The Real Science Radio Caveman Show

[Stripe]

It would make sense for them to either all be the same or all be different. But we find neither

:dizzy:

So when you design a lot of different things, they have to either be all the same or all different. That's your argument?

Calling me names was more convincing. lain:

WHY are they so similar Stripe? Why are whales closer to cows than any other mammal in that listing of creatures?

You know the answer to this. :thumb:

Not a scientific argument.

Of course it's scientific to point to the truth!

You have specific ideas about HOW God created. Saying "God just did it that way" is a total cop out. You're then saying God made it look like evolution without actually creating through evolution.

Evolutionists love to assume the truth of that which they hold dear and use it for evidence.

You mean all of them? I'm asking for YOU to use YOUR definition. I can give you examples of species, and why they are defined as such all day. If "kind" is so simple and obvious, you should have no trouble giving us examples ad nauseum.

:yawn:

All you've done in this entire thread is assert, obfuscate and dodge. You're a total waste of time.

Feel free to not talk to me. :thumb:

 

[Alate_One]

So when you design a lot of different things, they have to either be all the same or all different. That's your argument?

It makes sense to do that, to have similarities between organisms that have nothing apparent in common, it makes little sense to make them similar, when it's clearly not necessary.

If you were designing an animal, from scratch, to live in water for its entire life, why would you build it so it could only breathe air?

It would be like (to use part of your "analogy") reverse engineering a car into a boat rather than designing a boat from scratch.

You know the answer to this.

I do. They share the most recent common ancestor compared to the other animals in the list. (Cows and whales)

But I was asking for YOUR explanation. You know when YOU actually say something substantive in your own defense rather than attacking the other person? (Does that ever happen?)

 

[voltaire]

Except that it doesn't explain the evidence. WHY are whales much more similar to hippos, cows and deer than rhinos, pigs or camels? What similarity do they have that would explain that data?

If they were all created at about the same time from totally separate common ancestors, we'd expect the level of similarity between say the "cow kind" to be similar to that of the "deer kind" and that of the "camel kind" but they're not. Instead there's a pattern and anyone that can count DNA differences can find it.

I agree that whales came from a hippo like ancestor but that is because of mitochondrial DNA evidence. Hippos and Whales should share more proteins in common that Hippos and Camels. Is that true or is our knowledge base of proteins less than that of DNA?

 

[Stripe]

If you were designing an animal, from scratch, to live in water for its entire life, why would you build it so it could only breathe air?

What's wrong with breathing air? :idunno:

I do. They share the most recent common ancestor compared to the other animals in the list. (Cows and whales)

Even creationism is evolution to an evolutionist.

 

[The Barbarian]

I agree that whales came from a hippo like ancestor but that is because of mitochondrial DNA evidence. Hippos and Whales should share more proteins in common that Hippos and Camels. Is that true or is our knowledge base of proteins less than that of DNA?

Cytochrome C does that, and then there's this:

Evidence from milk casein genes that cetaceans are close relatives of hippopotamid artiodactyls.
http://mbe.oxfordjournals.org/content/13/7/954.short

And a summary here:
Hippos were determined to be the closest relative of whales, ruminants were related to a whale/hippo clade, and pigs were more distant. In addition to producing the controversial whale/hippo clade, these analyses debunked the idea that hippos and pigs are closely related. This had been a popular taxonomic hypothesis (Suiformes) based on similarities in morphological (physical) characteristics.

In addition to DNA and protein sequences, researchers tracked the movement of transposons called SINEs in the genome (see the method at retrotransposon marker). A transposon is a DNA sequence that will occasionally make a copy of itself and insert that copy into another part of the genome. It is considered highly unlikely that SINEs will insert themselves into exactly the same part of a genome by chance. The data indicate that several transposons inserted themselves at the same point in the genomes of whales, ruminants and hippos (sometimes referred to as "pseudoruminants" because although they have four-chambered stomachs like true ruminants, they do not chew the cud). This insertion point is not shared with camels and pigs.

This hypothesis has been tested with DNA sequences from a host of genes: the complete mitochondrial genome (as well as several of its genes independently), beta-casein, kappa-casein, von Willebrand factor, breast cancer 1, recombination activating genes 1 and 2, cannabinoid receptor 1, and several others. These sequence data and the transposons converge on the same conclusion that hippos and whales are more closely related to one another than either is to other artiodactyls.

Sequences analyzed in combined analyses with morphological characters have also produced the same results as sequences alone. Some have argued that the sheer number of characters (one for each nucleotide) in sequences swamps out the effects of morphology. There have been a few morphology-based studies that have suggested (weakly) the same results as the molecular results, but overall most morphological studies have conflicted with the whale/hippo hypothesis of Cetartiodactyla.

An important exception is a recent study conducted by Boisserie et al. (2005). They examined 80 hard morphological characters of fossil and extant cetartiodactylan taxa. Their results suggest that hippopotamids evolved from within a clade of anthracotheres. That anthracothere/hippopotamid clade appears to be sister to the Cetacea and supports the molecular results.
http://en.wikipedia.org/wiki/Cetartiodactyla

Your hypothesis is correct.

 

[voltaire]

I agree that whales came from a hippo like ancestor but that is because of mitochondrial DNA evidence. Hippos and Whales should share more proteins in common that Hippos and Camels. Is that true or is our knowledge base of proteins less than that of DNA?

Alate. Could you please answer this? It wasn't addressed to barbarian. I didn't say a thing about Cytochrome C. That is one protein (singular). I was asking about a plurality of proteins in common.

 

[Flipper]

Alate. Could you please answer this? It wasn't addressed to barbarian. I didn't say a thing about Cytochrome C. That is one protein (singular). I was asking about a plurality of proteins in common.

The casein genes are the obvious ones (there were three in the complex mentioned in that first paper); out of interest, I looked up the the others and it seems like they all code for proteins of various kinds.

Stripe can wiggle and evade all he likes, but creationism provides no good explanation of why multiple DNA sequences would point to hippos being the closest relatives to whales (providing corroborating details to a prediction of paleontology), unless God had a longer-term plan to make creationists look bad.

 

[Stripe]

Stripe can wiggle and evade all he likes, but creationism provides no good explanation of why multiple DNA sequences would point to hippos being the closest relatives to whales (providing corroborating details to a prediction of paleontology), unless God had a longer-term plan to make creationists look bad.

Animals with physical similarities require proteins of similar functionality just as buildings of similar physical structure require similar tools in their construction.

It's an explanation you must insist as "not good" solely because of the consequences.

 

[voltaire]

The casein genes are the obvious ones (there were three in the complex mentioned in that first paper); out of interest, I looked up the the others and it seems like they all code for proteins of various kinds.

Stripe can wiggle and evade all he likes, but creationism provides no good explanation of why multiple DNA sequences would point to hippos being the closest relatives to whales (providing corroborating details to a prediction of paleontology), unless God had a longer-term plan to make creationists look bad.

Again, I did not ask about genes. I asked for a plurality of proteins in common amongst various branches of the evolutionary tree. IOW, a snake and an alligator should have more proteins in common that a snake and a penguin. I am looking for the actual protein evidence that the statement is true. Talking about Cytochrome C or casein genes does nothing to answer the question. Still waiting for AlateOne.

 

[Flipper]

Animals with physical similarities require proteins of similar functionality just as buildings of similar physical structure require similar tools in their construction.

It's an explanation you must insist as "not good" solely because of the consequences.

I see you didn't actually get around to looking at the evidence for common descent in this case by bothering to read that paper on cetacean caseins, hey? Can't say I'm surprised.

If you had, you would have learned that they also compared sequences with the Harbor Seal (which I think we can both agree has much more in common in regards to lifestyle and in terms of gross morphology with the cetaceans than with the hippo). Yet the sequences tell the same story - the Harbor Seal is a significantly more distant relative to the whale than is the hippo. It's a more distant relation than the giraffe, pig or camel.

 

[Alate_One]

What's wrong with breathing air? :idunno:

Um drowning? Would it make sense for cows to breathe water?

Even creationism is evolution to an evolutionist.

Way to miss the point yet again.

 

[Yorzhik]

Why, with the "orchard model" are there clear evolutionary links between the trees that should be separated if they were indeed separately created?

The only clear evolutionary links between trees are the ones that can be imagined by cherry picking similar traits. I'll agree this is evidence, but very weak evidence. And against it is what should be a study by scientists how a supposed common ancestor could have evolved, 1 or a few mutations at a time into both a cow and a whale. In other words, once you claim to identify closely related species you must eliminate any stepping stone problem.

This also includes not only counting raw differences on two closely related species, but what those differences are. In other words, simply declaring the number of differences is quantitative when your problem is a qualitative one.

 

[Alate_One]

Alate. Could you please answer this? It wasn't addressed to barbarian. I didn't say a thing about Cytochrome C. That is one protein (singular). I was asking about a plurality of proteins in common.

Again, I did not ask about genes. I asked for a plurality of proteins in common amongst various branches of the evolutionary tree. IOW, a snake and an alligator should have more proteins in common that a snake and a penguin. I am looking for the actual protein evidence that the statement is true. Talking about Cytochrome C or casein genes does nothing to answer the question. Still waiting for AlateOne.

Genes = proteins essentially. You can get more information out of genes because most amino acids have several synonymous codons.

Protein alignments are often used when comparing very distant organisms because the DNA sequences won't have much homology. (Hence Barbarian's cytC example)

The whole genome alignment I gave you in an earlier post is far better than a simple comparison of proteins. Because DNA does a lot more than just encode proteins. And it's often non- protein coding DNA that makes the difference between species.

For example, if we compared proteins only between say humans and chimps there would be essentially no difference at all.

 

[Alate_One]

The only clear evolutionary links between trees are the ones that can be imagined by cherry picking similar traits.

Oh really? How do you explain the whole genome sequence tree I just posted? How do you cherry pick a whole genome? :rotfl: Anything to support your preconceived notion eh? :rotfl:

This also includes not only counting raw differences on two closely related species, but what those differences are. In other words, simply declaring the number of differences is quantitative when your problem is a qualitative one.

We're learning a lot about what those differences are. In the case of humans and chimps, most of them are in non-coding regions. And many (surprise surprise) are in regions associated with brain growth. There also appear to be a lot of rearrangements and duplications.

 

[Stripe]

Um drowning?

So you're saying there's a serious disadvantage to air breathing creatures living in water. Interesting. :think:

Would it make sense for cows to breathe water?

A miracle would do it. :chuckle:

 

[voltaire]

Genes = proteins essentially. You can get more information out of genes because most amino acids have several synonymous codons.

Protein alignments are often used when comparing very distant organisms because the DNA sequences won't have much homology. (Hence Barbarian's cytC example)

The whole genome alignment I gave you in an earlier post is far better than a simple comparison of proteins. Because DNA does a lot more than just encode proteins. And it's often non- protein coding DNA that makes the difference between species.

For example, if we compared proteins only between say humans and chimps there would be essentially no difference at all.

As you said, DNA does a whole lot more than just make proteins. That is my point. Two branches of the evolutionary tree may share a significant amount of DNA sequences but it doesn't tell you anything about common proteins. Two identical DNA sequences may produce two vary different types of proteins. How? RNA splicing. Two related branches on the evolutionary tree should slice and fuse RNA sequences in a very similar manner. If they don't, you will end up with different proteins being translated from the RNA. It is the proteins and enzymes that make organisms work. Two organisms may match in their DNA sequences by 98% but due to varying splicing, be functioning in quite radically different manners because they are operating with a different set of proteins.

 

[voltaire]

Oh really? How do you explain the whole genome sequence tree I just posted? How do you cherry pick a whole genome?

You don't cherry pick a whole genome; you cherry pick DNA sequencing from a list of other options such as Mitchondrial DNA, Cytochrome C, Protein analysis, Enzyme analysis, or comparing the whole Protein Genome, so to speak, of one animal with another.

 

[Alate_One]

As you said, DNA does a whole lot more than just make proteins. That is my point. Two branches of the evolutionary tree may share a significant amount of DNA sequences but it doesn't tell you anything about common proteins.

Um, sure it does. Proteins are encoded by DNA.

ATG GAC CCA GGT ACC TTG = Methionine, Aspartic Acid, Proline, Glycine

Of course those same amino acids can be encoded in multiple different ways which is why there is more information to be had at the DNA/RNA level vs. the protein level.

Two identical DNA sequences may produce two vary different types of proteins. How? RNA splicing. Two related branches on the evolutionary tree should slice and fuse RNA sequences in a very similar manner. If they don't, you will end up with different proteins being translated from the RNA.

Indeed this is true, but this is generally controlled by non-coding regions of DNA, introns etc. So whole genome sequence would cover that, albeit indirectly.

Really a better way of looking at what you're talking about directly is looking at EST/mRNA sequence - these are created by sequencing the RNAs (via turning them into cDNAs first). Then you can find the alternative splicing sites, noncoding RNAs etc. What you're looking for is called a transcriptome analysis. It isn't normally used for comparing distantly related species, since genome sequence includes regulatory sequences that cause the differences in the transcriptome between species. This is also not done because the transcriptome is different depending on the tissue/cell type in question and in some cases the sex of the individual.

Transcriptome analysis is more frequently used for comparing different tissues of the same organism. Though it can be used for comparing closely related species. There has been a lot done comparing human and chimp transcriptomes in different tissues, for example.

 

[Alate_One]

You don't cherry pick a whole genome; you cherry pick DNA sequencing from a list of other options such as Mitchondrial DNA, Cytochrome C, Protein analysis, Enzyme analysis, or comparing the whole Protein Genome, so to speak, of one animal with another.

Mitochondrial DNA is another option, but it's maternally inherited only (in most species), so it gives you a different set of information than whole genome sequence. Analysis at the protein and enzyme level is not really an alternative source of information since proteins and alternative forms of them all still ultimately derive from genome sequence (with some epigenetics worked in).

The bottom line is all those sets of information keep giving the same answer in the question we've been addressing: that whales descend from hoofed mammals.

 

[The Barbarian]

Again, I did not ask about genes. I asked for a plurality of proteins in common amongst various branches of the evolutionary tree.

I showed you that was the case with hippos and cetaceans. There's several proteins that fit. Can you think of one that doesn't?

IOW, a snake and an alligator should have more proteins in common that a snake and a penguin.

No. A penguin and an alligator should have more proteins in common than a snake and an alligator.

I am looking for the actual protein evidence that the statement is true. Talking about Cytochrome C or casein genes does nothing to answer the question.

It's true. I just showed you. It's for different forms of casein, cytochrome C (which is a protein), and so on. The information I found confirms the relationship.