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Sunday, February 10, 2013

Craig Venter Discusses the Tree of Life

I don't know where this clip comes from or when it was made but it's being promoted on YouTube as "Dr. Craig Venter Denies Common Descent in front of Richard Dawkins!" The link was posted by someone in a comment to a previous post on Sandwalk.

Everything that Ventor says is correct. He didn't need to quibble about the universality of the genetic code but it's true that there are variants.

His point about the tree of life is correct, especially in a discussion about the origin of life. It's unfortunate that Richard Dawkins repeatedly makes such an issue about the tree of life because he's on shakey ground when he does that. I assume that Dawkins hasn't studied the problem. However, he's in good company since most scientists don't understand the problems with the early tree of life. The early history of life looks more like a bush with many interconnecting branches due to horizontal gene transfer [The Tree of Life].

Here's a video of the complete debate. The relevant part, according to the creationists, begins at 9 mins.



266 comments :

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Piotr Gąsiorowski said...

@Diogenes

As far as I have been able to check, the new Antarctic basilosaurid -- stil unnamed -- is some 49.5 My old (if the taxonomic position of the incomplete jaw and the dating turn out to be correct), so it predates Rodhocetus by at least two million years.

The oldest known "quadruped" whales (Himalayacetus, Pakicetus) lived about 53 Mya. They were already quite diverse, so the actual "first whale" must have been still older.

Luther Flint said...

@Dodgyknees the paedo
Italics, bold, caps, caps, italics, bold, caps, bold. LOL Move on clown.

Mikkel Rumraket Rasmussen said...

@Luther
How is it question begging? The soul/mind (whatever you want to call it) interacts with matter in a way that is in principle inexplicable via any material processes.
That's the question begging part. There's no evidence of any external influence on matter. All observed behavior of brainmatter, or any other tissue, is explicable in purely physical and chemical terms. When your arm moves or you speak or whatever action you take, we can usually trace it back to electrical impulses emerging in your brain from certain chemical cascades.

That's not to beg the question, it's to answer it by giving you billions of examples of exactly the thing you say there's no evidence of.
There are "billions" of examples of souls interacting with matter?
That's an interesting claim. Since we're dealing with chemical reactions in your brain, you must be saying there's at some point a chemical reaction happening that emerges out of nothing with no prior affecting physical state. That would mean the brain would violate the laws of thermodynamics courtesy of being forced to react in certain ways due to input/stimuli from the alleged soul-entity. Consequently, you should be ready to give me billiosn of citations of brains producing energy without being fed nutrients and oxygen from the bloodstream, or at the very least a couple of millions of examples of reactions happening in violation known chemical activation energies.

Got any of that, Luther?

How much more evidence would you like?
One, single, credible, independently verifiable case of thermodynamic violations in brain tissue would be enough. Give me that, Luther.

Humans are not describable in purely material terms - deal with it.
That's the questionbegging part again Luther.

In contrast to your claim here you'll find that all actions human beings take fall within the laws of thermodynamics. Additoonally our movements are describable by standard newtonian mechanics, and no tissues, brain or otherwise, have ever been found spurred into action by immaterial soul-entities. You'll find, I'm afraid, that the electrons only start flowing when it is thermodynamically favorable to do so.

But according to you, somehow, somewhere, a chemical or physical reaction must be happening inside the brain, that does not follow or result from another physical and chemical state, because the soul-thing somehow reaches into our material realm and pokes atoms and molecules around so an electrical signal can be generated, run along your central nervous system, down into your limbs and move you around or make you speak or whatever.

So, Luther, time to cough up the "billions and billions" of examples of just that.

I won't be holding my breath, I also won't be able to promise that I can withold laughter in the face of all the flailing I'm about to recieve.

Piotr Gąsiorowski said...

Look, if the transition from amphibious "whales" to whale whales took place between 45-43 million years ago then there can't have been whale whales 49 million years ago. Or, the other way round, if whale whales existed 49 million years ago then the transition to fully aquatic whales couldn't have happened between 45-43 million years ago.

If the new findings are confirmed, we can narrow the transition down, temporally, to ca. 52-50 Mya. Which does not mean that morphologically primitive whales, looking like the ancestral type, did not survive longer.

Luther Flint said...

@ rumraket
There are billions of examples of influences on matter that are in principle inexplicable via any material processes. This sentence for example. Humans decide, in many cases, where matter goes - not vice versa. This is what you don't seem to understand - the idea that humans are completely describable in material terms is just your religion - it has no scientific evidence to back it up and flies in the face of some very simple facts - humans have intentional states for example.

As for "chemical interaction in your brain" - LOL. That's just your religious views getting the better of you again.

Diogenes said...

Luther Flint has been caught lying, and he thinks he can Gish Gallop and change the subject.

Let me re-state the questions no creationist dares to answer.

1. Are there fully aquatic whale fossils older than the first appearance of transitional, semi-aquatic forms like Ambulocetus?

2. Name three semi-aquatic transitional fossils that first appear after fully aquatic whale fossils. Provide citations to the scientific literature.

3. Will you admit that Gross' source says nothing about fully aquatic whale fossils appearing before the first appearance of semi-aquatic, transitional forms? Will you admit that Gross' cited source says nothing of the sort?

4. Since you present yourself as caring about science, and being knowledgeable about science, why do you never have citations to the scientific literature for imaginary fossils and other bizarre claims?

Luther Flint said...

@piotr
How short a time do we need to get down to before drastic revision to the ToE was needed? Is 6 weeks OK?

Luther Flint said...

@Paedo
I refer the dishonorable gentleman to the answer I gave some moments ago.

Diogenes said...

Rapey: I refer the dishonorable gentleman to the answer I gave some moments ago

Again, Luther is lying. He did not answer those questions.

1. Are there fully aquatic whale fossils older than the first appearance of transitional, semi-aquatic forms like Ambulocetus?

2. Name three semi-aquatic transitional fossils that first appear after fully aquatic whale fossils. Provide citations to the scientific literature.

3. Will you admit that Gross' source says nothing about fully aquatic whale fossils appearing before the first appearance of semi-aquatic, transitional forms? Will you admit that Gross' cited source says nothing of the sort?

4. Since you present yourself as caring about science, and being knowledgeable about science, why do you never have citations to the scientific literature for imaginary fossils and other bizarre claims?

Luther Flint said...

@Paedo
I refer the dishonorable gentleman to the answer I gave some moments ago. Yaaawn.

Mikkel Rumraket Rasmussen said...

@ rumraket
There are billions of examples of influences on matter that are in principle inexplicable via any material processes.

More questionbegging.

This sentence for example.
What about it?

Humans decide, in many cases, where matter goes - not vice versa.
Human beings are made of matter and never violate the laws of thermodynamics. There are no counterexamples.

This is what you don't seem to understand - the idea that humans are completely describable in material terms is just your religion
I don't do religion of any sort at all, you silly trolling is dismissed as just that.

it has no scientific evidence to back it up
Human beings are made of matter, all our actions follow known physical and chemical laws. Prove me wrong, it should be easy for you to give me examples of human beings violating the laws of thermodynamics, either by taking actions that lead to a reduction in total entropy without burning energy, or by showing me examples of chemical interactions arising in bodily tissues which weren't themselves caused by antecedent physical and chemical states.

and flies in the face of some very simple facts - humans have intentional states for example.
And if your claim is true, then at some point the material stuff of which human beings are made would show signs of violating known physical laws that all other matter obeys. So kindly give me those examples.

As for "chemical interaction in your brain" - LOL. That's just your religious views getting the better of you again.
Your feeble, knee-jerk dismissal borne out of a knowledge that you know your deep down that your position is refuted is duly acknowledged.

It's late in Denmark, I'll go have a good night's sleep, thinking while I do so, burning energy in the process, as one would expect on thermodynamic grounds from an informationprocessing system.

I'll be anxiously awaiting references to examples of thermodynamic violations of the behavior of matter tomorrow Luther.

Actually I won't, because I know all you have to repond with is an insistence that your inconsequential philosowibble takes precedence over scientific facts.

Diogenes said...

Why are creationists unable to answer simple questions relevant to the issues they raise? Because they're afraid.

Creationist Gross lied through his teeth about the transitional fossils to whales.

Rapey: I refer the dishonorable gentleman to the answer I gave some moments ago.

Outright lying. Rapey never answered these questions.

1. Are there fully aquatic whale fossils older than the first appearance of transitional, semi-aquatic forms like Ambulocetus?

2. Name three semi-aquatic transitional fossils that first appear after fully aquatic whale fossils. Provide citations to the scientific literature.

3. Will you admit that Gross' source says nothing about fully aquatic whale fossils appearing before the first appearance of semi-aquatic, transitional forms? Will you admit that Gross' cited source says nothing of the sort?

4. Since you present yourself as caring about science, and being knowledgeable about science, why do you never have citations to the scientific literature for imaginary fossils and other bizarre claims?

What are you afraid of, Rapey? Can't you just admit you were wrong?

Luther Flint said...

@Rumraket
Why should there be thermodynamic violations? It's more a matter of just deciding where stuff goes in a manner in principle inexplicable via any material processes - your religious views to the contrary notwithstanding. How do you account for intentional states, for example? Do you think humans have them? What do you take them to be? How might you characterise them in material terms?

Luther Flint said...

@paedo
I wasn't wrong, you were wrong.

Diogenes said...

Luther Flint: If you weren't wrong, why are you scared shitless to answer simple questions, relevant to the issues you raised?

Do these questions make you shit your pants?

1. Are there fully aquatic whale fossils older than the first appearance of transitional, semi-aquatic forms like Ambulocetus?

2. Name three semi-aquatic transitional fossils that first appear after fully aquatic whale fossils. Provide citations to the scientific literature.

3. Will you admit that Gross' source says nothing about fully aquatic whale fossils appearing before the first appearance of semi-aquatic, transitional forms? Will you admit that Gross' cited source says nothing of the sort?

4. Since you present yourself as caring about science, and being knowledgeable about science, why do you never have citations to the scientific literature for imaginary fossils and other bizarre claims?

The above questions, which are trivially simple, ridiculously easy to answer, make Luther shit his pants with fear.

Piotr Gąsiorowski said...

How short a time do we need to get down to before drastic revision to the ToE was needed? Is 6 weeks OK?

At the moment, we have evidence of only semiaquatic whales 52+ Mya, and there seems to be some evidence of a fully aquatic one 49.5 Mya. It was still a very primitive whale, definitely not anything like the modern cetaceans. It seems to be a reasonable guess that the transition to a fully marine way of life in at least one lineage occurred about 50 Mya. There's no reason to think that it took 6 weeks. It could have taken a few million years, for all we know. Note that a few decades ago we knew bugger-all about the earliest whales. Now we have plenty of fossils and are in a position to date some major transition with just a small margin of uncertainty -- +/- 1 My or so.

Luther Flint said...

@paedo
I've answered the questions. 1 - yes. 2. pick any three from any of the hundreds of semi-aquatic mammals though to have first emerged less than 45 million years ago. (Use rumraket's explanation of "transitional fossil" to see why this presents no problem.) 3. Who cares, it doesn't say lots of things. The point is taken from what it does say and what people were saying about the timescales for whale evolution. 4. Because my points are based on facts that are readily accepted and thus there is no need to cite a peer-reviewed scientific paper saying, eg, it's Friday today - requests for such sources being simply a ruse used by clowns (like you) to try to derail the pwnings you regularly receive from far more intelligent people (like me).
NEXT!

Diogenes said...

Rapey shits his pants in fear but refuses to answer simple questions!

I asked:

2. Name three semi-aquatic transitional fossils that first appear after fully aquatic whale fossils. Provide citations to the scientific literature.

Rapey has no reply:

pick any three from any of the hundreds of semi-aquatic mammals though to have first emerged less than 45 million years ago.

That is not an answer. That is Luther shitting his pants in fear and re-stating his thesis as evidence for this thesis.

I said "Name three".

Luther says there are "hundreds of semi-aquatic mammals though to have first emerged less than 45 million years ago."

Luther says there are hundreds, but cannot even name three! Simple questions make him shit his pants!

Luther: my points are based on facts that are readily accepted and thus there is no need to cite a peer-reviewed scientific paper

Why, Luther don't need no stinkin' evidence because he has "facts that are readily accepted"!

Note that "are readily accepted" is a PASSIVE TENSE verb. Accepted by whom? Outright liars switch to passive tense verbs to avoid specifying who, precisely, accepts these things where.

I said "Name three".

Luther says there are "hundreds of semi-aquatic mammals though to have first emerged less than 45 million years ago."

If there were hundreds, it would be easy for Rapey to name three.

He cannot because they don't exist. He shits his pants in fear.

Luther Flint said...

@Paedo
Otter, beaver, sea lion. All transitional creatures according the new expanded definition of "transitional". Anyway, why not tell us about three of the many thousands of transitional species that must have existed that are descendants of a land mammal like pakicetus and ancestral to a whale? Why not tell us about one?

Piotr Gąsiorowski said...

pick any three from any of the hundreds of semi-aquatic mammals though to have first emerged less than 45 million years ago. (Use rumraket's explanation of "transitional fossil" to see why this presents no problem.)

They won't do. When Rumraket wrote about "transitional features" he didn't mean simply a transitional way of life. The otter, for example, is semi-aquatic, but here the similarity ends. It is in no other way transitional between terrestrial artiodactyls and whales. Unlike Rodhocetus and the like, it shares no unique morphological innovations with whales -- innovations that appeared first in the common ancestor. Seals, water voles or muskrats don't qualify either. Even hippos don't, though they are pretty close relatives of whales. They are still an outgroup with no distinctive cetacean traits.

Luther Flint said...

@Piotr
I know. The reason it's difficult is because despite the fact that there must be (must be!) thousands of species descended from something akin to pakicetus and ancestral to the whale the supporters of the theory the earth goes round the sun just hasn't managed to turn any up yet. All they've got are creatures that lives at almost exactly the same time as the first whale whale but which weren't all that much of a whaley whale.

Piotr Gąsiorowski said...

@Luther,

Sorry for taking you seriously for a moment. I won't do that mistake again.

Unknown said...

Highlight of the full "Venter" Video:

http://thesciencenetwork.org/programs/the-great-debate-what-is-life/what-is-life-panel

Christopher McKay 5.53 NASA:

"As we study early life, it’s looking more and more like life appears very in early in earth history at a very complete and complex level already. It seems like Athena springing from the head of Zeus fully formed. It’s really quite a mystery and it’s forced some people to think “Well maybe it didn't develop here. It came here and landed here.” And that’s why we get this impression of incredible development and complexity so early."

Whata heck is Chris talking about? He couldn't be talking about the cambrian explosi'voe, could he? From what he's saying there must have been a cambrian miracle rather than cambrian biogenesis ...

Unknown said...

More Venter video:

Moron Krauss asks Venter uneducated question and gets an answer he can't handle because he is a moron that is it. Just listen. He has no clue...

What is the minimum to create life....(like he knows what his talking about....
Venter fires back at an moron:

"There won’t be a minimal gene set; there will be multiple ones. Because I’m not so sanguine as some of my colleagues here that there’s only one life form on this planet. we have a lot of different metabolism, different organisms. I wouldn’t call you the same life form as the one we have that lives in pH 12 base that would dissolve your skin if we dropped you in it… I think the tree of life is an artifact of some early scientific studies that aren’t really holding up… So there is not a tree of life. ~ Craig Venter 8.58

Unknown said...

Buhahahahahaha... You are going to tell Venter what he knows? You're stupid,stupid and ignorant moron, He said "...so there is no tree of life....!!!! Don't you get it? It's mainly because of endosybiosis of prokaryotic cells to eukaryotic that does not make sense... If you have scientific proof we will give you 1 milion dollars. You see you don't that's why I know you are an idiot. Oxy is not enogh...

Diogenes said...

Witton, you're a pathetic liar.

This video was labelled "Venter denies common descent."

In the video, Venter affirms common descent.

You quote Venter saying "...so there is no tree of life..." which is not a denial of common descent.

Your creationist hero, Michael Behe, affirms common descent.

Back to Venter says in the video:

1:10we found 12 that look like a very, very deep branching... perhaps forth domain of life

"Deeply branching" into WHAT!?

Branching into US. Branching into YOU. If they branch into the other domains of life, then they're are relatives and it's not a denial of common descent.

A fourth domain of life is not a separate tree and not a separate bush. It is "deeply branching" into OUR tree or OUR bush, take your pick, we are inter-twined with them.

So the creationist who labelled the video "Venter denies common descent" was lying.

More obviously, Venter never gets close to challenging that all eukaryotic life forms a tree. That includes animals, vertebrates, mammals, apes, and humans.

So humans and apes are of COMMON DESCENT, humans and mice are of COMMON DESCENT, humans and fish are of COMMON DESCENT, humans and arthropods are of COMMON DESCENT, humans and fungi are of COMMON DESCENT, humans and plants are of COMMON DESCENT, etc.

As for your additional Venter quote: "One question is, can we extrapolate back from this data set to describe the most recent common ancestor. I don't necessarily buy that there is a single ancestor. It’s counterintuitive to me. I think we may have thousands of recent common ancestors and they are not necessarily so common."

In this quote Venter, does not assert that evidence proves there is no universal comment ancestor, and even if he did, it would not be a "denial of common descent" as you claimed, because we and they are intertwined on the same bush, assuming his speculation (not evidence) is correct that there are "multiple COMMON ancestors."

Venter says common, common, common, common, and you assert that he denied common descent. NO, you put those words in Venter's mouth.

You and apes are of COMMON DESCENT and you cannot find any major scientist denying that-- not even Michael Behe!

If YOU deny common descent, then you go argue with Michael Behe, who called it "trivial"!

Diogenes said...

Witton: You're stupid,stupid and ignorant moron... I know you are an idiot.

You've presented no references or citations to the scientific literature or to any study denying common descent.

But again: Michael Behe, who works for the Discovery Institute, affirms common descent, he considers it obvious and "trivial." So let me fix your quote for you.

Witton should have written: Behe is stupid,stupid and ignorant moron... I know Behe is an idiot.

Andre said...

Whoa!!!! All this emotion..... Let me help you, since it seems you suffer from the very condition you accuse me of, So TOE had previously claimed as a fact that modern whales only came on the scene about 45 million years ago, this fact has been shoved down people's throats for a while now, but then they found fossil evidence that disproved that very shoved down our throat facts that a fully aquatic whale existed 5 million years prior to the just so story, of course for evolution its easy to shitf the goal posts by just chucking in a metaphysical claim that reads; things turned out different than once believed, which in plain English means we fucked up but let us am end our just so story because we don't want you to think it could be false.....

Andre said...

PS. Calling me a troll does not make it true, evidence that mutations cause cancer, knock yourselves out Darwin's acolytes!!!

http://cancer.stanford.edu/information/geneticsAndCancer/genesCause.html


http://m.cancer.org/cancer/cancercauses/geneticsandcancer/oncogenesandtumorsuppressorgenes/oncogenes-tumor-suppressor-genes-and-cancer-mutations-and-cancer

http://www.mayoclinic.com/health/cancer/DS01076/DSECTION=causes

Andre said...

Yes Tiktaalik was one until they found tetrapod tracks that predated Tiktaalik by 18 million years...... That really fucked things up for TOE.

Andre said...

So what can we conclude from this lesson?

1. Yo avarage Darwin disciple does not follow science.
2. 1+1=2 As mutation rates increase incidents of cancer increases.

Mikkel Rumraket Rasmussen said...

Hmm, it seems a portion of the exchange I had with Luther yesterday got deleted.

AllanMiller said...

PS. Calling me a troll does not make it true, evidence that mutations cause cancer, knock yourselves out Darwin's acolytes!!!

Andre, please! It is well known that mutations cause cancer. But that is not the same as saying ALL, or even most, mutations cause cancer. Cancer is unrestrained cell growth in multicellular organisms. Most mutations do not cause unrestrained cell growth. It does not even apply to most organisms on earth (think small). Where mutation is involved, it is typically in somatic cells, which do not get passed on, so those mutations have no evolutionary significance.

AllanMiller said...

Yeah, I believe we've been through this. I think Venter is wrong. A tree of descent is the fundamental expectation of any process of iterative copying, not an 'artifact' of some primitive scientific methodology. As to equivocation on 'life form' ...

You don't have to find a single ancestor, as a matter of fundamental principle, but - hey! - we do. The ribosomal tree is monophyletic, as is the 'tree of variant codes'. Therefore, all protein-coding genes converge on this ancestor, even if the path to it not always the same direct, vertical one for every gene.

Acknowledging universal monophyly on ribosomes but then calling it into question based on protein-coding gene sequences misses something rather fundamental about protein-coding genes.

Andre said...

Allan will peer reviewed material from nature convince you of my claim that the increase of mutations have increased the rate of cancer. Do you not get it? Mutations are far more harmful than neutral or good.

http://www.nature.com/news/past-5-000-years-prolific-for-changes-to-human-genome-1.11912


This was published in November 2012

Andre said...

More evidence, does the most prestigious scientific journal count?


http://www.nature.com/news/2008/080220/full/451876a.html

Andre said...

And this cannot point to common design at all only common ancestry?

Piotr Gąsiorowski said...

So TOE had previously claimed as a fact that modern whales only came on the scene about 45 million years ago,

No, the date has nothing to do with the theory of evolution. That's what paleontology suggested, not what any sort of theory predicted. The paleontological record is the source of raw evidence. We learn when a certain group appeared when we find its representatives -- or to be more precise, their appearance in the fossil record gives us a lower bound on its age, which may turn out to be greater. As the earliest basilosaurids were known from ca. 41 Mya, it was tentatively assumed that they evolved about that long ago. The date has no mystic importance to anyone. A new find may always push it back.

this fact has been shoved down people's throats for a while now

What a stupid comment. Most people don't know or care what a cetacean is. You don't know what you are talking about either. A whale from, say, the Middle Jurassic woukld shake the foundations of what we know of the evolution of mammals. Pushing back the oldest basilosaurid even by 9 million years is no big problem. There are still earlier primitive cetaceans known today, and there's little doubt more will be found soon, given the brilliant progress of paleontology in recent years.

Piotr Gąsiorowski said...

What the heck is "common design"? Define it and explain why it should mimic the nested hierarchy predicted by models of common ancestry.

Andre said...

And there you have it TOE is not science because you can chop and change the story anyway you like.

Luther Flint said...

@rumraket
Look harder.

Luther Flint said...

@Piotr
I'd imagine "common design" would yield a nested hierarchy in the way human designs can be placed in a nested hierarchy. Think of a department store, and the stuff sold there.

Luther Flint said...

Full video is here

http://thesciencenetwork.org/programs/the-great-debate-what-is-life/what-is-life-panel

some of the philosophy is so unsophisticated as to be cringeworthy, bet hey, that's to be expected I guess.

Luther Flint said...

@John
He's not talking about the Cambrian at all. He's talking about much much earlier than that. He's talking about the very origin of the single celled organisms that appeared, already extraordinarily complex, almost as soon as the earth could physically sustain such things. This is the abiogenesis mystery - the Cambrian explosion is a completely different mystery concerning the sudden explosion, seemingly without precursors, of a huge variety of complex multicellular creatures including representatives of all the body plans we see today.

AllanMiller said...

Andre - the word 'cancer' appears in neither article.

Cancer is a predominately a disease of old age, in multicellular organisms, due (in part) to certain mutations in somatic cell lines. We are living longer, so more people are living long enough to die of it; additionally we expose ourselves to certain specific carcinogens (eg smoking).

That doesn't have a huge amount to do with the role of mutations in evolution.

AllanMiller said...

The hierarchy of Life is objective, particularly on molecular criteria. There are no criteria other than commonality of sequence - we don't place organisms in order of size, or who can eat who, or which ones you could sit on.

If common design, that design would need to include signals deliberately intended to fool diligent analysis into thinking that it was common descent. 'Fluff' - nonfatal inversions, deletions, insertions etc - are copy errors, and they follow the nested hierarchy. There is no explanation for variations of the genetic code on a Common Design paradigm. It's absolutely essential that Mycoplasma has a spare tryptophan codon instead of a STOP? Yeah, sure it is.

At some point, common descent must form an explanation for commonality. Whenever Designers aren't Designing, organisms' genomes are being copied, and that copying is the dominant source of commonality among any individual and all its non-tinkered-with descendants.

Maybe LUCA was designed, and everything since has been evolution.

The whole truth said...

Allan Miller asked:

"I'll ask again in a more direct fashion: why is 4 million years too short?"

I think that one of the big problems creationists of the YEC variety have is that they can't comprehend how long one million years is, let alone 4 million, 100 million, a billion, etc. It's just way past their mental capabilities, and they don't even try to change that.

Creationists, especially of the YEC variety, are basically children who never mentally grew up. They may have gone through physical puberty but they still have the mental immaturity of a child. They are afraid to grow up and expand their minds.

The whole truth said...

andre said:

"And there you have it TOE is not science because you can chop and change the story anyway you like."

Actually, andre, scientific theories are all subject to change as more evidence is found. Unlike religious beliefs, science must ultimately adjust to the evidence, whereas religious zealots constantly try to ignore or adjust the evidence to fit their fairy tale beliefs. Science isn't a belief system like your religious dogma, so change is actually expected, rather than despised. Yeah, sometimes proper change is resisted by some scientists (they're humans after all) but proper changes in theories will occur as more evidence is found and hypotheses/inferences/explanations are refined, and that doesn't necessarily mean that the scientific theories are completely wrong.

The whole truth said...

andre said:

"Yes Tiktaalik was one until they found tetrapod tracks that predated Tiktaalik by 18 million years...... That really fucked things up for TOE."

That comment really shows how little you know and how limited your mind is, as if your other comments weren't enough.

Piotr Gąsiorowski said...

I think that one of the big problems creationists of the YEC variety have is that they can't comprehend how long one million years is...

It's some 170 times longer than whet *they* believe to be the correct age of the planet. And yet, somehow, it seems too short for them. It's unfathomable!

Unknown said...

100 Years of Fruit Fly Tests Show No Evolution...Why???
"July 22, 2010, marked the 100th anniversary of genetic investigations using fruit flies. The first such study appeared in Science in 1910 and described the unexpected appearance of a male fruit fly with white eyes after generations of flies with pigmented eyes.1 This began a century of focused studies on fruit fly mutations, but what has really been learned by all this tinkering?

For most of the past century--and especially since the discovery of DNA as a physical molecule carrying heritable information--the prevailing concept of neo-Darwinian evolution has held mutations to be the central generator of new and useful information. Thus, mutations have been given ample opportunity to prove themselves, if they are naturally selected, as having "the power to drive the evolution of all living things in the direction of positive improvement."2

Fruit flies, with their short generation times and only four pairs of chromosomes, presented prime testing ground for evolution. In laboratories worldwide, they have been subjected to all manner of mutation-inducing phenomena, including hosts of chemicals and radiation treatments, to try and accelerate evolution-mimicking mutations. After all this, fruit flies should have certainly exemplified evolution by now.2 But they haven't.

So, having achieved no evolutionary progression in fruit flies by these random means, researchers made them the focus of countless purposeful gene manipulation studies. The most popular, from an evolutionary perspective, were experiments with what are called HOX genes.

HOX, an abbreviation of "homeobox," are genes used by the organism during embryonic development. Many reasoned that it would be simpler for evolution to operate by mutating these genes, since a small alteration could produce a large effect in the fly's body. However, this was before recent studies showed that embyronic development is more heavily influenced by regulatory DNA, not genes. And mutating (through substituting, deleting, or duplicating) developmental genes like HOX has only ever yielded a dead fly, a normal fly (if the mutation happened to have no noticeable effect), or a tiny monster. None of these results match the "positive improvement" expected of Darwinian evolution.

Extra body segments, an extra set of wings, or legs in the place of antennae characterized the weird forms that were generated. Three generations of specifically designed DNA alterations were required to produce fruit flies with four wings--but they couldn't fly. The extra wings had no muscles and were dead weight. One recent exploration of neo-Darwinism remarked:

The mutants that produce four-winged fruit flies survive today only in a carefully controlled environment and only when skilled researchers meticulously guide their subjects through one non-functional stage after another. This carefully controlled experiment does not tell us much about what undirected mutations can produce in the wild.3

In his book Evolution, Colin Patterson summarized the lost hope of finding evolution from HOX investigations:

The spectacular effects of homeobox gene mutations were first seen in Drosophila, early in the history of genetics. Carriers of some of these mutations certainly qualify as monsters--though without much hope.4

Whereas fruit fly studies have provided critical information about how genes, nerves, longevity, and other biological machines and processes operate, no progress whatsoever has been made in the quest to accelerate these insects' "evolution" by ramping up their mutations. The survivors of 100 years of lab torture are still just fruit flies.
http://sandwalk.blogspot.ca/2013/02/craig-ventor-discusses-tree-of-life.html#comment-form

The whole truth said...

Yeah, unfathomable.

YECs must believe that every extant species on Earth evolved during about the last 4,000 years only from what the bible says was taken on the ark. Either that or they must believe that MANY new genera/species have been poofed into existence by the designer-god during that 4,000 years.

Apparently, with the help of a designer-god, evolution (or poofing) is WAY FAST, but without such help evolution has to always be slooooooooooooooooooooooooooooow.

Andre said...

Now why would Nature journal lie for Jesus?

http://www.nature.com/nature/journal/v463/n7277/edsumm/e100107-01.html

I wonder......

The point here is that the stories keep changing, everything is a FACT until the next find.....

Andre said...

TWT

Are yo denying that mutations cause cancer?

Andre said...

Allan

Your assertion that cancer is for old people is claptrap, on a personal level, I have lost 3 friends that died of cancer in their teens.

Andre said...

Cancer does not have much to do with mutations in evolution, your words...


Really?




http://cancer.ucsf.edu/evolution

Andre said...

I would say this statement contradicts yours don't you think?

"Cancer progression is an evolutionary process Evolution is fundamental to the generation of cancer and our difficulty in curing cancer. A neoplasm is a microcosm of evolution with a mosaic of mutant clones competing for resources. Progression to malignancy occurs through a dynamic of natural selection within the neoplasm, as cells acquire the hallmarks of cancer and out-compete their surrounding cells."

Unknown said...

Once upon the time there was endosymbiosis...

Part 1.

"On the Origin of Mitochondria: Reasons for Skepticism on the Endosymbiotic Story

With regret, ENV recently noted the passing of biologist Lynn Margulis. Margulis, a scientist whom I admired greatly, was never a stranger to controversy, going so far as to call neo-Darwinism "a complete funk" and asserting that "The critics, including the creationist critics, are right about their criticism. It's just that they've got nothing to offer by intelligent design or 'God did it.' They have no alternatives that are scientific." She was a scientist who wasn't afraid to think creatively, disregarding the scorn of her colleagues. According to the Telegraph, a response to one grant application she made said: "Your research is crap. Don't ever bother to apply again."

Lynn Margulis took a controversial view on how evolution works, stressing the importance of symbiotic and co-operative relationships over competition. This concept of evolution inspired what is now recognized as her most notable idea, the notion that the eukaryotic mitochondrion -- the power plant of the cell -- was acquired by virtue of an endosymbiotic event. Endosymbiotic theory essentially maintains that mitochondria arose by virtue of a symbiotic union of prokaryote cells. The nearest living relative to the mitochondrion is thought to be the alpha-proteobacteria Rickettsia (Emelyanov, 2000; Andersson et al., 1998). Chloroplasts are also thought to have arisen in a similar manner from the photosynthetic cyanobacteria.

In November 2010, I drew attention to a paper in Nature by Nick Lane and Bill Martin, who showed that the prokaryote-to-eukaryote transition was effectively impossible without the energy demands, pertinent to the biggest event of gene manufacture in the history of life on earth, being met by the mitochondrial processes of oxidative phosphorylation and the electron transport chain. The bacterial cell alone could not meet these energy demands.

The evidence that is typically offered for endosymbiotic theory includes the following:
Mitochondria possess a circular genome (lacking in introns and independent from the nuclear DNA) in which transcription is coupled to translation, characteristic of bacterial DNA. There are also some other notable similarities. For example, in both mitochondria and Mycoplasma, the codon UGA specifies the amino acid Tryptophan (Hayashi-Ishimaru et al., 1997; Martin et al., 1980; Inamine et al., 1990; Yamao, 1985), whereas in the conventional code it serves as a stop codon.
Mitochondria divide and replicate independently of host cell division and do so in a manner akin to binary fission, possessing homologues of the bacterial division protein FtsZ (Kiefel et al., 2004).
They are enclosed by a double-membrane.
Mitochondria and bacteria are of a similar size and shape."

Unknown said...

Once upon the time there was endosymbiosis...

Part 2.

"On the Origin of Mitochondria: Reasons for Skepticism on the Endosymbiotic Story

The Size and Shape of Mitochondria
The argument based on the size and shape of mitochondria is one that has been turned on its head in recent years, being transformed from an argument for endosymbiosis to one against it. These organelles are now acknowledged in the literature to be better understood as dynamic reticular structures (see this link for references).

Electron micrographs displaying cross-sections of mitochondria portrayed the mitochondrion as a sphere. However, when one looks at 3D models of the organelle, the reality is somewhat different. You can take a look at some of these images by going here, here, here, or here.

The Lack of a Mechanism

By far the most potent challenge to the endosymbiotic origin of eukaryotic mitochondria is the lack of a viable mechanism, perhaps most particularly with respect to the transfer of genes from the mitochondrion to the nucleus.

For one thing, there are the variants on the conventional genetic code. This means that, over the course of their transfer to the nucleus, the genes would need to be "recoded" so as to comply with the conventional genetic code. For example, recognizing UGA as a stop codon instead of the codon for Tryptophan (or vice versa) would cause cellular mayhem.

Secondly, mitochondrial proteins made at the ribosomes in the eukaryote cytoplasm need to be identified as such to ensure that they are properly dispatched (this is normally done by attaching a "label" in the form of an extra length of polypeptide to the protein). This would require a coincidental modification of the correct structural gene (which seems unlikely). Biologist Timothy G. Standish notes,"

Unknown said...

“Once upon the time there was endosymbiosis... Part 3. "On the Origin of Mitochondria: Reasons for Skepticism on the Endosymbiotic Story ...

"G. Standish notes,

If genes were to move from the mitochondria to the nucleus they would have to somehow pick up the leader sequences necessary to signal for transport before they could be functional.

While leader sequences seem to have meaningful portions on them, according to Lewin (1997, p251) sequence homology between different sequences is not evident, thus there could be no standard sequence that was tacked on as genes were moved from mitochondria to nucleus.

Alternatively, if genes for mitochondrial proteins existed in the nucleus prior to loss of genes in the mitochondria, the problem remains, where did the signal sequences come from? And where did the mechanism to move proteins with signal sequences on them come from?
Albert de Roos explains,
All evolutionary theories must offer an explanation in mechanistic terms of how it should or could have happened in order to be tested. The difficult thing with the endosymbiotic theory is that it proposes no real mechanism and most textbooks show the simplistic picture of a cell that swallows another cell that becomes a mitochondrion. Unfortunately, it is not so simple as that. There is a difference between the process of endosymbiosis and its incorporation in the germline, necessitating genetic changes. What were those changes? What was the host? Was it a fusion, was it engulfment, how did the mitochondrion get its second membrane, how did two genomes in one cell integrate and coordinate? The theory is also strongly teleological, illustrated by the widely used term 'enslavement'. But how do you enslave another cell, how do you replace its proteins and genes without affecting existing functions? The existence of obligate bacterial endosymbionts in some present eukaryotes is often presented as a substitute for a mechanism, but they remain bacteria and give not rise to new organelles. So, before we can speak of the endosymbiotic as a testable scientific theory, we need a mechanistic scenario which is lacking at the moment.
When we do try to envision a mechanistic scenario based on the endosymbiotic theory, we quickly run into problems. Genetic mutations that allow bacteria to thrive in the cytoplasm would not be strategic for survival. Anaerobic cells normally do not survive in environment that contains oxygen, while the endosymbiont would need oxygen in order to present fitness advantage. The two organisms would initially compete for energy sources since bacteria are users of ATP and do not export it. The extensive gene transfer that is needed in the endosymbiotic theory would wreak havoc in a complex genome since frequent insertion of random pieces of mitochondrial DNA would disrupt existing functions. Furthermore, gene transfer is a multi-step process were genes need to be moved to the nucleus, the different genetic code of mitochondria needs to be circumvented, the genes need to be expressed correctly, as well as imported back into the mitochondria in order to be functional. All in all, mechanistic scenarios for the endosymbiotic theory imply many non-functional intermediates or would just be plain harmful to an organism. Therefore, the endosymbiotic theory is in contrast with the concept of gradualism that forms the basis of modern evolutionary theory."

Unknown said...

“Once upon the time there was endosymbiosis... Part 4. "On the Origin of Mitochondria: Reasons for Skepticism on the Endosymbiotic Story..."

"Furthermore, this gene transfer must have taken place at a time extremely early in the history of eukaryotes, substantially reducing the window of time in which gene transfer could have occurred.
Summary and Conclusion

While we find examples of similarity between eukaryotic mitochondria and bacterial cells, other cases also reveal stark differences. In addition, the sheer lack of a mechanistic basis for mitochondrial endosymbiotic assimilation ought to -- at the very least -- give us reason for caution and the expectation of some fairly spectacular evidence for the claim being made. At present, however, such evidence does not exist -- and justifiably gives one cause for skepticism..."

Well... No comment needed...;)

AllanMiller said...

Andre,

This will be my last response to you, as you clearly don't understand the material you wish to argue over, and the thread is already well over-spammed.

1) Cancer incidence increases during life. The fact that you know people who died young does not invalidate that. I could show you a lot more old people with tumours than young ones. The longer people avoid dying of other things, the more surely they will die of cancer.

2) The fact that you can dig out a quote by googling 'cancer' and 'evolution' invalidates nothing I have said. Cancer is evolutionary, because it involves genetic changes in cell lines, but these occur in somatic cells, which do not get passed on - the mutations last for one organismal generation, no more and no less. This has nothing to do with 'building whales', etc - the long game of evolutionary change.

Cancer mutations - undoubtedly deleterious - persist in a way that deleterious alleles in a population cannot because 'Reproductive success' of cells in a body is the last thing you want. Because that's cancer. But in a wider population, producing more offspring than your rivals is exactly what you want. So your (unattributed) quote somewhat undermines your 'mutations = bad' argument. Rate-increasing mutations that are bad in a body are good in a lineage battling against rivals in a population.

Toodles!

Anonymous said...

John,

You are an ass-hole. here a question that will show you how if you dare to investigate: where do these variants to the standard genetic code exist?

Clue 1: mitochondria: they have such a little number of genes that changes in the code were not bound to be catastrophic. The changes are not so big though. Obviously third variant genetic code is a descendant of the standard one.

Other places where we find variants to the standard code it is a derived code that works on very small genomes/chromosomes. Again, not catastrophic, still only small variations.

Also, if Dawkins is wrong, and if there was multiple origins of life, that would not undermine evolution one bit. Dawkins would be wrong about universal common ancestry, but you are an ape and share common ancestry with chimps and gorillas, and many more animals regardless of your triumphant tone. That's undeniable, undebatable, and you are still an ass-hole. Grow up your mind ass-hole. Your rhetorical bullshit and your absolutism about how wrong Dawkins could be does not lead you away from reality.

Anonymous said...

Larry. I forgot to ask you about this. Why do you agree with Ventor that mycoplasma's genetic code would not work in human cells? I thing it would work it wouldn't be as efficient. What's your thought? I don't like Ventoer. He thinks he knows it all.

Leyo said...

Yes, it would seem extraordinaryly unlikely to imagine that life originated twice independently, both evolved the same genetic code relatively simultaneously and then horizontally transferred seqeunces between them that just happened to work well in both "species" upon translation.
Perte de cheveux chez la femme

Anonymous said...

which evolution? By what mechanisms? You only know how to say "something" has evolved, but do not know empirically and observationally explain natural processes and mechanisms that produced it all. I can say this thing has evolved, however, as it has evolved? By what process? Natural selection does not explain the evolutionary mechanism. "Aculo of mutations and variations" does not explain macroevolution, since both natural selection, as mutations and variaçãoes are limited and work with existing genetic stuff! They do not produce new genetic information: at least until today any natural evolutionary process or mutation producing new genetic information but new sequences was not observed, but with existing genetic material. Where's the evolution? Assumptions do not prove evolution!

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