Deep Homology and Front-loading

It's an argument based on what we know about biology: life requires a fairly specific core set of genes . . .

Actually, we don't even know if life requires DNA, much less a certain set of genes. Again, you are painting the bull's eye around the bullet hole. You are taking one result out of possibly billions and claiming that this is the only way of doing it. You are assuming that eukaryotes and metazoans were the goal instead of demonstrating that they are the goal.

What are the chances that the same mutation will occur at the same base in 5 different species? Quite slim. It is possible, but improbable.

Doesn't that depend on the length of the sequence?

If were just dealing with AAAA and AAAT, then having AAAT pop up twice isn't all that improbable. (Stats was the only math class I hated and I ain't gonna figure this one) Plus, considering the chemistry of it, some of it ain't even all that random, is it?

As to size . . . as large as possible.

Sweet. E aho laula.

If you are trying to reconstruct the entire ancestral genome then you will try to find ALL of the shared DNA you can. You need to keep in mind that DNA will be lost in different lineages, so phylogenetic information is also important to determine when that deletion occurred.

Seems to me that the phylogeny speeks better, I don't see how you could come to much of a conclusion from the sequences. I'm not liking Geno's approach... but don't get me wrong folks, I'd love to see some good evidence showing some planning involved in the evolution of life on Earth.

Ubiquitin being ubiquitous

Just now getting that, thanks.

I don't see how the large presence of ubiquitin would point more towards either FLE or "darwinian" evolution.

Nice thread, Geno.

Thanks.

But how unlikely is it, really? Maybe its inevitable, no? Given that its all spontaneous chemistry, and that proteins work because of thier shape, why wouldn't we expect these kinds of similarities even without FLE?

I don't think there's anything in the blind watchmaker that makes it inevitable for a specific fold to arise, in the absence of specified initial conditions. I.e., starting with just a few basic folds, there's no real guarantee that the blind watchmaker will be able to piece together a specific novel fold.

Is there any reason to think it is inevitable for any fold to arise?

I mean it's obvious that the trend of evolution will be towards greater complexity but beyond that, is there anything that seems inevitable?

This quote exemplifies the problems with FLE. It is Texas Sharpshooting, plain and simple. The Texas Sharpshooter falacy is where a sharpshooter makes the claim that he can hit a target the size of a quarter from 1,000 yards away on the first try. The sharpshooter fires his shot into a crowded suburb, finds the bullet hole (presumably in the side of a house), and draws a quarter sized bull's eye around the bullet hole. Voila, amazing sharpshooting exhibition, right?

From Wikipedia:
"The Texas sharpshooter fallacy is a logical fallacy in which pieces of information that have no relationship to one another are called out for their similarities, and that similarity is used for claiming the existence of a pattern. This fallacy is the philosophical/rhetorical application of the multiple comparisons problem in statistics, and apophenia in cognitive psychology. It is related to the clustering illusion, which refers to the tendency in human cognition to interpret patterns in randomness where none actually exist.

The name comes from a joke about a Texan who fires some shots at the side of a barn, then paints a target centered on the biggest cluster of hits and claims to be a sharpshooter."

And:

"The Texas sharpshooter fallacy often arises when a person has a large amount of data at their disposal, but only focuses on a small subset of that data. Random chance may give all the elements in that subset some kind of common property (or pair of common properties, when arguing for correlation). If the person fails to account for the likelihood of finding some subset in the large data with some common property strictly by chance alone, that person is likely committing a Texas Sharpshooter fallacy."

Now that we've defined our terms, I ask the following question: in what way do I have "a large amount of data at their disposal, but only focuses on a small subset of that data. Random chance may give all the elements in that subset some kind of common property"?

This is exactly what FLE is. It assumes that the biodiversity we see today is the biodiversity that was intended. Genomicus is drawing the bull's eye around the bullet hole. What Genomicus just can't understand is that eukaryotes DID NOT NEED TO EVOLVE. There is nothing in the history of life that requires the existence of eukaryotes, much less eukaryotes with calmodulin. NOTHING. It is a happenstance of occurences that resulted in eukaryotes evolving. If we went back in time before eukaryotes emerged could we use FLE to predict that eukaryotes would emerge, and that they would all require calmodulin? No. Genomicus has not put forward one methodology within FLE for predicting which proteins will become important in future lineages. None. All FLE does is look at what did evolve and then claim that this was the target. This is Texas Sharpshooting.

One of the premises of Darwinian theory is that all species are related by common ancestry. Meanwhile, the premise of the front-loading hypothesis is that the Metazoa etc. that we see today was the result of intent. If we take this as a basic premise of our hypothesis, we can then develop testable predictions. Confirmation of those predictions strengthens the hypothesis.

Suppose, for example, that we received a radio signal from space that consisted of a long string of prime numbers. From here, it would be perfectly reasonable to hypothesize that the sequence of the radio signal was the intended outcome by some alien intelligence. And this allows us to make testable predictions. For example, we might predict that after the first 50 prime numbers, the 51th prime number will appear next. Etc. As far as I can tell, FLE is similar. The FLE hypothesizes that the eukaryotes and Metazoa that we see today are an intended outcome. Taking this as our basic premise, predictions can be gleaned and tested.

Even worse, the predictions of FLE are exactly what we would predict from the non-teleological process of evolution.

Please read the OP and respond to the specific points I make there, where I argue that there is a prediction of the FLE that we would not make from the non-teleological model.

Is there any reason to think it is inevitable for any fold to arise?

Unless there are specific initial conditions, I would answer "no."

I mean it's obvious that the trend of evolution will be towards greater complexity but beyond that, is there anything that seems inevitable?

Well, for example, I would say the evolution of anti-biotic resistance to certain drugs is pretty inevitable.

But the only known initial condition is that the first life was single celled and so it was inevitable that any evolution would tend towards more complex critters.

Well, for example, I would say the evolution of anti-biotic resistance to certain drugs is pretty inevitable.

Which of course is totally irrelevant to this topic even though it is directly predicted by conventional Evolution Theories.

I don't think there's anything in the blind watchmaker that makes it inevitable for a specific fold to arise, in the absence of specified initial conditions. I.e., starting with just a few basic folds, there's no real guarantee that the blind watchmaker will be able to piece together a specific novel fold.

The thing in the blind watchmaker is chemistry. Proteins work because of their shape, they get their shape based on the chemistry of their interactions. The blind watchmaker would just offer every possible fold and the ones that work would stick and the ones that didn't would be discarded.

In hind sight, it might look like the ones that stuck were meant to be, but you're not looking at all the ones that didn't make it. That's were the sharpshooting fallacy comes into play. How many folds were tried and how many of those succeeded? If you had a brazillion folds and a handful make the cut, then looking back on only the handful to come to a conclusion of improbability wouldn't be good thinking.

It sure looks like the puddle was designed to fit within the pothole, and when you zoom in it might not make sense why that particular water molecule ended up in that particular place. The water is trying to go everywhere, but gravity pulls it into the puddle. Similarly, the proteins were trying to fold in every shape, but chemisty decides what works and what doesn't.

If you've got a lock and somebody keeps randomly making keys, its inevitable that eventually you'll get a key that unlocks it.

Doesn't that depend on the length of the sequence?

It depends on the mutation rate and the size of the genome. For most metazoans, the chances of the same mutation moving to fixation in two separate populations is low enough that it can be ignored for most purposes, but it should always be lurking in the background.

Seems to me that the phylogeny speeks better, I don't see how you could come to much of a conclusion from the sequences.

You might be interested in this article:

quote:

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Heidmann and his colleagues set out to re-activate one family of HERVs, called the HERV-K(HML2) family, an evolutionarily “young” family of retroviral elements. They aligned HERV-K(HML2) elements, determined their consensus sequence, and then constructed a retrovirus—Phoenix—from the consensus sequence by mutating existing HERV-K(HML2) copies.

In addition, the researchers showed that Phoenix could form particles capable of infecting mammalian cells in culture. Infectivity was very low, presumably because host cells have evolved mechanisms to resist uncontrolled virus propagation, as has been repeatedly observed for retroviruses from experimental animals.
http://genome.cshlp.org/site/press/Herv_K.xhtml

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I'm not liking Geno's approach... but don't get me wrong folks, I'd love to see some good evidence showing some planning involved in the evolution of life on Earth.

I do appreciate Geno bringing a breath of fresh air into these discussions. At least he has an informed opinion even if it turns out to be wrong.

Now that we've defined our terms, I ask the following question: in what way do I have "a large amount of data at their disposal, but only focuses on a small subset of that data. Random chance may give all the elements in that subset some kind of common property"?

That would be easy. You are focusing on what evolution did instead of what could have evolved. You claim that ubiquitin was front loaded while ignoring all of the other proteins that did not become functionally important in the metazoan lineage. You are looking for a bullet hole, and then painting a bull's eye around it.

One of the premises of Darwinian theory is that all species are related by common ancestry.

No it isn't. It is one of the CONCLUSIONS. It is what the evidence demonstrates. We don't need to assume common ancestry. We can demonstrate it. I am asking you to do the same for FLE.

Meanwhile, the premise of the front-loading hypothesis is that the Metazoa etc. that we see today was the result of intent.

Then I challenge that premise. Demonstrate that metazoans are the result of intent. Demonstrate that ubiquitin was intended to become functionally necessary in eukaryotes and how you are able to determine which proteins will become necessary in future generations.

Suppose, for example, that we received a radio signal from space that consisted of a long string of prime numbers. From here, it would be perfectly reasonable to hypothesize that the sequence of the radio signal was the intended outcome by some alien intelligence.

This is a poor analogy for a process that occurs through non-intelligent process (i.e. biological reproduction) right in front of our eyes.

Please read the OP and respond to the specific points I make there, where I argue that there is a prediction of the FLE that we would not make from the non-teleological model.

There is really only one point worth replying to which is the main point:

"From here we can make a prediction: key eukaryotic proteins will share deep homology with functional but unnecessary prokaryotic proteins. "

This is consistent with non-teleological evolution as well. You have not distinguished FLE from evolution in a testable manner. Since we can observe evolution in action, but lack any observation of your supposed designers, then it makes us wonder why evolution is not a satisfactory answer for the data in hand.

Edited by Taq, : No reason given.

From here we can make a prediction: key eukaryotic proteins will share deep homology with functional but unnecessary prokaryotic proteins. This is also what we would expect from non-teleological processes like evolution. In fact, Hermann Muller predicted that evolution would produce these relationships clear back in 1918...

No, Hermann Muller predicted that traits that are at first merely beneficial can become necessary. He did not predict anything at all along the lines that crucial eukaryotic proteins will share deep homology with functional but unnecessary (for life) prokaryotic proteins.

You also make the mistake of equating unnecessary with useless.

No. From the OP:

"So, by 'unnecessary but functional' I mean a gene that is not required by the basic prokaryote cell plan but does carry out a functional role in the LUCA."

One of the MAJOR problems with your model is assuming that a minimalistic genome comprised of only "necessary" proteins would be viable. It wouldn't.

Yes, it would be. At one point, under the non-teleological model, life consisted of only a few genes. In arguing against the possibility that the LUCA could have, under the non-telic model, consisted of only a minimal genome, you are going against what a number of scientific papers have proposed or implied.

For example:

"...the common belief that the hypothetical genome of LUCA should resemble those of the smallest extant genomes of obligate parasites is not supported by recent advances in computational genomics. Instead, a fairly complex genome similar to those of free-living prokaryotes, with a variety of functional capabilities including metabolic transformation, information processing, membrane/transport proteins and complex regulation, shared between the three domains of life, emerges as the most likely progenitor of life on Earth, with profound repercussions for planetary exploration and exobiology." ("A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective," 2006)

And:

"We argue that there is a commonality of mechanisms and protein sequences, shared between prokaryotes and eukaryotes for several modes of DNA repair, reflecting diversification from a minimal set of genes thought to represent the genome of the LUCA." ("DNA repair systems in archaea: mementos from the last universal common ancestor?" 1999)

Also:

"One hands-on approach to trying to uncover the biology of the LUCA has been to look for genes that are universal — that is, genes that all life forms possess. Once a list of these genes has been made, they also lead to another possibility: perhaps this list encapsulates the essence of cellular life — the minimum number of genes required to make a cell. In 1996, with the sequences of the first two bacterial genomes (Mycoplasma genitalium & Haemophilus influenzae) in hand, Arcady Mushegian & Eugene Koonin [Mushegian & Koonin 1996] tried exactly this...

...they tentatively concluded that LUCA stored its genetic information in RNA, not DNA, and made suggestions on how to further reduce the number of genes in their minimal genome. The work heralded the arrival of comparative genome studies, and there is no doubt that a good number of the genes in their 256-strong list do date back to the LUCA." (My Name is LUCA—The Last Universal Common Ancestor, Anthony Poole)

That RNA, and not DNA, was present in the LUCA is compatible with non-teleological evolution but isn't compatible with FLE.

All of this demonstrates that, not only is it compatible with non-teleological evolution that the LUCA had a minimal genome, but it's not at all unlikely from that perspective.

No, Hermann Muller predicted that traits that are at first merely beneficial can become necessary. He did not predict anything at all along the lines that crucial eukaryotic proteins will share deep homology with functional but unnecessary (for life) prokaryotic proteins.

"Functional but unnecessary" is the same as beneficial. They are one in the same. If these proteins did not produce beneficial function in prokaryotes then they would not be around 3 billion years later. They would have long since accumulated knockout mutations and gone the way of the dodo. In order for a protein to stick around in lineages it needs to be preserved by positive selection.

At one point, under the non-teleological model, life consisted of only a few genes. In arguing against the possibility that the LUCA could have, under the non-telic model, consisted of only a minimal genome, you are going against what a number of scientific papers have proposed or implied.

An organism with a minimal set of genes necessary for reproduction will go extinct as it is outcompeted by organisms that have functional but unnecessary genes that allow it to gain access to more resources. Any organism resembling LUCA would have those types of genes as LUCA is already well along a path of evolution. LUCA is not the first life. It is the last common ancestor of all extant life. Universally shared genes makes up the minimum genome for LUCA, not the entire thing.

You still have not demonstrated that the life we see today was even intended, much less intended by your proposed designers. You need to show us the bull's eye without a bullet hole in it, and then show us the bull's eye with the bullet hole in it. Do you understand what I am saying?

IOW, FLE is nothing more than the hope of some supernatural guidance in a nominally non-teleologic process.

Since when did the supernatural, gods, deities, etc., enter this discussion?