell walls and depends on the 2 kingdom system created in the 1700s as an authority that they are plants.

As far as I can tell he suffers from a number of pathologies, including a crisis of identity. In short, he thinks he is the second messiah, given the authority to reveal the esoteric meanings behind scientific knowledge that reveal the bible to be scientifically accurate. For this reason he thinks it is okay to manipulate the data in order to make it "fit" Genesis. If it weren't against forum rules I would also tell you that he is a habitual liar.

Most of the "evidence" he points to are a combination of contextomy and outright forgeries having nothing to do with the work of the people he attributes it to. ("The 7 spiritual Freudian archetypes", for example, which appears nowhere in the body of Freud's work.)

The "bacteria are plants" is just another manifestation of him trying to make the bible literally true.

verysincere · Apr 8, 2012

Zaius137 said:
A question I have always wanted to ask of an evolutionist.

What is the molecular mechanism for evolution?

Chemical bonds.

.

Jazer · Apr 8, 2012

CabVet said:
God "speaks" to people differently.

If you read your Bible you would see that God confused the languages so that people can not communicate with each other. For what it's worth I believe the atonement is two fold. Jesus died to reconcile us with the Father. HE also died to reconcile us with each other. We use to have a saying in Church that God will give to us what He can get through us to others.

Naraoia · Apr 8, 2012

Zaius137 said:
Then what is your comment on the following?

It's way cool?

Huram Abi said:
No. He just wants others to believe this.

He claims that "the plant kingdom DID establish itself before the animal kingdom" and says that this is science that supports the genesis account.

Because it has been demonstrated that animals came before plants, he now has pulled bacteria into the conversation so that he can still say that plants came before animals and that science supports Genesis.

Funnily, if he actually knew anything about the history of life on earth, he could legitimately say that plants came before animals by pointing to red algae, which are known from over a billion years ago and are included in Plantae sensu lato. (Still not land plants, let alone flowering plants, but at least phylogenetically close...)

Instead, he goes for bacteria, which aren't even remotely related to plants except through chloroplasts.

Most of the "evidence" he points to are a combination of contextomy and outright forgeries having nothing to do with the work of the people he attributes it to.

Contextomy is my new favourite word.

JustMeSee · Apr 8, 2012

thompsonb24 said:
Hi,

Welcome to CF!

bjt2024 · Apr 8, 2012

JustMeSee said:
Welcome to CF!

Hello Thank you!

JustMeSee · Apr 8, 2012

thompsonb24 said:
Hello Thank you!

You are welcome. This end of CF can get rather interesting. I wish you much patience.

Huram Abi · Apr 8, 2012

Naraoia said:
It's way cool?

Funnily, if he actually knew anything about the history of life on earth, he could legitimately say that plants came before animals by pointing to red algae, which are known from over a billion years ago and are included in Plantae sensu lato. (Still not land plants, let alone flowering plants, but at least phylogenetically close...)

Well, his only determining factor for what is a plant is if they have cell walls. The first cells, of course, weren't that complex and were a simple fatty, permeable lipid chain.

Using his own ill-informed understanding of taxonomy is his "2 Kingdom System" to follow it to its logical conclusion, it still can be said that "animals" (those organisms without cell walls) still came before "plants"(organisms with cell walls).

Huram Abi · Apr 8, 2012

And contextomy, I agree, is a good word.

Zaius137 · Apr 8, 2012

thompsonb24 said:
I do continue to persist however that evolution is the process by which, organisms more suited to survival in their environment are more likely to survive and therefore reproduce and pass on their desirable characteristics.

I do not disagree with organisms adapting to there environment. Concentrations of alleles in certain individuals (genetic drift) can improve an organisms chance of survival. But genetic drift will not add new innovative features to an organism such as legs from fins. Such a change must involve specific changes to the expression of DNA as my quoted article suggests. What is that mechanism?

I was not aware of this mechanism, but after reading the evidence I believe that it is less involved in the survival of an organism than the pre-determined genetics such as height, ability to hear, resistance to extreme cold for example.

Such changes by this mechanism are either deleterious or add specific benefit and if specific irreducible systems are involved (say metabolic pathways that synthesize complex chemicals or proteins) they will probably be deleterious unless many beneficial alterations occur spontaneously.

If you are talking about predetermined genetics changing there must be a molecular mechanism driving that change.

Zaius137 · Apr 9, 2012

thompsonb24 said:
Scientists present facts, data and evidence in charts and graphs which allow clear representation and easier interpretation. A genetic tree allows a person to understand where a clear divergence in speciation occured. Scientists aren't about convincing anyone, we're not a "church" or a "political party". We are about finding out the truth about why things happen. About explaining, the unexplained.

I have another question I would like to ask I dont mean to blitz you with too many questions so please take your time. You seem to be familiar with the Homo pan divergence.

There is one thing you can specifically answer that other participants on this forum have failed to. It relates to the homo pan divergence time given by:

Filling in the equation with current values I get.

t= number of generations since divergence (Generation =20 years)
k= percentage of sequence divergence Estimated at 4%
Ne= effective size of population ~9.6*10^4
(u)=mutation rate 2.3 × 10-8 per base pairs (130 mutation per generation)

From http://www.genetics.org/content/156/1/297.full

t= .5(k/u-4Ne)

t~678k (13.5 million years)

The problem is specifically a divergence around 5 million years is universally claimed by evolution but the most optimistic number I get is 13.5 million years. What is the problem?

Zaius137 · Apr 9, 2012

thompsonb24 said:
What exactly is dominant life? I would say that Mycobacterium tuberculosis is pretty dominant over humans as it can eliminate humans with ease. I believe that bacteria are far superior to other forms of life, they sustain all life. New species of bacteria are constantly evolving in order to survive to changing conditions.

I highlighted the statement in red which interests me the most which new species are you talking about? I might venture a guessBut.

sfs · Apr 9, 2012

Zaius137 said:
There is one thing you can specifically answer that other participants on this forum have failed to. It relates to the homo pan divergence time given by:

Filling in the equation with current values I get.

t= number of generations since divergence (Generation =20 years)
k= percentage of sequence divergence Estimated at 4%
Ne= effective size of population ~9.6*10^4
(u)=mutation rate 2.3 × 10-8 per base pairs (130 mutation per generation)

From Estimate of the Mutation Rate per Nucleotide in Humans

t= .5(k/u-4Ne)

t~678k (13.5 million years)

The problem is specifically a divergence around 5 million years is universally claimed by evolution but the most optimistic number I get is 13.5 million years. What is the problem?

The problem is simple: the human/chimpanzee divergence isn't 4%. The divergence that matters here is the number of mutational events that separate the two species. Using just single-base substitutions (which corresponds to the mutation rate you're using from the cited Genetics paper), the divergence is 1.23%. If you want to include insertions and deletions (which is a bad idea because they're poorly measured), increase the estimated mutation rate (from that paper) by 10% and the divergence by 14% (from the chimpanzee genome paper).

(Note: the mutation rate you're using is roughly a factor of two higher than current estimates.)

Zaius137 · Apr 9, 2012

sfs said:
The problem is simple: the human/chimpanzee divergence isn't 4%. The divergence that matters here is the number of mutational events that separate the two species. Using just single-base substitutions (which corresponds to the mutation rate you're using from the cited Genetics paper), the divergence is 1.23%. If you want to include insertions and deletions (which is a bad idea because they're poorly measured), increase the estimated mutation rate (from that paper) by 10% and the divergence by 14% (from the chimpanzee genome paper).

(Note: the mutation rate you're using is roughly a factor of two higher than current estimates.)

I think you and I have been over this before. Your opinion about the differences in the chimp human genome are not current or up to date with general scientific evidence. As we discussed before the raw mutations still had to fix in both genomes (which took time). Your statements remind me of the original staments by evolutionists that claimed the 90% of the human genome was junk DNA; not anymore…

“As expected, only 1 percent of the coding that was common to both the human and the chimp genomes was different, due to single-pair substitutions in the code. Researchers found that an additional 1.5 percent of the human DNA coding was not found in chimps, and 1.5 percent of the chimp coding was missing in humans — bringing the total difference between the two genomes to 4 percent.(my highlight)”

Chimp genetic code opens human frontiers - Technology & science - Science - msnbc.com

In our previous go around I showed…

“Now the evolutionists are further compromised by ignoring the fact that only 2.4Gb of the human 3.1Gb aligned at all. 2.4/3.1 ~ 77%. Sorry but this 23% of the genome can not be ignored. Try ignoring 23% of the book “Huckleberry Finn” and see if you get the same reading.”

Now have they sequenced those last .7Gb?

Here is another conformation of noted differences:

A genome-wide comparison of recent chimpanzee and human segmental duplications : Article : Nature

There is even greater estimates of divergence….

“If we focus on the human/chimp comparison, it turns out that the human genome contains 1,418 genes that do not have orthologs in the chimpanzee genome. What this means is that if we look at the identical sections of human and chimp chromosomes one of them will have a gene that the other one does not have at that position. It turns out that the human genome has 689 genes not present in the chimp and the chimp has 729 genes not present in humans. If there are 22,000 genes in the genome, then this total of 1,418 differences represents 6.4% of the genes.”

Sandwalk: Mammalian Gene Families: Humans and Chimps Differ by 6%

Yes lets include a more realistic evaluation of the chimp human genome.

sfs · Apr 9, 2012

Zaius137 said:
I think you and I have been over this before.

I know. Do you ever intend to learn anything about this subject, or are you going to continue wasting everyone's time by repeating the same mistakes over and over?

Your opinion about the differences in the chimp human genome are not current or up to date with general scientific evidence.

Your arrogance is notable but misplaced.

As we discussed before the raw mutations still had to fix in both genomes (which took time).

Nothing had to fix. The formula you quoted is for the difference between one copy of the chimpanzee genome and one copy of the human genome. Some of the differences between them will be fixed and some won't. In any case, what does this have to do with the fact that you're using the wrong number for the human/chimpanzee divergence?

As expected, only 1 percent of the coding that was common to both the human and the chimp genomes was different, due to single-pair substitutions in the code. Researchers found that an additional 1.5 percent of the human DNA coding was not found in chimps, and 1.5 percent of the chimp coding was missing in humans bringing the total difference between the two genomes to 4 percent.(my highlight)

Since I was an author of that paper, this is not exactly news to me. The mutation rate you cited was the rate at which mutations occur. To apply it to human/chimpanzee divergence, you have to count the number of differences between them, that is, the number of mutations that have occurred. What you don't do is count the number of bases that differ between them, since some mutations add or subtract thousands or millions of bases. So the 4 percent has nothing at all to do with the mutation rate you quoted. This is really not a complicated idea.

The mutation rate for insertions and deletions -- which contributed the bulk of that 4% difference -- was estimated in the chimp genome paper to be one-seventh the single base substitution rate, and in the other paper you cited to be 10% of the single base rate. Those are the numbers you should be using.

In our previous go around I showed

Now the evolutionists are further compromised by ignoring the fact that only 2.4Gb of the human 3.1Gb aligned at all. 2.4/3.1 ~ 77%. Sorry but this 23% of the genome can not be ignored. Try ignoring 23% of the book Huckleberry Finn and see if you get the same reading.

I went to great lengths to explain why this argument was utterly mistaken. Go back and read that thread again. (Also note that this argument contradicts the 4% you were claiming in the last post. Not that it matters, since this argument is just dumb.)

Here is another conformation of noted differences:

A genome-wide comparison of recent chimpanzee and human segmental duplications : Article : Nature

There is even greater estimates of divergence.

If we focus on the human/chimp comparison, it turns out that the human genome contains 1,418 genes that do not have orthologs in the chimpanzee genome. What this means is that if we look at the identical sections of human and chimp chromosomes one of them will have a gene that the other one does not have at that position. It turns out that the human genome has 689 genes not present in the chimp and the chimp has 729 genes not present in humans. If there are 22,000 genes in the genome, then this total of 1,418 differences represents 6.4% of the genes.

Sandwalk: Mammalian Gene Families: Humans and Chimps Differ by 6%

Yes lets include a more realistic evaluation of the chimp human genome.

You seem to be under the impression that these findings somehow contradict the divergence estimates I cited. They don't. They're more detailed studies of some of the five million insertions and deletions that distinguish humans and chimpanzees genetically. You should still be using either 1.23% or 1.4% (the latter if your mutation rate includes insertions and deletions, the former otherwise).

verysincere · Apr 9, 2012

sfs said:
I know. Do you ever intend to learn anything about this subject, or are you going to continue wasting everyone's time by repeating the same mistakes over and over?

I don't claim the gift of prophesy but I think I can predict this one.

sfs said:
Your arrogance is notable but misplaced.

If the Dunning-Kruger Foundation starts funding endowed chairs, I know of a stellar candidate. (Perhaps for a folding chair?)

.

bibleblevr · Apr 9, 2012

Please explain the process in which new information is added to the genome via mutations and how they can remain and be passed down despite the dna's redundancies that try to prevent the proliferation of theses mutations. How often do the mutations get passed down and how often are these mutations helpful?

This is an area of evolution that I am not educated on as I am sure you can tell from the questions.

I would love some good links if you know of any to read more on the subject

Thanks

sfs · Apr 9, 2012

bibleblevr said:
Please explain the process in which new information is added to the genome via mutations and how they can remain and be passed down despite the dna's redundancies that try to prevent the proliferation of theses mutations. How often do the mutations get passed down and how often are these mutations helpful?

This is an area of evolution that I am not educated on as I am sure you can tell from the questions.

I would love some good links if you know of any to read more on the subject

Lots and lots of mutations get through DNA replication and its error-checking, or occur by other mechanisms where there can be no error-checking. Very roughly, 50 new mutations per person. Once those mutations are in your offspring, they're free to spread or not, based on chance and natural selection. What fraction of those add information to the genome depends on how you define information. If you use a simple and straightforward definition of information, such that there are two bits of information for every base in the genome, then a significant fraction, perhaps 5%, of mutations add information, by adding bases to the genome.

For a look at the kind of functional information that can be added, you can look here.

Zaius137 · Apr 9, 2012

sfs said:
Since I was an author of that paper, this is not exactly news to

sfs said:
me.

I must apologize Mr. Boyle I did not read in the parenthesis behind your name…

By Alan Boyle(alias sfs) Science editor
msnbc.com

The mutation rate you cited was the rate at which mutations occur. To apply it to human/chimpanzee divergence, you have to count the number of differences between them, that is, the number of mutations that have occurred.

I used the same priori number that the divergence calculation implied except my calculation worked backward from the empirical findings of the human genome as a mutation rate. Again you need a math course and a better understanding of my principle calculation.

From http://www.genetics.org/content/156/1/297.full

What you don't do is count the number of bases that differ between them, since some mutations add or subtract thousands or millions of bases. So the 4 percent has nothing at all to do with the mutation rate you quoted. This is really not a complicated idea.

You still got the numbers mixed up my mutation rate is from actual empirical findings (u rate). The actual sequence divergence is the (k rate) Estimated at 4%. You are backwards on this. Again I must teach you the math…

The mutation rate for insertions and deletions -- which contributed the bulk of that 4% difference (this again is not mutation rate (u)) -- was estimated in the chimp genome paper to be one-seventh the single base substitution rate, and in the other paper you cited to be 10% of the single base rate. Those are the numbers you should be using.

I am having real problems with your understanding of such things. First you say “Yes there is a 4% difference in the genome”, then you say “no there isn’t a 4% difference in the genome”. The evolutionist must draw finer and finer obscuration around the simple reasoning, finer divisions and finer definitions like 24 separate definitions of a species.

By the way did you also write the paper on the 6% variation in genomes between chimps and humans? I see at least four primary authors cited. Please do not claim that…

Zaius137 · Apr 9, 2012

sfs said:
Lots and lots of mutations get through DNA replication and its error-checking, or occur by other mechanisms where there can be no error-checking. Very roughly, 50 new mutations per person. Once those mutations are in your offspring, they're free to spread or not, based on chance and natural selection. What fraction of those add information to the genome depends on how you define information. If you use a simple and straightforward definition of information, such that there are two bits of information for every base in the genome, then a significant fraction, perhaps 5%, of mutations add information, by adding bases to the genome.

For a look at the kind of functional information that can be added, you can look here.

Actually the newer number is about 130 new mutations per individual an that includes the non protein coding segments stay up on the new findings please.

No No No no new information has ever been observed to be added spontaneously by point mutations that is a fact. Many if not all of these point mutations turn out to be deleterious increasing the genome loading and the calculated (U) value.

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