[asking]

Why are there not spontaneously "evolved" native chihuahuas or poodles or pomeranians or any other breed that can be traced back to wolves WITHOUT
direct human knowledge and manipulation?

InTheBox: That's the whole point; there are! There are more than one million named species of organisms living on Earth today, which evolved from a common ancestor over 3.8 billion years. That is, they can be traced back to common ancestors because they are all related to one another. Biologists think there may be many more species alive today--perhaps 10 million or even 30 million. These millions of species--which evolved without the intervention of intelligent beings, human or otherwise--represent just 1% of all the species that have ever lived on Earth. The other 99% went extinct during the billions of years since life first arose on Earth. Many of them left fossils, but obviously not all.

From among all those millions of species, there are all KINDS of different dog-like animals, some still living, some extinct. Here -- at the website below -- are a tiny fraction of the members of the dog family, dogs that ALL "evolved without direct human knowledge and manipulation." Of course, they aren't dogs! But they are related to dogs; they are jackals, coyotes, foxes, wolves, wild dogs, raccoon dogs, bat-eared foxes, and a fennec. Take a look! They are beautiful.

ADW: Canidae: Pictures

Each of these species includes a huge amount of genetic diversity, so that if you started selecting for long legs (or short legs), short snouts (or long ones), you could very soon have a whole lot of "pomeranian fennecs" or "great dane fennecs," and so on. Almost anything you want. There's very little difference between natural selection and artificial selection. The only difference is that in one case, the environment selects the dogs that are best suited to that particular environment, and they end up having the most puppies, while in the other case, human breeders decide which dogs get to have the most puppies.

Same story with plants. For example, Europeans farmers took a single species of "mustard" plant and made cabbage, broccoli, Brussels sprouts, cauliflower, and of course mustard. All from one species. If there's that much variation in one species, think how much there is in a whole family of animal species such as the "canids," or dogs. It's the miracle of life.
Cheers,
Asking

[asking]

Lots of good stuff in JEM's post..

First, how to make more genes:

[QUOTE=jem02081]You want answers?
1. Gene duplication.
2. Gene transfer.

And chromosome duplication, too.

It been a long time since someone thought that “higher organisms” should have more chromosomes. It used to be mentioned in the first chapter of genetics textbooks, but I haven’t looked in a while.

I just looked in a college genetics textbook and don't see it. Still, I just read an article in Science or similar in the last couple of months that commented once more on the amazing fact that "simpler" organisms sometimes have more DNA than more complex ones... Yawn.

An interesting question (with a convincing answer) is why all of the great apes have 48 chromosomes and humans have only 46

.

Um, so, JEM, what is the answer? I'm on the edge of my seat... :)
Why do the other great apes have an extra pair of chromosomes? I hadn't realized we'd mislaid a pair, like losing a pair of socks at the laundromat?

“genes are the key to life.” is an interesting phase. There are whole schools of the thought in evolutionary biology which start from that point. Ever hear of the term “selfish gene”.

To me, “genes are the key to life” is 99% rhetoric. What isn't the key to life? DNA? Cell membranes? Ribosomes? Evolution itself? Water? Every master switch is a weak link. I'm not saying genes aren't important, but much else is too. And there's the sticky question of defining what exactly a gene is.

Asking

[asking]

An interesting question (with a convincing answer) is why all of the great apes have 48 chromosomes and humans have only 46.

And the answer is that one of our chromosomes is actually two chromosomes fused together (and of course they come in pairs, hence 46 instead of 48).

YouTube - Ken Miller on Human Evolution

[red_cartoon]

chances are zero if the world is ten thousand years old & most people who have studied this think the chance is almost a certainity if the earth is billions of year old.

Well said.

[red_cartoon]

... Europeans farmers took a single species of "mustard" plant and made cabbage, broccoli, Brussels sprouts, cauliflower, and of course mustard. All from one species.

Wow, I did not know that. Can you please suggest some links on this topic, I would really like to do some reading on it. Thanks in advance :)

[inthebox]

You want answers?
Let’s start at the top.

There are many ways with many books written about each of then. Le’s start with two methods that came to my mind.
1. Gene duplication. There are numerous examples in the human genome. Here are a couple of which you might be familiar with. Look up why people are red green colorblind or what causes (alpha or beta) thalassemia. Of course, this isn’t restricted to humans.
2. Gene transfer. Have you heard of MRSA? This is an example of horizontal gene transfer of antibiotic resistance genes. This also happens outside of the human influenced biosphere, but human are less interested in reading about that. Influenza H5N1? This is an example of the genetic recombination of genes between different types of viruses. I can give you human examples as well (endogenous retroviuses).


This question has been asked & answered and the answers aren’t controversial. But you need to be a bit of a science historian to remember when this question was first asked and answered. It been a long time since someone thought that “higher organisms” should have more chromosomes. It used to be mentioned in the first chapter of genetics textbooks, but I haven’t looked in a while.

An interesting question (with a convincing answer) is why all of the great apes have 48 chromosomes and humans have only 46.

“genes are the key to life.” is an interesting phase. There are whole schools of the thought in evolutionary biology which start from that point. Ever hear of the term “selfish gene”.

chances are zero if the world is ten thousand years old & most people who have studied this think the chance is almost a certainity if the earth is billions of year old.

Any questions on these topics?

If don’t want your questions answered then why are you lurking here?

You have not explained anything, let alone providing links to explain what you assert.

and what you assert is factually wrong

Thalassemia - Wikipedia, the free encyclopedia
"Thalassemia produces a deficiency of α or β globin, unlike sickle-cell disease which produces a specific mutant form of β globin.

β globin chains are encoded by a single gene on chromosome 11; α globin chains are encoded by two closely linked genes on chromosome 16. Thus in a normal person with two copies of each chromosome, there are two loci encoding the β chain, and four loci encoding the α chain.[2]



DELETION of one of the α loci has a high prevalence in people of African-American or Asian descent, making them more likely to develop α thalassemias. β thalassemias are common in African-Americans, but also in Greeks and Italians"

deletion not duplication.
Also note that most gene mutations are actually deleterious to survival
- down's, sickle cell, cystic fibrosis etc...


Show me a link a explaining how dna came about via evolution.

This is my main assertion of my posts.

I agree that dna, molecular biology, modern techniques are facts, I was once a lab tech working on frog mitochodria of all things.

Francis Crick of Dna double helix fame could not explain the origin of dna - he even thought of panspermia - look it up.

You have to remember that when Darwin came out with his theory he did not have the technology to know that a single cell was so complex - having its own organelles etc.

He did not know of DNA or RNA - each scientific discovery makes evolution less and less likely.

Look at stem cells from skin cells. Scientists directly manipulated cells and still there are draw backs - like potential cancer causing genes in these transformed cells.

This is a directed process - not random chance.

Think again - how did this come about?

Computer programs - less complex than fruitfly genome - did they come about randomly?

[asking]

wow, I did not know that. Can you please suggest some links on this topic, I would really like to do some reading on it. Thanks in advance :)

Here's one.
Evolution 101: Evolutionary Change

And you are welcome! I didn't even mention kohlrabi, either. In each case, they selected for a different thing--big flower buds (broccoli), huge stems kohlrabi, huge leaves (kale), and so on.
Asking

[asking]

Show me a link a explaining how dna came about via evolution.

This is my main assertation of my posts.

I agree that dna, molecular biology, modern techniques are facts, I was once a lab tech working on frog mitochodria of all things.

Francis Crick of Dna double helix fame could not explain the origin of dna - he even thought of panspermia - look it up.

I have to go to an appt, so I write in haste.
It seems to me you were asking about NEW DNA in earlier posts, that is, how organisms increase the amount of DNA they have or make new genes. Those questions were answered clearly by JEM. (although you'd have to do some reading elsewhere to get all the details).

NOW you are asking about the origin of life, which is an entirely different question than whether evolution explains the origin of species. Given a single cell 4 billion years ago, evolution by means of natural selection (and other ancillary mechanisms) explains how we have millions of species, from green algae to redwood trees, one-celled organisms and mushrooms, whales, fennecs (see left!), and human beings.

If you want to discuss the origin of that cell, you get into deeper waters and you are correct, there is less certainty about the origin of the first DNA or RNA-loaded cell. But that's not to say there's no explanation for the cell, just that--unlike evolution--it is more speculative. But if you start with a cell, evolution explains the origin of new species of organisms, and that's what most people mean by evolution.

The origin of living cells is certainly not what the original question was about ("is it true that humans are descendants of apes").
Asking

[asking]

Another source of new genes

Another source of new genes, it turns out, are viruses that insert themselves into the DNA of sperm or eggs. At conception, the viral genes in the sperm or egg becomes part of the DNA of a new human being and the virus is passed on to the next generation.

About 8 percent of our DNA is composed of fragments of viral DNA, some of which is inserted itself into our DNA millions of years ago. Like fossil diseases, they are remnants of infections that afflicted our ancestors.
Asking

[jem02081]

You have not explained anything, let alone providing links to explain what you assert.

and what you assert is factually wrong

Thalassemia - Wikipedia, the free encyclopedia
"Thalassemia produces a deficiency of α or β globin, unlike sickle-cell disease which produces a specific mutant form of β globin.

β globin chains are encoded by a single gene on chromosome 11; α globin chains are encoded by two closely linked genes on chromosome 16. Thus in a normal person with two copies of each chromosome, there are two loci encoding the β chain, and four loci encoding the α chain.[2]

DELETION of one of the α loci has a high prevalence in people of African-American or Asian descent, making them more likely to develop α thalassemias. β thalassemias are common in African-Americans, but also in Greeks and Italians"

deletion not duplication.
Also note that most gene mutations are actually deleterious to survival
- down's, sickle cell, cystic fibrosis etc...

Dear inthebox,
Sorry for the slow response but the Patriot’s game was more important ;)

I was wrong on 2 counts. First, I thought that both alpha & beta thalassemias were due to the same spectrum of mutations and I should have focused on alpha thalassemia where one of the main types of mutations is a gene deletion. Second, I didn’t provide you with enough information to understand what I meant.

Your right that a deletion isn’t a duplication, but deletions are linked to amplifications. The most common mechanism for a deletion is what is called “unequal crossing over” (see definition at ghr.nlm.nih.gov/ghr/glossary/unequalcrossingover or unequal crossing-over - Encyclopedia.com) You can find a detailed review in a PNAS article titled” Processes of copy-number change in human DNA: The dynamics of alpha-globin gene deletion” Inaugural Article: Processes of copy-number change in human DNA: The dynamics of {alpha}-globin gene deletion -- Lam and Jeffreys 103 (24): 8921 -- Proceedings of the National Academy of Sciences

The loss of 1 alpha gene has occurred several times in modern humans, but this is a rare event so the number of affected individuals is quite small.
And as you point out “most gene mutations are actually deleterious”, however the operative word is “most”. Both thalassemia & sickle cell anemia occur in areas where malaria is endemic. Both are recessive traits which are quite harmful to those who are homozygous for the mutant form of the genes. However the carriers of the trait (heterozygous) are protected from malaria. (see the PNAS paper or Synthetic Theory of Evolution: Natural Selection or most any other genetics website)

This explanation predicts that chromosomes missing an alpha globin gene (deletion) will be under positive selection (That’s Darwin’s “natural selection”) in areas where malaria existed. This will match what you wrote “thalassemias are common in African-Americans, but also in Greeks and Italians"
This explanation also predicts that the chromosome containing 3 alpha genes (duplication) will remain rare since it isn’t under positive selection.

The other example I gave earlier (red-green colorblindness also has a similar spectrum of deletion... amplification in the human population)

Show me a link a explaining how dna came about via evolution.

Are you asking about the origins of life? Start with Wikipedia.

I actually prefer the RNA world hypothesis (also in Wikipedia) but it is far from certain.

[kp2171]

I'm not taking a stand here cause I'm too damn tired to fight it out... but PLEASE don't count chromosomes and use the numbers to explain complexity.

If you think the human genome project was the end of the mapping process you are clueless. Introns, exons, and coding "oh my"!.

The next generation of mapping will involve understanding how the regulation of genes is encoded... those who simply count genes don't have a clue about the real complexity of the human genome.

[inthebox]

Another source of new genes

Another source of new genes, it turns out, are viruses that insert themselves into the DNA of sperm or eggs. At conception, the viral genes in the sperm or egg becomes part of the DNA of a new human being and the virus is passed on to the next generation.

About 8 percent of our DNA is composed of fragments of viral DNA, some of which is inserted itself into our DNA millions of years ago. Like fossil diseases, they are remnants of infections that afflicted our ancestors.
Asking

Link?
Which virus[es]?

So in theory, our generation, on average, should have more genes or at least more dna base pairs, than the average human say 10 generations ago?


...



Perhaps I found your source..

Annals of Science: Darwin's Surprise: Reporting & Essays: The New Yorker

The New Yorker - hardly a name peer reviewed scientific journal - I know..

Here are some interesting excerpts:

Page 1 fourrth paragraph:

"Like dinosaur bones, these viral fragments are fossils. Instead of having been buried in sand, they reside within each of us, carrying a record that goes back millions of years. Because they no longer seem to serve a purpose or cause harm, these remnants have often been referred to as “JUNK DNA.” Many still manage to generate proteins, but
scientists have never found one that functions properly in humans or that could make us sick."


Page 5 third pargraph

"They focussed on chimpanzees, our closest relatives. Chimpanzees are easily infected by the AIDS virus, but it never makes them sick. That has remained one of the most frustrating mysteries of the epidemic. How did nearly identical genetic relatives become immune to a virus that attacks us with such vigor? The most dramatic difference between the chimp genome and ours is that chimps have roughly a hundred and thirty copies of a virus called Pan troglodytes endogenous retrovirus, which scientists refer to by the acronym PtERV (pronounced “pea-terv”). Gorillas have eighty copies. Humans have none."

Theoretically are not humans suppose to be closest to chimps an gorillas are off on a different branch?



Contrast scientific results with gene therapy

Gene Therapy

"The Food and Drug Administration (FDA) has not yet approved any human gene therapy product for sale. Current gene therapy is experimental and has not proven very successful in clinical trials"



There are instances of viruses that can cause cancer.

Burkitt lymphoma and Burkitt-like lymphoma : Cancerbackup
"The Epstein-Barr virus is able to survive and 'transforms' the normal B-lymphocytes into cancerous cells."


Human T-lymphotropic virus - Wikipedia, the free encyclopedia


So it appears that viral genetic additions are actually useless or cause harm [ in humans at least ] - hardly a good thing for a species.

[KBC]

So basically, someone out there can show how humans crossed the land bridge from ASIA to NORTH AMERICA some 15,000 years ago, as hunters and eventually settlers, and we are still on the concept of when(or how) man was developed VS the written theological word?

Seems like undeniable proof to me folks, but what do I know?

KEN

[inthebox]

I'm just pointing out the questions that evolution can't answer.

I'm just pointing out the inconsistencies in evolution.

[charlotte234s]

Honestly, I feel there's more inconsistencies in creationism than in evolution, and evolution is presented by scientists, creation is taught by people who know nothing about science and the human genetics, dna, the like, however, I am a Christian so I believe that perhaps God made us and also made evolution to help us get better over time.

[asking]

IntheBox, are you saying that because Gene Therapy is a bust, that proves that viruses are bad, which proves that evolution is inconsistent? I want to make sure I understand your point. (This is a bit ironic for me, because I've been arguing that Gene Therapy is not going to work ever since they started hyping it in the early 80s.) But if that's what you mean, I'll try to address that.

And yes I admit my secret vice: I was reading the New Yorker last night. Michael Specter makes lots of errors when writing about evolution, which bothers me. Especially when he gets above the level of the cell. But the substance of what he says in this article is coming from the researchers and makes sense. Has been published elsewhere in journals. If you can read the original articles and show that Specter is SUBSTANTIVELY wrong, I'll listen. I think he makes too many big claims, but I didn't mention those. Like, he said that endogenous retroviruses are the best evidence yet for human evolution. I think it's great evidence, but there is lots of excellent evidence out there. I hate it when writers try to make their bit of science, their researcher, seem more important than it is, just for the sake of hyping one article.
Asking

[asking]

So in theory, our generation, on average, should have more genes or at least more dna base pairs, than the average human say 10 generations ago?

No. I don't think that's the prediction. We can get new genes, we can lose genes. I don't know that anyone is making claims about a constant net gain of DNA, especially over time spans as short as 10 generations. For example, birds have LESS DNA than their ancestors. They have lost DNA for some reason.

The question was how can evolutionary theory account for the accumulation of new genes or new DNA. This allows us to have new sequences, new traits, new material for natural selection to work on.

Some answers:
Gene Duplication
Gene Transfer
Chromosome duplication
Endogenous retroviruses

[inthebox]

im not taking a stand here cause im too damn tired to fight it out... but PLEASE dont count chromosomes and use the numbers to explain complexity.

if you think the human genome project was the end of the mapping process you are clueless. introns, exons, and coding "oh my"!....

the next generation of mapping will involve understanding how the regulation of genes is encoded... those who simply count genes dont have a clue about the real complexity of the human genome.

Exactly the point.


As science discovers more and more about genetics and molecular biology the complexity increases, and

It becomes harder and harder to fit all this with the theory of evolution.


Now it is up to the individual to draw their own conclusions about this.

[asking]

As science discovers more and more about genetics and molecular biology the complexity increases, and

It becomes harder and harder to fit all this with the theory of evolution.

Now it is up to the individual to draw their own conclusions about this.

Hi Inthebox,
I'm fine with people drawing their own conclusions if they have access to relevant information (or really even if not, because they will anyway! :) ).

But why do you think molecular biology is "hard to fit" with evolution? My point actually was that everything discussed in this thread DOES fit with the theory of evolution. Every new fact --whether it's from molecular biology or ecology--that is consistent with what's already known and understood about how evolution works further supports evolution.

Because of the way science works, you can disprove things, but you can never prove something is true. So you can't prove that gravity exists everywhere and for all time. (But most reasonable scientists accept that it's a general law of natural science because everything is consistent with it's being a general truth.) For the same reason, you can't outright prove evolution. But as hundreds of years go by and NO discovery DISproves it and virtually all of biological science supports it, it is hard to understand why a person would hold out hope for a single discovery that would finally come along and prove it wrong. Duplication, Gene Transfer, Chromosome duplication,and Endogenous retroviruses are all consistent with the theory of evolution. As far as I know, they fail to disprove evolution.

For example, in the case of endogenous (built-in) viruses: if our ancestors were infected with viruses with a unique sequence of DNA (like a unique bar code) millions of years ago and if other apes carry the same viral bar code, then it's logical to conclude that we and they are descended from the same ancestor, the one infected by the virus. It's pretty straightforward. Where's the inexplicable complexity?

Analogously, if the package of Cheetos I bought at Safeway taste the same, look the same, and have the same packaging as the Cheetos I bought at 7/11, then I'm going to conclude they are the same basic product. If later, I notice they have the same barcode, too, that's going to tend to convince me I'm right EVEN MORE. Endogenous retroviruses are like that barcode; they seal the deal on humans and apes being related. We already look alike, act alike,and so on. Now we discover that we share an invisible bar code. How cool is that?

Do you see it differently, IntheBox?
Asking

[excon]

Hello:

The problem with most lay people is that they don't understand the words "scientific theory". They think it means a proposition that hasn't been proven yet.

Nope. That's not what it means. Not even close. In fact, evolution has been proven time, and time again, just like gravity has...

excon