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Thursday, May 26, 2011

Junk & Jonathan: Part 8—Chapter 5

This is part 8 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the link to Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

Pseudogenes are the classic example of junk DNA and, as pointed out by many evolutionary biologists, they represent a difficult challenge for Intelligent Design Creationists. It's especially difficult to explain pseudogenes that are located in the same place in different species.

Chapter 5: Pseudogenes—Not so Pseudo After All

Chapter 5 is Pseudogenes—Not so Pseudo After All. This is the chapter where Jonathan Wells takes the standard creationist approach to the problem of pseudogenes—he denies that they exist!

Wells begins the chapter by reminding us that several evolutionary biologists have challenged the IDiots to come up with an explanation for pseudogenes, especially those that are found in closely related species. The usual suspects are quoted: Ken Miller, Douglas Futuyma, Jerry Coyne, Richard Dawkins, and John Avise. All of these challenges are based on solid evidence that most pseudogenes are actually pseudogenes (non-functional, degenerate copies of functional genes). But Wells says, "Yet there is growing evidence that many pseudogenes are not functionless, after all."

Types of Pseudogenes

There are three kinds of pseudogenes [Pseudogenes]. The first category contains genes that used to be functional in our ancestors but currently are non-functional. The best example is the human GULOP pseudogene that used to encode a key enzyme in the pathway for synthesis of vitamin C [Human GULOP Pseudogene]. This gene is active in most animals but it has become a pseudogene in primates and, independently, in a few other animals.


UPDATE: see: Creationists questioning pseudogenes: the GULO pseudogene

The second category includes genes that arise from a gene duplication event followed by inactivation of one of the copies. These pseudogenes tend to be located near their active siblings and they retain most of the features of the original gene except they can't produce an active product. Many of them are transcribed, especially if they have only recently become pseudogenes.

The third category is called "processed" pseudogenes. They arise when a mature mRNA molecule is copied into DNA by reverse transcriptase and the resulting DNA is integrated into the genome. Processed pseudogenes will usually not have any introns and when they integrate they will not be near a promoter. Many of them are truncated because the copying process was not complete. Processed pseudogenes were never able to produce their original functional product (protein or RNA) and they accumulate mutations at the rate expected from fixation of neutral alleles by random genetic drift.

The first two categories of pseudogene will also accumulate mutations once they become inactive. It's a characteristic of pseudogenes that the older they are the more mutations they have. Thus a pseudogene that is only found in chimpanzees and humans will have fewer mutations than one found in monkeys and apes and even fewer that one found in both rodents and primates.

The human genome contains about 20,000 pseudogenes, about the same as the number of genes. Many of these pseudogenes belong to the same family so not every gene has a corresponding pseudogene. About 6,000 of these pseudogenes arose from duplication events and 14,000 are processed. (The first category is rare.)

The pseudogenes in the "duplicated" category tend to be associated with large families of related genes. For example, in the human genome there are 414 pseudogenes in the olfactory receptor gene family [Olfactory Receptor Genes, The Evolution of Gene Families]. It's difficult to imagine how any substantial number of these genes could have a function.

As expected, the processed pseudogenes are scattered thoughout the genome because they insert at random. Roughly 2,000 of them are found in introns and this is further evidence that introns are mostly junk. Of course, if a processed pseudogene plunks down in an intron sequence it will be transcribed. Processed pseudogenes tend to come from functional genes that are abundantly expressed in the germ line. That's because the processed pseudogene has to be integrated into germ line DNA in order to be passed on to the progeny. Most of these genes are standard housekeeping genes. For example, there are 1300 pseudogenes derived from ribosomal protein genes.

Jonathan Wells describes the three categories but doesn't explain any of the other things I just mentioned.

Transcribed Pseudogenes

The first important section of his chapter is "Transcribed Pseudogenes." He quotes a number of papers showing that some pseudogenes are transcribed in humans, cows, and plants. In humans he claims that about one-fifth of pseudogenes are transcirbed at some time or another. This is probably an upper limit since most workers suggest that only 10% are transcribed.

I'm sure that some pseudogenes are transcibed. Many of the pseudogenes derived from gene duplication events will still be transcribed from active promoters even though they may not produce a functional product. Many of the processed pseudogenes will be transcribed because they are found within a gene (introns) or have fortuitously integrated near a promoter.

'Pseudogenes' That Encode Proteins

The key question is whether any pseudogenes produce a functional product and that's addressed in the next section: "'Pseudogenes' That Encode Proteins." Wells describes five studies where presumed pseudogenes were found to be genes after all (three in humans and two in fruit flies). Interesting but irrelevant. These genes are not junk. What about the other 20,000 real pseudogenes? Here's what Wells says at this point in the chapter ...
To be sure, only a relatively small proportion of known pseudogenes have been shown to encode proteins. But there is growing evidence that RNAs transcribed from pseudogenes perform essential functions in the cell
Here's where we get to the most important part of the chapter. It's in a section called "RNA Interference."

RNA Interference

RNA interference arises when one RNA molecule interferes with the expression of another. The easiest example to understand is when part of a gene is transcribed in the opposite direction producing what's called "antisense" RNA. This antisense RNA will hybridize to the functional mRNA and either block translation or induce degradation. In either case, less protein is made.

If a pseudogene is transcribed in the opposite direction then its antisense RNA could interfere with the expression of the normal gene. Wells gives us three examples of this phenomenon: one famous one from snails (1999), one from mouse oocytes (2008), and one from rice (2009). I don't know whether all these results have been confirmed but even if they have it doesn't amount to much. All kinds of strange things happen in biology and the fact that a few pseudogenes might have acquired a regulatory function isn't shocking. What about the other 20,000 pseudogenes?

Pseudogene Enhancement of Gene Expression

Theme

Genomes
& Junk DNA
Well, there's always the possibility that pseudogenes could enhance gene expression. The next section is "Pseudogene Enhancement of Gene Expression." Jonathan Wells begins this section with a description of the results on the mouse Mkrn-1-p1 pseudogene. The authors of this famous 2003 Nature paper claim that transcripts from the pseudogene protect the functional mRNA by shielding it from degradation. The title of their paper is "An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene" (Hirotsune et al., 2003).

Wells devotes three paragraphs to this important paper. There's only one slight problem. This work has been discredited in a 2006 PNAS paper with the title "The putatively functional Mkrn-1-p1 pseudogene is neither expressed nor imprinted nor does it regulate its source in trans." (Gray et., 2006) Oops!

Wells knows about this 2006 paper because he discusses it in Chapter 8 when he attacks the defenders of junk DNA. In chapter 5 he adds the following remark in parentheses, "Other biologists later challenged the Makorin-1 pseudogene results, which remain controversial." I think this is the only time when he mentions any legitimate scientific controversy.

There are three other examples of pseudogenes that might have an enhancement function: one from plants and two from humans. I don't know if these studies have been confirmed but even if they have they don't have much of an impact on the possible functions of the remaining 20,000 pseudogenes.

Sequence Conservation

The only significant evidence of widespread functionality of pseudogenes comes from two studies on sequence conservation. Wells covers this in a one-page section on "Sequence Conservation." The studies purport to show that pseudogene sequences are much more conserved than expected if they are really junk DNA. These studies have not been reproduced, as far as I know, and they fly in the face of much evidence to the contrary—evidence that Wells forgets to mention.

The first paper is a review by Balakirev and Ayala (2003). They review the possible functions of some pseudogenes in Drosophila and mammals. Some of them show evidence of sequence conservation. They conclude that most pseudogenes are probably functional. A study published that same year looked at all the known pseudogenes in the human genome and concluded that 95% of them evolved as though they had no function (i.e. they were not conserved) (Torrents et al., 2003)

The second paper that Wells mentions is Khachane and Harrison (2009). They identify 68 human pseudogenes whose sequences appear to be conserved in at least two other mammals. These are good candidates for functional genes.

The strange thing about this argument is that Wells doesn't believe in common descent so the evidence of sequence conservation really shouldn't have any meaning for him. Nevertheless, he says ...
How odd! As we saw in Chapter 2, Kenneth Miller, Richard Dawkins, Douglas Futuyma, Michael Shermer, Jerry Coyne and John Avise argue that pseudogenes confirm Darwinism because they are non-functional. But if we assume that Darwinism is true and then compare the DNA of unrelated organisms, sequence similarities imply that many of their pseudogenes are functional. So nonfunction supposedly implies Darwinism, but Darwinism plus sequence conservation implies function. When it comes to conserved pseudogenes, it seems, Darwinism saws off the very branch on which it sits.
For the record, if the majority of pseudogenes really are more conserved than expected from random mutations and fixation by random genetic drift then this would, indeed, be evidence that something is going on. Maybe they do have a function we don't know about. I don't think the evidence points in this direction at all—in fact much of the evidence contradicts it. Balakirov and Ayala (2003) are just speculating. I prefer the evidence of Torrents et al. (2003) suggesting that only a small number of potential pseudogenes have a function. This is consistent with the results of Khachane and Harrison (2009).

[If all 1,000 presumed pseudogenes turned out to be real genes then this moves about 0.06% of the genome from the junk category to the functional category. This isn't enough to save the IDiots.]

The Vitamin C Pseudogene

Finally, there's a section I haven't covered. It's titled "The Vitamin C Pseudogene." Wells has to address this particular pseudogene because it's the one that comes up most often when evolutionary biologists (e.g. Ken Miller and Jerry Coyne) criticize Intelligent Design Creationism. Here's what Wells says,
The evidence is not as straightforward as Miller and Coyne make it out to be, however, and their argument is ultimately circular. In any case, common ancestry and intelligent design are two different issues, and the vitamin C story would take us on a detour from the issue of junk DNA that's the focus of this book, so the details are omitted here and included in an appendix.
Which brings us to the Appendix: "The Vitamin C Pseudogene."

The main argument of scientists like Ken Miller and Jerry Coyne is not that the GULOP pseudogene exists. It's that the GULOP gene and its pseudogene are at the same location in the genomes of all mammals. In the primate lineage this gene is non-functional due to a number of mutations that make it impossible to produce a functional protein. Some of the same deactivating mutations are found in related species such as humans and chimpanzees. This suggests strongly that the non-functional pseudogene was inherited from a common ancestor. How do Intelligent Design Creationists deal with this evidence?

How does Wells respond?
... intelligent design and common ancestry are two different issues. Major ID proponents pointed this out before Miller wrote his book....Although some ID proponents (including me) question universal common ancestry on empirical grounds (as do some evolutionary biologists), intelligent design is not necessarily inconsistent with common ancestry.
I'm not sure what this means. Does it mean that people like Wells are completely bamboozled by this data since they can't refute either the evidence of common descent or the evidence of bad design? Other IDiots, like Michael Behe, only have to explain the bad design?

Jerry Coyne has published a similar argument but Wells attacks him on two fronts. First, he claims that human and chimpanzee Y chromosomes differ by 60 million nucleotide substitutions. If they really have a common ancestor then one would expect much greater sequence similarity. According to Wells, "If similarities in the vitamin C pseudogene are evidence for common ancestry, then differences in the Y chromosome are presumably evidence against it."

The Y chromosome paper is Hughes et al. (2010). Their results show that in orthologous regions of the Y chromosomes the human and chimp sequences are 98.3% identical. However, the chimp and human chromosomes differ in other regions because of large inserts and deletions. This is still evidence of common ancestry.

As usual, Wells is wanting to have his cake and eat it too.

The second attack is based on a number of quibbles. Coyne said that all primates need vitamin C in their diets but Wells points out that prosimians are primates and they can make vitamin C. Furthermore, according to Wells the requirement for vitamin C has only been established in nine species of monkeys. There are 251 other species and we don't know if they need vitamin C. Not only that, Coyne claimed that all primates have the same single nucleotide deletion in their GULOP pseudogene but Wells is quick to point out that only five primate sequences have been published.

Put that in your pipe and smoke it, Jerry Coyne! I assume that Wells is completely incapable of answering the challenge that's been issued and that's why he resorts to red herrings.

Continuing with this shotgun approach we quickly encounter several other arguments that are designed to distract from the main topic.
  • "Miller and Coyne rely on speculations about the motives of the designer or creator that have no legitimate place in natural science." (I hope you turned off your irony meter before reading that.)
  • Miller and Coyne have not provided any evidence to justify their claim that the GLO pseudogene is completely nonfunctional.
  • (Turn off your irony meter!) Their argument is circular. The similarities in sequence between chimp and human pseudogenes could be due to natural selection. "To break the circle, Miller and Coyne would either have to establish the recent ancestry of humans and chimps on other grounds (but why then bother invoking the vitamin C pseudogene at all?), or they would first have to establish that the vitamin C pseudogene has no function whatsoever (but this is impossible). So their argument not only fails to refute ID, but it also fails to establish that humans and chimps are descended from a common ancestor."
I feel a bit sorry for Ken Miller and Jerry Coyne. If this is the best the IDiots can do then why bother trying to argue with them in the first place?

Thus endeth Chapter 5.


Gray TA, Wilson A, Fortin PJ, Nicholls RD. (2006) The putatively functional Mkrn1-p1 pseudogene is neither expressed nor imprinted, nor does it regulate its source gene in trans. Proc. Natl. Acad. Sci. USA 103:12039-12044. [PDF]

Hirotsune, S., Yoshida, N., Chen, A., Garrett, L., Sugiyama, F., Takahashi, S., Yagami, K., Wynshaw-Boris, A., and Yoshiki, A. (2003) An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423:91-6. [PDF]

Hughes, J.F., Skaletsky, H., Pyntikova, T., Graves, T.A., van Daalen, S.K., Minx, P.J., Fulton, R.S., McGrath, S.D., Locke, D.P., Friedman, C., Trask, B.J., Mardis, E.R., Warren, W.C., Repping, S., Rozen, S., Wilson, R.K., and Page, D.C. (2010) Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature 463:536-539. [Nature]

Khachane, A.N., and Harrison, P.M. (2009) Assessing the genomic evidence for conserved transcribed pseudogenes under selection. BMC Genomics 15:435-449. [PDF]

Torrents, D., Suyama, M., Zdobnov, E., and Bork, P.. (2003) A genome-wide survey of human pseudogenes. Genome Res. 13:2559-2567. [PDF]

416 comments :

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Anonymous said...

Negative Entropy posted:
"OK, I have no idea which mutations occurred, nor how many were available in the wolves ancestral to our dogs."

So Negative Entropy cannot even give ballpark numbers for any creatures.
Can anyone else answer the type of questions that I have been asking?

What size groups are we talking about?
We might be talking about a group of primitive creatures that became horses. How many in such a group? Being generous perhaps 500? 1,000? 2,000?

How about groups of pre-humans? Groups of 50? 100? 500?

Just pick any creature and provide answers on these questions. The numbers will never be exact of course but ballpark numbers will get us started.

Anonymous said...

Moran referred to the 300 million people in the US and posted:

"Scientists have wrapped their minds around that fact for fifty years. It's one of the reasons why evolution is so very probable."

In other words according to Moran, "scientists" (ie. evolutionists) have been thinking that because the probabilities in a group of 300 million people is high, therefore evolution theory is probable.

If he really means that, then evolutionists have all made the same mindbogglingly foolish error that Moran has made. They have all used an irrelevant and incorrect number like 300 million as the size of groups that in the past are claimed to have evolved.

Is anyone going to acknowledge this or will everyone go quiet as if the facts will just go away?

Larry Moran said...

anonymous the IDiot asks,

Just pick any creature and provide answers on these questions. The numbers will never be exact of course but ballpark numbers will get us started.

OK. I'll play your silly game. I pick primitive nematodes. Population size 100 trillion.

Go for it. Prove that evolution is impossible.

Anonymous said...

Boy that Moran is a wily rascal. I have been asking about situations like wolves, horses, humans etc.
And he pulls out trillions of worms.

How about we deal with the wolves, horses, humans type of situation that I have been repeatedly asking about.

Nobody has offered up anything on them.

But how about this?
How about we take a population of 500 creatures. (They could be creatures leading to wolves, horses, humans whatever).

At the rate of 1 in 100 million mutations PER GENERATION, do people see that it is completely impossible for those mutations to actually accumulate in any creature to lead to the origin of a new genus?

This is the question that evolutionists never focus on.

Anyone here willing to look at this honestly and objectively?

What will happen now is a huge amount of tap dancing around the question.
And eventually someone will say that current thinking is that mutations that drive evolution do not occur at the nucleotide level but at the gene level.

Perhaps we could save time and have someone put forward that idea and save us all a lot of time that would be wasted showing that the rate of nucleotide change can never result in what we see in the fossil record.

Anonymous said...

To save time consider this:

http://www.ncbi.nlm.nih.gov/pubmed/15042088
"Powerful masticatory muscles are found in most primates, including chimpanzees and gorillas, and were part of a prominent adaptation of Australopithecus and Paranthropus, extinct genera of the family Hominidae. In contrast, masticatory muscles are considerably smaller in both modern and fossil members of Homo. The evolving hominid masticatory apparatus--traceable to a Late Miocene, chimpanzee-like morphology--shifted towards a pattern of gracilization nearly simultaneously with accelerated encephalization in early Homo. Here, we show that the gene encoding the predominant myosin heavy chain (MYH) expressed in these muscles was inactivated by a frameshifting mutation after the lineages leading to humans and chimpanzees diverged. Loss of this protein isoform is associated with marked size reductions in individual muscle fibres and entire masticatory muscles. Using the coding sequence for the myosin rod domains as a molecular clock, we estimate that this mutation appeared approximately 2.4 million years ago, predating the appearance of modern human body size and emigration of Homo from Africa. This represents the first proteomic distinction between humans and chimpanzees that can be correlated with a traceable anatomic imprint in the fossil record."

AND

http://en.wikipedia.org/wiki/Frameshift_mutation
"A frameshift mutation is a genetic mutation caused by indels (insertions or deletions) of a number of nucleotides that is not evenly divisible by three from a DNA sequence. Due to the triplet nature of gene expression by codons, the insertion or deletion can change the reading frame (the grouping of the codons), resulting in a completely different translation from the original."


Change is brought about by a package of related nucleotide changes.
And saltation is brought about by a package of related gene changes.

Larry Moran said...

anonymous says,

Boy that Moran is a wily rascal. I have been asking about situations like wolves, horses, humans etc.
And he pulls out trillions of worms.


Actually, you said, "Just pick any creature ..." So I did.

Now that you have implicitly conceded the point—that you are talking nonsense—we can chase the moving goalposts.

You've now focused attention on a specie of evolving mammal with a small population size. I know I'm going to regret this, but what the heck.

Evolutionary theory deals with this situation. If the effective population size is 1000 or less then modern evolutionary theory predicts that the population will probably go extinct. This has nothing to do with mutation rates.

However, lets assume an ancient wolf species with an effective population size of 1000. The average number of mutations in every newborn wolf cub will be approximately 129 [Mutation Rate]. Let's round that down to 100 mutations per individual per generation so you don't get too confused by the math.

So, in a population of 1000 primitive wolves that means roughly 100,000 new mutations per generation in the population.

I don't know what the generation time of ancient wolves might have been but let's assume that it's five years. Thus, in 5000 years there will be 1000 generations of wolves in this population. That means 100,000,000 new mutations in the population.

Most of these mutations will be in junk DNA and that's a good thing because otherwise such a massive amount of mutation would have killed the species. If 90% of the mutations are in junk DNA that still leaves 10 million mutations that could could lead to the evolution of a new species.

And that's only 5000 years—a mere blink of the eye in terms of evolution.

You task, should you have the courage to accept it, is to explain why 10 million new mutations is insufficient to account for evolution.

(Oops. I almost forgot. You don't accept the mutation rate I've used in this calculation. You prefer to use 30 new mutations per individual instead of 100. Okay. Explain why 3 million mutations is insufficient.)

Anonymous said...

Anus. The Utmost IDiot shows then unimaginable level of dishonesty and stupidity are required to remain an IDiot:

So Negative Entropy cannot even give ballpark numbers for any creatures.

Thus humans produced those dog breeds by magic?

Anus., I knew you would do this exactly. Thanks for giving us such clear examples of your dishonesty, here by ignoring the rest of my comment?

Again in case you want to pretend you missed it: Did humans use magic to produce those dog breeds?

Good bye you perfect example of an imbecile.

Anonymous said...

Well at least Moran is beginning to actually deal with the issue. That is a good step.
But notice that for some reason he changed my already very generous estimate of 500 up to 1,000.

Also note that Moran says:
"Oops. I [Moran] almost forgot. You don't accept the mutation rate I've used in this calculation. You prefer to use 30 new mutations per individual instead of 100."

I prefer to use the latest estimate from the study that was published this month. If that number is wrong then Moran had better show why. Instead he tries to sneak the idea by that that estimate is "my preference".

Also notice that the study estimated 60 mutations, not 30.
http://www.sciencedaily.com/releases/2011/06/110613012758.htm

Anonymous said...

Here is why Moran had to choose 1,000:
He posted:
"Evolutionary theory deals with this situation. If the effective population size is 1000 or less then modern evolutionary theory predicts that the population will probably go extinct. This has nothing to do with mutation rates."

That alone refutes evolution theory at the nucleotide level. Remember that current evolution theory bases itself greatly on groups that split from large groups. And it is claimed that evolution occurs in these small break-away groups.
This is an example where evolution ideas contradict each other, as I have mentioned.

Evolution at the nucleotide level is simply impossible.

Evolution [change] at the gene level is actually how change occurs.

Anonymous said...

Analyzing this a bit more. Consider:

http://www.ncbi.nlm.nih.gov/pubmed/15042088
"The evolving hominid masticatory apparatus--traceable to a Late Miocene, chimpanzee-like morphology--shifted towards a pattern of gracilization nearly simultaneously with accelerated encephalization [increased brain size]in early Homo [pre-humans].

Note it says that the myosin gene change was nearly simultaneous with the accelerated brain size increase.
Think about that for a moment. Think about how many other gene changes were required in total for that leap in brain size.
And they all must have happened "almost simultaneously".
Of course that is EXACTLY my point.
The saltation is a package of changes.

Anonymous said...

Anus. The Incredibly IDiotic IDiot said,

To save time consider this: [couple of abstracts about frameshift mutations, which Anus, in her incredible wisdom interpreted as a need for mutations to come in packages to produce a change]

Sorry Anus, but a frameshift mutation can happen with just one nucleotide inserted, just one deleted. The explanations tells you about any number, not a necessity for it to be a large number, as long as it is not divisible by three. Otherwise it is not a frameshift mutation. If the insertions/deletions were divisible by three you would still have a mutation, only not a frameshift one, and those mutations also produce changes. Anus. such an ignorant and imbecile troll.

You really have to go study first. Do you really think that playing with words such as "a number" will work better than understanding what these articles really talk about? Are you that much of an imbecile? Ups, yes you are! You are an IDiot! You don't care about knowledge, but about obfuscation and rhetoric. After all, that's what being a creationist is all about. Thanks for reminding me once again. Bye now Anus.

Anonymous said...

http://email.eva.mpg.de/~paabo/pdf1/Chou_Inactivation_PNAS_2002.pdf

"Thus, we used independent molecular approaches
to estimate that the inactivating mutation in the hydroxylase occurred just over 2 mya. No single one of these approaches is free of potential error. However, when taken together, they allow us to reasonably date the inactivation of the hydroxylase to the period just before the appearance of Homo."

"It is intriguing to note that, in all mammals studied so far (1), including the chimpanzee (4), the amount of Neu5Gc in the brain is always very low, no matter what the levels are in other organs of the body. This seems to be explained by selective down-regulation of CMAH gene expression in the mammalian
brain (44). A potentially testable hypothesis is that the low levels of residual brain Neu5Gc in other mammals somehow limited
brain expansion and that the human CMAH mutation released our ancestors from such a constraint."


AND

http://www.pnas.org/content/99/18/11736
"Taken together, these studies indicate that the CMAH gene was inactivated shortly before the time when brain expansion began in humankind's ancestry, ≈2.1–2.2 mya."

The CMAH mutation [change] is part of the package of changes that occurred at the dawn of pre-humans.

Boojum said...

He's really out done himself with his last point about frameshifts and packages. Tip from the wise anon one is a number not evenly divisible by three.

Larry Moran said...

anonymous the IDiot says,

Blah, blah, blah ...

I think you forgot the question. Let me help you out.

"Your task, should you have the courage to accept it, is to explain why 3 million new mutations over a period of 5,000 years is insufficient to account for evolution in a group of 1000 wolf-like mammals."

You seem to get easily distracted so I'll remind you of the question from time to time. After all, it was you who demanded that the facts be explained to you.

If you prefer to make it 6 million mutations then I'll be happy to accept that number as well.

Anonymous said...

http://en.wikipedia.org/wiki/Mutation#Harmful_mutations
"Studies of the fly Drosophila melanogaster suggest that if a mutation does change a protein, this will probably be harmful, with about 70 percent of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial."


Perhaps Moran was not familiar with this.

Anonymous said...

Here is why Moran had to choose 1,000:
He posted:
"Evolutionary theory deals with this situation. If the effective population size is 1000 or less then modern evolutionary theory predicts that the population will probably go extinct. This has nothing to do with mutation rates."

That alone refutes evolution theory at the nucleotide level. Remember that current evolution theory bases itself greatly on groups that split from large groups. And it is claimed that evolution occurs in these small break-away groups.
This is an example where evolution ideas contradict each other, as I have mentioned.

Evolution at the nucleotide level is simply impossible.

Evolution (change) at the gene level is actually how change occurs.

Anonymous said...

Anus the Utmost IDiot,

WHile yu keep at being an imbecile, and while Larry already showed you that you can get many mutations within a few generations, here is another question for you to ponder after the quote to your stupidity:

The CMAH mutation [change] is part of the package of changes that occurred at the dawn of pre-humans.

Do you think Anus, that it is impossible for mutations to occur in different individuals, then get together when those individuals mate and reproduce?

That's but one little detail that creationist rhetorics forgets, obvious things such as sex.

I could go on with a few others displays of stupidity on your part. But I think that's enough.

You are the utmost kind of imbecile. One who is proud of being one.

Jud said...

Anonymous writes:

Do people see the trick that Moran is playing here.

Yeah, it's called "mathematics."

Why are you still commenting if you've been reduced to characterizing math and science as "tricks"?

Anonymous said...

The 70% estimate of negative mutations means that 30% of mutations are neutral or weakly beneficial.
Applying this to the 500 size group that I suggested we get
900,000 single letter changes (neutral or weakly beneficial changes) over 5,000 years.

In fact, the situation is actually must worse than that when we analyze it further, but is that enough to show that evolution at the nucleotide level (point mutations) cannot be the correct explanation?

Anonymous said...

Moran posted:

"Evolutionary theory deals with this situation. If the effective population size is 1000 or less then modern evolutionary theory predicts that the population will probably go extinct. This has nothing to do with mutation rates."

Does this mean that evolution occurs only in groups greater than 1,000?

Anonymous said...

"The 70% estimate of negative mutations means that 30% of mutations are neutral or weakly beneficial.
Applying this to the 500 size group that I suggested we get
900,000 single letter changes (neutral or weakly beneficial changes) over 5,000 years.
In fact, the situation is actually must worse than that when we analyze it further, but is that enough to show that evolution at the nucleotide level (point mutations) cannot be the correct explanation?"


Does anyone think that a rate of 900,000 neutral or weakly beneficial mutations over 5,000 years (in a group of 500) is a sufficient rate to support the claims of evolution theory?

Anonymous said...

Let's look at another aspect of this.
What happens when a creature with a particular single letter mutation mates with another creature? That other creature does not have the same particular single letter change. After mating, the offspring will have a 50% chance of having that mutated single letter. Similarly with the next mating and each one afterwards.
The original single letter mutation will fade way. The chances of it continuing are astronomically low.
So not only do we have very few single letter mutations to begin with, but they fade away over the generations.

Is there anyone who can acknowledge this?

Larry Moran said...

anonymous the IDiot asks,

So not only do we have very few single letter mutations to begin with, but they fade away over the generations.

Is there anyone who can acknowledge this?


Me.

The probability of fixation of an allele depends on it's selective advantage (s) and the effective population size (N).

Most new alleles will be lost before they are fixed. This is basic population genetics. I'm sure you know all about it since you are an expert on evolution. I bet you could even give me the exact probability that an neutral allele (s=0) will become fixed in a population of 1000 wolves? Right?

Larry Moran said...

anonymous the IDiot asks,

Does anyone think that a rate of 900,000 neutral or weakly beneficial mutations over 5,000 years (in a group of 500) is a sufficient rate to support the claims of evolution theory?

I do. Why do you ask?

What do you think will happen as some of those weakly beneficial alleles become fixed in the population over time? Why wouldn't it be evolution since it meets the definition? Would it also be an example of Intelligent Design Creationism?

Anonymous said...

Moran is not getting it. Or pretending not to get it.
The mutations fade away, as I explained.
The assumed 900,000 single letter mutations do not even accumulate. Mutations arise and disappear over each generation.
Neither the neutral nor the weakly beneficial alleles become fixed in the population over time.
They arise and disappear as I explained.

Is everyone as confused as Moran?

Anonymous said...

Since Moran does not get it, perhaps he did not read this:

What happens when a creature with a particular single letter mutation mates with another creature? That other creature does not have the same particular mutated single letter. After mating, the offspring will have a 50% chance of having that mutated single letter. Similarly with the next mating and each one afterwards.
The original single letter mutation will fade way. The chances of it continuing are astronomically low.
So not only do we have very few single letter mutations to begin with, but they fade away over the generations.

Anonymous said...

Perhaps this is not clear.
I posted:
"After mating, the offspring will have a 50% chance of having that mutated single letter. Similarly with the next mating and each one afterwards.
The original single letter mutation will fade way."

The point is that with each generation it is 50% of the previous chance. For example the second generation is only a 25% chance (50% of 50%).
The third generation it is only 12.5% chance.
ETC.
Till it fades away completely.
Single letter mutations disappear over time. They do not accumulate.

If this is not clear please let me know.

Jud said...

Anonymous writes:

If this is not clear please let me know.

Oh, it's clear all right - clearly, demonstrably, and unequivocally wrong.

More than a century after Hardy-Weinberg was published, and many decades since its correctness has been demonstrated with real data so many times that anyone with a couple of brain cells to rub together must accept it as true, you put forward the population genetics equivalent of 2+2=5 and ask whether everyone understands you clearly.

M. Dionis said...

Anonymous wrote:

The point is that with each generation it is 50% of the previous chance. For example the second generation is only a 25% chance (50% of 50%).
The third generation it is only 12.5% chance.
ETC.
Till it fades away completely.
Single letter mutations disappear over time. They do not accumulate.


For the sake of the discussion, let's suppose your argument holds.
Now, let's read your own previous statement:

Evolution at the nucleotide level is simply impossible.

Evolution (change) at the gene level is actually how change occurs.


Let a gene mutate (whatever that would mean, in your last phrase) and look for its fate over time. The first generation of mating between the mutant and a normal individual has a probability of 50% to bear it [actually, it is not "probability to have it" but something more like "offspring gene frequency" since the mutant alleles necessarily exist in the 1st generation offspring]. The second generation will go down to 25% and so on.
Now, please explain why would your line of reasoning apply rather to single letter mutations but not to your "gene level mutations"?!

For the sake of biology, let's mention that the argument you produced is fallacious. Why? Because it supposes that mutant individuals (i.e. those having at least one mutant allele/gene) will mate only individuals which don't have it. This might be true for the first generation but less and less likely for the next generations (unless you don't consider that any couple produces only one offspring / generation, a birth rate which would neccessarily lead to the extinction of the population; we speak here about populations which survive over time). If the size of the population is relatively small, the mating choice is limited so the probability that a mutation gets fixed becomes higher. Of course, this probability is even more increased in case of favorable mutations (in the sense of fitness) since the average number of mutant offspring individuals is, by definition, higher than for non-mutants.

Anonymous said...

M. Dionis posted:
"Because it supposes that mutant individuals (i.e. those having at least one mutant allele/gene) will mate only individuals which don't have it."

We are working with the estimate of 60 single letter mutations per generation.
http://www.sciencedaily.com/releases/2011/06/110613012758.htm
"Each one of us receives approximately 60 new mutations in our genome from our parents."

AND

http://www.sciencedaily.com/releases/2011/06/110613012749.htm
"Your genome, or genetic code, is made up of six billion pieces of information, called nucleotides,"

If one creature has a mutation in a particular spot (letter), the chance that his mate has one at that spot is 1 in 100 million. (60 in 6 billion).

And even if that happens, the chance the offspring will find a mate like that is again 1 in 100 million.

Single letter mutations disappear.

After we get that settled, we can talk about genes.

Boojum said...

It's pretty appalling he is ignorant to this extent but we might as well explain exactly why he is wrong, instead of just marveling at the fact he's this stupid.

Say there is one initial point mutation, it has a 50% chance of being passed on to each of the organisms offspring, the organism breeds twice. There is a 25% chance the mutant allele will be passed to both offspring, a 25% chance it will be lost and a 50% chance it will be passed to only one of the two, i.e. 25% chance it will increase/decrease in frequency and a 50% chance it will remain constant.

Going down each generation the probability of any one descendant having the mutation halves but the allele frequency stays constant because the number of descendants doubles as you go down a generation. Your scenario seems to assume that each organism only produces one offspring which would mean that all alleles would be decreasing in frequency because the population would be halving each generation.

M. Dionis said...

Anonymous wrote:

If one creature has a mutation in a particular spot (letter), the chance that his mate has one at that spot is 1 in 100 million. (60 in 6 billion). [...]

You have completely missed the idea.
Fixation of a mutation doesn't point on two unrelated individuals who mate and have by chance the very same point mutation. It's about individuals with a common mutant ancestor which no longer form a negligible fraction of the population after some generations, so the chances for a mutation bearer individual to find another one for interbreeding are increasing. The HW law mentioned by Jud refers to essential conservation of two fixed mutant alleles and has been already established long time ago; if one mutation confers a slight fitness advantage over "normality", then the normal evolution of the population is to shift to the advantageous configuration (if some random fluctuation doesn't eliminate all advantaged individuals in an early stage). Go back to the basic tenets of (population) biology and reexamine them before posting nonsense.

Anonymous said...

Anus. The Utmost IDiot keeps showing amazing intellectual bankruptcy.

Anus., your calculations are naive ones at best. This is why there is a whole field called population genetics.

Example: if two individuals, each bearing 30 mutations, mate, then the offspring can have any number of such mutations, from 60 to 0 (plus newly introduced ones). The probability that no mutation would survive has to be calculated on the basis of the probability of each situation, the size of the population, and whether (and how much) the mutation confers a selective advantage/disadvantage, not in simple 50%s as you did. Be warned that this is also oversimplified, population genetics is much more and much better than that. Once you understand it you can answer Larry's question about the probability of fixation of a neutral mutation. Only after understanding population genetics can you claim that somebody else "doesn't get it." In the meantime you just show off yourself as an imbecile. Not an imbecile who just "doesn't get it," but one who tries hard and with pride not to get it. Also, changes in genes are mutations you IDiot.

Anus. by this time you should notice that we have mentioned population genetics these many times for very good reasons.

Now please go to hell.

Anonymous said...

"Does anyone think that a rate of 900,000 neutral or weakly beneficial mutations over 5,000 years (in a group of 500) is a sufficient rate to support the claims of evolution theory?"

Moran posted:
"I do. Why do you ask?
What do you think will happen as some of those weakly beneficial alleles become fixed in the population over time? Why wouldn't it be evolution since it meets the definition? Would it also be an example of Intelligent Design Creationism?"

The issue is whether a mutation rate that small will lead to the kind of changes we see in the fossil record. In other words will we see the origin of new species at different points in time (requiring extensive gene changes) being possible from such a low rate of single letter changes.

We also still have the problem of requiring groups larger than 1,000 which we can analyze later.

Anonymous said...

I have a question based on Moran's post:

"Evolutionary theory deals with this situation. If the effective population size is 1000 or less then modern evolutionary theory predicts that the population will probably go extinct. This has nothing to do with mutation rates."

Is evolution theory based on the idea that evolution only took place in groups of over 1,000?

Anonymous said...

In the example we have been developing, we have a population of 500 and we have calculated a total of 900,000 single letter mutations in 5 years.
We have assumed that each individual in this group of 500 has 6 billion single letters.
This mean that if we looked at the genomes of the 500 individuals we would be looking at 500 x 6 billion letters. In other words, 3 trillion letters.
And sprinkled within those 3 trillion letters are 900,000 mutated letters (neutral and weakly beneficial mutations).

Now I think that calculation is correct but before I continue could someone verify that please?

Anonymous said...

Another question is how do changes that require more than one letter occur?
Take our example.
Are we to think that randomly some mutated single letters form (for example) a 10 letter word IN ONE INDIVIDUAL? And the 10 letter combination has meaning. In other words a valid word.
This is something I have wondered about for a long time. Can someone explain that?

Jud said...

Anonymous writes:

And the 10 letter combination has meaning. In other words a valid word.

This is something I have wondered about for a long time. Can someone explain that?

I doubt you'll bother learning enough to understand the correct explanation, so I'm not going to trouble myself to lay out something extensive. I'll tell you a few things that should be enough to get you on the right track should you wish to bestir yourself.

- You're likely thinking about this the wrong way regarding "has meaning" and "valid word." Hint: If the odds against winning the lottery are huge, why does it happen so frequently?

- A one letter change can cause a difference in function (or change from non-function to functionality) in 10, or lots more than 10, other letters.

- If a change in function requires multiple mutations, those mutations need not happen simultaneously. They can happen over eons. (Your previous posts show you don't know the first thing about population genetics, and refuse to learn on your own even after being told where to go for the information, so I don't expect you to understand this point.)

Anonymous said...

It is useless to try talking to Jud (as I have said before).
I will remind people of the rate of change that we have seen in the example Moran and I worked out.
That rate of change cannot create changes quickly enough for what we see in the fossil record and the size of groups involved.
Not even close.
That is where we are in this discussion.

Is the rate that we have established, fast enough for the origin of new species within the time frames we see in the fossil record?
If anyone thinks so please explain how that would actually work - at that rate.

While we are it, nobody has answered the simple question:
Is evolution theory based on the idea that evolution only took place in groups of over 1,000?
If nobody can answer this question, you might as well give up trying to defend evolution theory.

Anonymous said...

In the example we have been developing, we have a population of 500 and we have calculated a total of 900,000 single letter mutations in 5 years.
We have assumed that each individual in this group of 500 has 6 billion single letters.
This mean that if we looked at the genomes of the 500 individuals we would be looking at 500 x 6 billion letters. In other words, 3 trillion letters.
And sprinkled within those 3 trillion letters are 900,000 mutated letters (neutral and weakly beneficial mutations).

Now I think that calculation is correct but before I continue could someone verify that please?

Can anyone answer this or is everyone going quiet again?

Anonymous said...

Moran posted:
"You've now focused attention on a specie of evolving mammal with a small population size. I know I'm going to regret this, but what the heck."

Now we see that Moran was right in regretting looking at the actual facts.
Evolution theory does not stand up to analysis.

But why would any honest researcher regret looking carefully and honestly at the facts?

Will everyone go quiet again, in order to not have to look at facts that contradict their preferred theory?

Anonymous said...

When we take a realistic look at the rate of mutation, the size of groups and the time-frames, we see that point mutations cannot explain the fossil record.
Point-mutation "errors" have nothing to do with the origin and development of species.

Evolution theory does not stand up to objective analysis.

Anonymous said...

As an analogy, let's consider a writer taking a book and using it as a base for writing a related but different book.
Does the author do that by modifying one letter here and another letter there? Hardly.
The author uses words and rearranges them in an ordered and meaningful way.
AND the author uses some of the IDEAS that were in the original book and brings them across to the new and different book.

That is the model.
We just need to look for what corresponds to "words" and "ideas" in the origin and development of creatures.

M. Dionis said...

Anonymous wrote:

As an analogy, let's consider a writer taking a book and using it as a base for writing a related but different book.
Does the author do that by modifying one letter here and another letter there? Hardly.
The author uses words and rearranges them in an ordered and meaningful way.
[...]
That is the model.


Not a perfect model but one has to hail it (since mutations are acting effectively "by modifying one letter here and another letter there", your "Hardly" is a nice comment regarding hypothetical author's writing skills, that is against ID). There is no known genome displaying a breaktrough brand new arrangement of the genes to be attributed to a wise designer playing hi-tech genetical engineering. The eventual major differences between related genomes are to be asserted mainly to casual replication non-point incidents somewhere on the evolutionary path (because they look like these).

Anonymous said...

Here is a first cut:

http://www.kedgley.school.nz/Kedgley/animalsite/Conservation%20Fact%20Sheets/DOCS/2/gecko.htm
DNA stands for deoxyribonucleic acid, and it is a bit like a little alphabet that has only four letters: A,G,C,and T. (Adenine, Guanine, Cytosine, and Thymine). So a gene is like a word made up of these four letters; a chromosome is like a sentence made up of gene-‘words’; and a cell is like a paragraph made up of chromosome-‘sentences’.


Nucleotide – letter
Base pair - ?
Gene- word (4 letters)
Chromosome – sentence
Cell – paragraph
? - section
Tissue/organ – chapter
Creature – book

Anonymous said...

M. Dionis posted:
"Not a perfect model but one has to hail it (since mutations are acting effectively "by modifying one letter here and another letter there", your "Hardly" is a nice comment regarding hypothetical author's writing skills, that is against ID). There is no known genome displaying a breaktrough brand new arrangement of the genes to be attributed to a wise designer playing hi-tech genetical engineering. The eventual major differences between related genomes are to be asserted mainly to casual replication non-point incidents somewhere on the evolutionary path (because they look like these)."

Does anyone understand what M. Dionis is saying?

Jud said...

M. Dionis writes:

Not a perfect model but one has to hail it (since mutations are acting effectively "by modifying one letter here and another letter there"

A better analogy IMO, and one that has been used before, is language changes. Through single-letter misspellings, other "mutations" brought about by variations in dialect/pronunciation, and borrowings from other languages through trade and invasions (which can be likened to genetic changes left through viral or bacterial-endosymbiotic action), languages change over hundreds or thousands of years into forms that would be unrecognizable to the speakers/writers of the ancestral tongue(s). As with genetic mutations eventually leading to speciation, though two language forms separated in time can be quite distinct from each other, there is always at every point along the timeline a community of speakers who all more or less understand roughly the same common language.

There is no known genome displaying a breakthyrough brand new arrangement of the genes

True, though one can find books with wholesale rearrangements of source wording - "design proponents" substituted for "creationists" for example - and even intermediate forms, such as "cdesign proponentsists."

Anonymous said...

To clarify:

Nucleotide – letter (A,C,G,T)
Base pair - ?
Gene- word
Chromosome – sentence
Cell – paragraph
? - section
Tissue/organ – chapter
Creature – book

M. Dionis said...

Anonymous wrote:

Does anyone understand what M. Dionis is saying?

Apparently yes, see Jud's comments. Basically, it goes like this: point mutations do occur in practice, an author willing to write a "related but different book" would "hardly" use this method to output it (according to your own considerations), so you produced an argument against ID. What we observe in the genomes doesn't look like the action of an mastermind overlord knowing what he's doing with "words" of definite meaning, but like the result of myriads of meaningless tests of a perfect ignorant (some of which are functional, therefore more or less preserved by natural selection). The Occam's razor cuts off the completely useless perfect ignorant from the theory.

Jud says:

A better analogy IMO, and one that has been used before, is language changes.[...]

Yes, this is a popular choice but it is somehow flawed since underlying mechanisms are ultimately distinct and not all the aspects of biological evolution can be put into correspondence with linguistic traits. I think the main utilities of the linguistic analogy are the idea of natural continuously occurring changes (with eventual variations in the speed) and the mental representation of speciation events.
Of course, analogy is the simplest method to obtain quick and erroneous results, so any analogy should be taken cum grano salis. For what's worth, I prefer to make a parallel between the genome and some programming language source code which has to be compiled and executed (after all, the genes are more like a set of instructions than a technical book). Compilation would be analoguous with creating proteins and running the compiled code would be equivalent to make function the organism (starting from the basic chemical level). Inactivation of a gene would be equivalent with commenting a piece of code and so on.
One has to hint a crucial difference with usual programming: while a programming language uses only a few key words and the overwhelming majority of "letter mutations" touching one of these reserved words produces a compilation error (the syntax becomes faulty), changing a genome base is usually not an absolute invalidating process at this level (some protein will still correspond to the mutated genome): that is due to the fact that programming languages are designed in a rational way, unlike the blind chemical machine translating DNA into polypeptidic chains.
Within this analogy, life is the replication of the source code with possible errors: the new generated codes might produce a scarse executable (or no executable at all) but the few ones which use better system resources will produce more offspring generation codes. The replication should happen ideally as Ctrl-A (Select All)/Ctrl-C (Copy)/Ctrl-V (Paste in new window), but actually there is no Ctrl-A: the copying system is more like a hasty Ctrl-C/Ctrl-V done successively on each letter of the original source code (an error-introducing procedure).
Finally, since genomes do look like source codes within which the traces of historical Ctrl-C/Ctrl-V are perfectly recognizable (which is remarkably significant when looking at similar "meaningless commented lines" with no functional role), one can make a strong case for common descent (i.e. the codes can be traced back to some original piece of code from the past which served as a basis for further spurious modifications occurred during Ctrl-C/Ctrl-V processes). Of course, one should always keep in mind the limits of this analogy: if one might simulate a silent gene as a conditional compilation source code (following say an #ifndef blabla), the genomes and the corresponding organisms exhibit a much more complex behavior than our analogic codes and executables.

Anonymous said...

M.Dionis posted:
"Basically, it goes like this: point mutations do occur in practice, an author willing to write a "related but different book" would "hardly" use this method to output it (according to your own considerations), so you produced an argument against ID."

I did not say that "the author" (which is NATURE) used point mutation. Quite the opposite.
I don't think you have been following what I have posted.
("Hardly" means not at all.)

AND
I have shown that at the rate of mutation and the size of groups and the timeframes we see for the origin of new creatures - we must conclude that evolution based on point mutations cannot come close to explaining what we see in the fossil record.

Because evolution based on point mutations is impossible, we must look at a different form of explanation.

Anonymous said...

Sweden debt clock:
http://www.weidemyr.com/debt/index-en.shtml

U.S. debt clock:
http://www.usdebtclock.org/

Canada debt clock:
http://www.debtclock.ca/

The phrase "we are all socialists now" can be restated as "we are all in big debt now".

Anonymous said...

Update:

Nucleotide – letter (A,C,G,T)
Base pair - ?
Gene - word
Chromosome – sentence
Cell – paragraph
Tissue/organ - section
Tissue/organ system – chapter
Creature – book
NATURE - library


Can anyone suggest how base pairs fits into this picture?

Jud said...

M. Dionis writes:

I think the main utilities of the linguistic analogy are the idea of natural continuously occurring changes (with eventual variations in the speed) and the mental representation of speciation events.
Of course, analogy is the simplest method to obtain quick and erroneous results, so any analogy should be taken cum grano salis.


First, let me say that somehow "with a grain of salt" sounds better in Latin. :-)

I agree with the points you make in favor of the language evolution analogy, plus one other I particularly like: today's mistakes become tomorrow's new languages/species, without the necessity of any overall guiding plan. In fact guidance in both cases is in the direction of continuing the old species/language, so without unintended, unguided errors there would be no evolution.

In both cases, evolution is inevitable and effortless (in the sense that no effort directed toward change is required). On the other hand, I would guess it is the case that a greater proportion of language errors is assimilated into the lingua franca than the proportion of mutations that becomes fixed in a population. (Would love to see some academic linguistic history papers to get a better idea of this.)

There are certainly also advantages in analogizing to programming, though as you point out, in programming there is the opposite problem that almost no "mutations" become fixed.

Anonymous said...

Nucleotide – letter (A,C,G,T)
Base pair - ?
Gene - word
Chromosome – sentence
Cell – paragraph
Tissue/organ - section
Tissue/organ system – chapter
Creature – book
NATURE - library

It might be interesting to analyze this a bit more. For example, is there good reason to compare chromosomes (composed of genes) to sentences?

Beginning with genes:
http://en.wikipedia.org/wiki/Gene
"A gene is a unit of heredity in a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism."

http://en.wikipedia.org/wiki/Chromosome
"A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.
Chromosomes are the essential unit for cellular division and must be replicated, divided, and passed successfully to their daughter cells so as to ensure the genetic diversity and survival of their progeny."

To be continued.

Anonymous said...

There is some reason to compare chromosomes to sentences.
A sentence is made up of words. But there is a new element as well. Some words function as subjects, some as verbs, some as objects. And the sentence has a structure (rules) about how the words can be "packaged".

We might compare the rules and packaging of words in constructing sentences to the rules and packaging of genes etc. into a chromosome.

But a word (eg. table) is inert on its own. It has a meaning but no action. It takes a sentence to have action. (Eg. "The boy threw the ball").
So if we compare a gene to a word then we are overlooking the fact that the gene itself can be used to drive action. To drive the generation of a protein.

So perhaps the gene is more like a sentence.
Thoughts?

Anonymous said...

Just came upon this:
http://www.sciencedaily.com/releases/2011/06/110629132546.htm

"Palaeontologists have uncovered half-a-billion-year-old fossils demonstrating that primitive animals had excellent vision. An international team led by scientists from the South Australian Museum and the University of Adelaide found the exquisite fossils, which look like squashed eyes from a recently swatted fly.
Their discovery reveals that some of the earliest animals possessed very powerful vision; similar eyes are found in many living insects, such as robber flies. Sharp vision must therefore have evolved very rapidly, soon after the first predators appeared during the 'Cambrian Explosion' of life that began around 540 million years ago."

Once more we see that evolution by point-mutation cannot explain the fossil record.
But certainly feel free to make up some story and tap dance around this as much as you like.

People who are willing to look at this subject objectively will realize it is necessary to look for some other kind of theory.

Anonymous said...

Anonymous ID advocate says,
People who are willing to look at this subject objectively will realize it is necessary to look for some other kind of theory.

Yes, and you are the shining example of objectivity.

A single point mutation did not create an eye. A series of incremental steps, from an existing simple photo receptor to many different solutions to the same problem in different animal phyla exactly fits the evolution paradigm.

Sadly your criticism is so predictable that there is already a blog about it.

http://whyevolutionistrue.wordpress.com/2011/06/29/eyes-from-the-deep-past/

http://pandasthumb.org/archives/2011/06/complex-eyes-in.html

/TheOtherJim

Anonymous said...

The other Jim posted:
"A single point mutation did not create an eye. A series of incremental steps, from an existing simple photo receptor to many different solutions to the same problem in different animal phyla exactly fits the evolution paradigm."

That is the standard summary of evolution thinking.
The problem with that thinking is that as I have shown, with the rate of mutation, the time frames and the size of groups it cannot explain what we see in the fossil record.

I have shown that, with the example that Moran and I were working through.

Larry Moran said...

anonymous, the IDiot, says,

I have shown that, with the example that Moran and I were working through.

Not on this planet, you didn't.

Anonymous said...

It looks like Dr. Moran is still here. I thought he had left when we analyzed it down to the specifics of rate of mutation and group size.

Since Moran is here, let me ask this basic question again:
"Is evolution theory based on the idea that evolution only took place in groups of over 1,000?"

Boojum said...

If you actually did a basic maths check you'd kinda realize you've shown nothing anon. For example take the chimp genome and compare it to the human genome, around 40 million mutations separate the two, which comes out as 20 million per lineage over 4 million years, or around 5 a year. While your maths 900,000/5000 shows a mutation rate of 180 per year. You then take this to somehow magically shows evolution is impossible without any further steps and scratch your head at why everyone here thinks your a moron.

Anonymous said...

40 million randomly distributed neutral and weakly beneficial mutations?
40 million randomly distributed point-mutations? We have not even scratched the surface of the problem.

And another question for you Boojum:
"Is evolution theory based on the idea that evolution only took place in groups of over 1,000?"

Folks will have to do a lot more than throw out insults.

Jud said...

Dr. Moran writes:

Not on this planet, you didn't.

Oh sure he did, by his own standards of "proof." But why bother with such a boring conversation about a rather interesting article?

It's wonderful that we've now got fossils of a rarely fossilized body part from "only" about 25-30 million years after the beginning of the Cambrian, and about 100 million years after molecular biology retrodicts the initial evolution of eyes.

Jud said...

The mathematics of population genetics were worked out a long time ago. Have a look at faculty.uca.edu/benw/biol4415/PopGNotes.pdf for example. There's also plenty of scholarly literature on effective population size and human evolution, available for anyone who wishes to study it.

The Other Jim said...

@ ID-Anonymous, who claims

That is the standard summary of evolution thinking.
The problem with that thinking is that as I have shown, with the rate of mutation, the time frames and the size of groups it cannot explain what we see in the fossil record.


Sorry, but you have not shown anything but a deep misunderstanding.

Doesn't it seem odd to you that many other groups are quite satisfied that the math fits?

http://genome.cshlp.org/content/early/2011/04/25/gr.119636.110.abstract

As with all ID'ers, you start with the belief that evolution is not possible without God (and cut the bullshit pretending the intelligence can be something else). Then, with the intellectual honesty of Ben Stein, you pretend that napkin math in a blog post upends a major theory. If this idea was so revolutionary, the big journals like Nature and Science you fall over themselves to publish something that killed a major theory. So why don't you take your post and attempt to publish them?

/TheOtherJim

Boojum said...

Anon spoke:
"40 million randomly distributed neutral and weakly beneficial mutations?
40 million randomly distributed point-mutations? We have not even scratched the surface of the problem."

Um are you retarded? If I restricted myself to point mutations that would drive the required mutation rate down to less than 4.37 per year which makes you math even worse.

Anonymous said...

Is evolution theory based on the idea that evolution only took place in groups of over 1,000?

Could someone answer this question please?

Anonymous said...

Here is a quote from the reference that was recommended above:
http://faculty.uca.edu/benw/biol4415/PopGNotes.pdf
"So if you have a population of 100 elephant seals, 50 males and 50 females, N = 100,
but Ne = 200/51 = 3.9. In other words, a population of 100 elephant seals in which only
one male mates will have as much genetic drift and inbreeding as a population of four
elephant seals in which all members could mate! This has a lot of implications for
conservation and breeding programs."


The example uses a group size of 100.
But Moran has already said:
"Evolutionary theory deals with this situation. If the effective population size is 1000 or less then modern evolutionary theory predicts that the population will probably go extinct. This has nothing to do with mutation rates."

So which is it?

Will someone actually face up to this question?

Jud said...

Just fascinating stuff on genetics and human evolution. Here are two quotes from a 2008 paper by Relethford in the journal Heredity:

The three out-of-Africa expansions detected in Templeton's multilocus analysis correlate temporally in an interesting way with the fossil record (Relethford, 2007). The earliest range expansion corresponds to the initial appearance and dispersal out of Africa of H. erectus. The second range expansion corresponds to a rapid increase in cranial capacity that took place about 700 000 years ago and overlaps with the appearance of H. heidelbergensis. The third and most recent out-of-Africa expansion corresponds to dates suggested for the dispersal of anatomically modern humans. Given the large confidence intervals typical of coalescent analysis, this correspondence should be taken as suggestive and not conclusive, but the apparent congruence of the fossil and genetic records is interesting and deserves continued attention, particularly as data on more low-recombination DNA regions become available.

* * *

When applied to data from living human populations, such estimates typically suggest a long-term average of 10 000 individuals of reproductive age (Relethford, 2001b). Because long-term population size reflects a harmonic mean over time, this figure further suggests that humans have recently expanded from a relatively small number of ancestors.... The situation is not that simple, however, as the genetic estimates of population size are effective population sizes that can differ greatly from actual census size and the latter is not a proxy for the former. Effective size can be considerably less than census size. Eller et al. (2004) show that a model of extinction and recolonization of local populations with reasonable parameters could result in a long-term census size of several hundred thousand individuals and still produce an effective population size of about 10 000.

Anonymous said...

http://www.sciencedaily.com/releases/2011/06/110629132546.htm
"The fossil compound eyes were found on Kangaroo Island, South Australia and are 515 million years old. They have over 3000 lenses, making them more powerful than anything from that era, and probably belonged to an active predator that was capable of seeing in dim light.
Their discovery reveals that some of the earliest animals possessed very powerful vision; similar eyes are found in many living insects, such as robber flies. Sharp vision must therefore have evolved very rapidly, soon after the first predators appeared during the 'Cambrian Explosion' of life that began around 540 million years ago."

Let's analyze this and be more precise.
According to wikipedia the Cambrian period began ~540 mya and the Cambrian Explosion began ~530 mya.

They date the fossil eye found, at ~515 mya.
The article says that:
"Sharp vision must therefore have evolved very rapidly, soon after the first predators appeared during the 'Cambrian Explosion'"

Putting this together we have the eye appearing ~515 mya and the presumed evolution of that eye taking place after the beginning of the Cambrian Explosion (after ~530 mya).
So that period of "very rapid evolution" is claimed to occur in the 15 million year period between 530 mya and 515 mya.

Correct so far?

Anonymous said...

Here is where we are in the analysis:

Putting this together we have the eye (MENTIONED IN THE ARTICLE) appearing ~515 mya and the presumed evolution THAT LED TO THAT EYE taking place after the beginning of the Cambrian Explosion (after ~530 mya).
So that period of "very rapid evolution" is claimed to occur in the 15 million year period between 530 mya and 515 mya.

But that 15 million year estimate is still much overestimated.
Let's consider what the article said.
It said:
"Sharp vision must therefore have evolved very rapidly, soon after the first predators appeared during the 'Cambrian Explosion"

The article does not say that sharp vision evolved very rapidly after the beginning of the Cambrian Explosion (~230 mya). It says that rapid evolution occurred "soon after the first predators appeared during the 'Cambrian Explosion".

So when did the "first predators" begin to appear? Evolutionists would not say they appeared right at the beginning. Evolutionists would claim it took some time.
So we are not looking at the period from ~530 million years back but from some later period, for example from ~520 mya.

In which case, the rapid eye evolution would have taken place in 5 million years (520 minus 515).

Right?

Anonymous said...

Here is where our analysis so far has led:
"The rapid eye evolution would have taken place over 5 million years (520 minus 515)."

But this still overestimates the time frame.
Here is what the article says:
"The fossil compound eyes were found on Kangaroo Island, South Australia and are 515 million years old."

If this compound "powerful vision" eye was around at 515 mya, the great likelihood is that such an eye existed prior to that as well. It would be quite unusual if the one found was the very earliest example of that kind of eye.

We could consider that that form of eye could well have existed 5 million years earlier, making it 520 mya.
That would make it the same time period as the rapid appearance of the creatures associated with the Cambrian Explosion (520 mya)
In other words, the explosion of new creatures included the new form of eyes.

If that is the case (and it looks like it may well have been) then we are looking at a SALTATION.

If anyone disagrees with this, please let us know specifically where your disagreement lies with what I have said.

Jud said...

Nice to see yet another confirmation of the predictions of evolutionary theory, see http://www.jstor.org/pss/49593 .

Anonymous said...

Is evolution theory based on the idea that evolution only took place in groups of over 1,000?

The Other Jim said...

@ID-Anonymous,

Your 520mya estimate is incorrect.

Cnidera and Arthropods share a number of "master switch" genetic regulators in eye development, implying common ancestry (http://www.pnas.org/content/107/32/14263)

Cnidera and arthopods shared a common ancestor ~990mya, so the "origin" of this share pathway, and therefore the eye, is >990mya.

Jud said...

Anonymous writes:

The example uses a group size of 100.

But Moran has already said:
"Evolutionary theory deals with this situation. If the effective population size is 1000 or less then modern evolutionary theory predicts that the population will probably go extinct. This has nothing to do with mutation rates."


So which is it?

Will someone actually face up to this question?

The question of why people use lowish "round" numbers like 100 in examples? Why, to make the math simple enough even an IDiot should be able to grasp it, of course. Did you seriously not understand that 100 was used in the example to make the math easy?

Then why did Dr. Moran use 1000 in his statement? Because it is a statement of fact, rather than a math example for beginners. Are you able to grasp the distinction? This is not intended to be an insult - the types of questions you ask lead me to honestly wonder how much you are understanding of what you read.

Jud said...

Anonymous writes:

First, quoting Dr. Moran:

If the effective population size is 1000 or less then modern evolutionary theory predicts that the population will probably go extinct.

Then, speaking for himself:

Is evolution theory based on the idea that evolution only took place in groups of over 1,000?

With apologies to The Princess Bride: You keep using that phrase, "groups of over 1,000." I do not think it means what you think it means.

If you'd like to begin to get some idea of the vast gap between what Dr. Moran actually said and what you appear to be saying, you could start by reviewing the second quoted paragraph from my July 4th 9:55 am comment.

And that's only one aspect of your apparent misconception. Another is that Dr. Moran said that chances are groups with effective population sizes of 1000 or lower would go extinct, which is not at all the same as saying evolution doesn't take place within those groups, or that those groups cannot contribute to the evolution of larger populations. (E.g., studies appear to show genetic contributions to modern humans from extinct groups such as Neanderthals.)

Anonymous said...

Finally someone supports Moran's statement that evolution theory is based on the idea that evolution only took place in groups of over 1,000.

A corollary of this concerns allopatric speciation.
The idea is that a small group breaks away from a larger group and evolution occurs in the small breakaway group.
We can conclude then that these break away groups were over 1,000.
And the groups they broke away from must have been much larger than 1,000.

The question is whether there is fossil evidence for the existence of such large groups in ALL the situations where evolution is claimed to have occurred.

Anonymous said...

The other jim posted:
"Your 520mya estimate is incorrect.
Cnidera and Arthropods share a number of "master switch" genetic regulators in eye development, implying common ancestry (http://www.pnas.org/content/107/32/14263)
Cnidera and arthopods shared a common ancestor ~990mya, so the "origin" of this share pathway, and therefore the eye, is >990mya."

I just knew that someone would choose to misinterpret what I am saying.
I am talking about the "very rapid evolution" that the article is talking about. Not any supposed "evolution" that occurred before that.
The "very rapid evolution" that the article is talking about seems to have occurred as a saltation circa 520 mya.

Anonymous said...

By the way, saltations such as I am pointing out were hypothesized by people such as Goldschmidt. We are now finding evidence of those saltations.

And if anyone wants to learn about how the intelligence of the cell and of NATURE directs "evolution" (change), check out the work of James A. Shapiro.

The Other Jim said...

The "very rapid evolution" that the article is talking about seems to have occurred as a saltation circa 520 mya.

Sigh. If you bothered to read the links I posted on Sunday, July 03, 2011, you would have noticed that;

1) Trilobites of the same age already have complex eyes. Yes, these ones are thought to be more complex, but the distant ancestor of both already had complex eyes.
2) So did Anomilacarus, also a big -eyed arthopod of the same age, found way back with the Burgess Shale discoveries.
3) The Cambrian Explosion is just an explosion of hard-bodied organisms. Not the "start" of animal life as is claimed. Molecular evidence suggests animals are much older. For instance, the ~980 mya estimate was for the divergence between jellyfish and arthropods.

So, in short, do your homework. It is painful to see someone argue so much about completely incorrect facts.

Jud said...

Anonymous writes:

Finally someone supports Moran's statement that evolution theory is based on the idea that evolution only took place in groups of over 1,000.

Of course that's the precise opposite of what I said. I pointed out your abysmal misunderstanding, I did not join in it.

Whether it's stubbornness, ignorance, stupidity, or a combination of all three I don't know (and that's giving you credit for honesty, which may or may not be merited), but it really doesn't matter in the end.

Anonymous said...

http://www.sciencedaily.com/releases/2011/06/110629132546.htm
"Sharp vision must therefore have evolved very rapidly, soon after the first predators appeared during the 'Cambrian Explosion' of life that began around 540 million years ago."

Folks here seem to want to ignore this.

I have shown that this rapid evolution likely took place around 520 mya.

Anonymous said...

Jud,

By now you should be able to notice that Anus. The Utmost IDiot does not care to understand. Anus. will quote-mine you in your face. That Anus. would not know what the word "probably" does when put before the words "go extinct" should shock us for the level of plain stupidity. But it is not stupidity but plain dishonest rhetoric (in other words bullshitery), when Anus uses that phrase to conclude that evolutionary theory means that evolution only (so he knows that some words modify the meaning of a sentence!) happens in populations of more than 1000 individuals.

This is not just ignorance. This is plain dishonest crap. I would let the imbecile alone with those ramblings. We have enough to show what is required to support ID: dishonesty, rhetorics, wilful ignorance. But we should not be too surprised. After all, imagine what it must be if you lie to try and disguise cherished beliefs, such as the belief in a god, as if it were science, knowing that it is such a big lie. Knowing that those cherished beliefs are being dressed in hypocrisy. Something has to break inside of them. Anus. The Utmost IDiot is a clear example of the kind of low-life that either you have to be, or you have to become to support ID.

Jud said...

Negative Entropy writes:

This is not just ignorance. This is plain dishonest crap.

Well, without bothering to make accusations of dishonesty, we certainly know it's crap. The somewhat remarkable thing about Anonymous, even among IDiots who've commented on this blog, is that surely he realizes at this point the only persuasion he's engaged in as regards ID is negative, i.e., no one could look at what Anonymous has written and find it coherent or informed, let alone persuasive. Quite the opposite, he's elicited a great deal of persuasive pro-evolution science in response to his comments, and has obviously not been able to deal scientifically with any of it. It seems to me that under these circumstances, there is something compulsive and almost pathetic about his continued comments, and continued pleading for others to respond.

I would let the imbecile alone with those ramblings.

You're right, of course.

The Other Jim said...

Anonymous continues to claim

I have shown that this rapid evolution likely took place around 520 mya.

No you have not.

There were arthropods in the Precambrian. Parvancorina, Bomakellia, and the "soft bodied trilobite" from the Flinders site. Since all Cambrian arthropods have eyes, common ancestry suggests that the origin of the eye is older than 520 mya. Spriggina may be an arthropod (but may not be). It also had pits on it's head, consistent with a place for eyes. Again, older eyes.

To borrow your tactic, I have shown that eyes are older than 520 mya. Intelligent design proponent trolls here seem to want to ignore this.

Anonymous said...

The folks here do not have the evidence on their side.
That is why they ignore the evidence and concentrate on attacking me.

We have seen saltations in the development of human beings and we are now seeing one in the development of the eye.
The article on the eye is not saying that before 520 mya there was no eye type structure. The article says that sharp vision must have evolved very rapidly from whatever was there before.
In other words there was a saltation.

People can pretend all they like and attack me.
I am interested in the facts as they are described in scientific articles.

Anonymous said...

It is surprising to me that people argue so strenuously against saltations.

Saltations are not contrary to evolution theory.
If someone presented very compelling evidence for saltations, evolutionists would say that that was consistent with evolution theory.

In fact, evolutionists would point to people like Goldschmidt (and others) and say that saltations had been hypothesized and predicted.

Anonymous said...

http://www.sciencedaily.com/releases/2011/06/110629132546.htm
"Their discovery reveals that some of the earliest animals possessed very powerful vision; similar eyes are found in many living insects, such as robber flies. Sharp vision must therefore have evolved very rapidly, soon after the first predators appeared during the 'Cambrian Explosion' of life that began around 540 million years ago."

Anonymous said...

From the published scientific article:
http://www.nature.com/nature/journal/v474/n7353/full/nature10097.html#/comments
"The eyes are more complex than those known from contemporaneous trilobites and are as advanced as those of many living forms. They provide further evidence that the Cambrian explosion involved rapid innovation in fine-scale anatomy as well as gross morphology, and are consistent with the concept that the development of advanced vision helped to drive this great evolutionary event."

The eye saltation was part of the larger set of Cambrian Explosion saltations.

That is why it is called an "explosion".

The Other Jim said...

Let's focus on my point. I will go very slowly.

From the article...

The evolution of powerful vision is one of the most important correlates of the Cambrian explosion and has been proposed as a trigger for this event. However, although the overall shapes of eyes are known for many Cambrian organisms intricate details of the visual surface are known only for trilobites and the tiny stem-crustacean cambropachycopids, which have bizarre, proportionately huge and medially fused compound eyes. In addition, indistinct ommatidia are preserved in a few Chengjiang fossils, including the non-biomineralized arthropods Isoxys and Cindarella. Isoxys inhabited both dim and bright pelagic environments whereas Cindarella probably inhabited a bright benthos. The specimens described here represent the first microanatomical evidence confirming the view that highly developed vision in the Early Cambrian was not restricted to trilobites . Furthermore, in possessing more and larger lenses, plus a distinct bright zone, they are substantially more complex than contemporaneous trilobite eyes, which are often assumed to be among the most powerful visual organs of their time.

[references removed]

So triolbites already had eyes. So did a bunch of other arthropods. There are fossils interpreted as relatives of trilobites ~555 mya (as stated in my post above). Some people people think it is much older, like ~698mya (see http://www.timetree.org/pdf/Pisani2009Chap29.pdf). But we will go with 555mya, as a conservative estimate. Assuming the arthopod "proto-eye" evolved once, it is older than 555 mya.

And the age of the fossils in the paper?

We have recovered exceptionally preserved, large compound eyes (Fig. 1) from the Early Cambrian (Series 2, Stage 4; ~515 Myr ago) Emu Bay Shale Konservat-Lagerstätte at Buck Quarry, Big Gully, on Kangaroo Island in South Australia

555,000,000 - 515,000,000 = 40,000,000

Assuming the arthopod LCA had no eye, then the oldest this could be is 698,000,000 - 515,000,000 = 183,000,000

Is an event that took >40 million years (i.e. 60% of the time since the KT boundary) a saltataion?

I am going to have to say no.

The Other Jim said...

Second point.

In response to learning that eyes did not poof into the fossil record ~520mya, you say;

The article on the eye is not saying that before 520 mya there was no eye type structure. The article says that sharp vision must have evolved very rapidly from whatever was there before. In other words there was a saltation.

Are you now you are calling the refinement of an already existing, complex organ from from having "not-so-sharp vision" to "sharp vision" a saltation?

Anonymous said...

http://www.nature.com/nature/journal/v474/n7353/full/nature10097.html#/comments
"The eyes are more complex than those known from contemporaneous trilobites and are as advanced as those of many living forms. They provide further evidence that the Cambrian explosion involved rapid innovation in fine-scale anatomy as well as gross morphology, and are consistent with the concept that the development of advanced vision helped to drive this great evolutionary event."

I have already shown that the conservative estimate of this "rapid innovation" ("as advanced as those of many living forms") is that it occurred circa 520 mya.

Anonymous said...

http://www.nature.com/nature/journal/v474/n7353/full/nature10097.html
Here we report exceptionally preserved fossil eyes from the Early Cambrian (~515 million years ago) Emu Bay Shale of South Australia, revealing that some of the earliest arthropods possessed highly advanced compound eyes, each with over 3,000 large ommatidial lenses and a specialized ‘bright zone’."

AND

Editor's note:
"Well-preserved fossils found in Early Cambrian shales from South Australia show that some of the earliest arthropods known had eyes very like those of some insects alive today, consisting of more than 3,000 individual lenses (ommatidia), with a zone of enlarged lenses generating binocular forward vision."

Anonymous said...

http://pandasthumb.org/archives/2011/06/complex-eyes-in.html
"What's wonderful about the eyes is that they are relatively large and contain numerous ommatidia, the individual facets of a compound eye. They have over 3,000 lenses, and there's also evidence of regional specialization in the eye. These were highly visual animals that were capable of forming a good image of the world around them.

"The hard part in the evolution of the compound eye was the development of the signal transduction mechanism, followed by the developmental rules that governed the formation of a regular, repeating structure of the eye."


This eye appeared in the early Cambrian.

Anonymous said...

"The new fossils reveal that some of the earliest arthropods had already acquired visual systems similar to those of living forms, underscoring the speed and magnitude of the evolutionary innovation that occurred during the Cambrian explosion."

Jud said...

All right, time to put Mr. Anonymous to bed by accurately quoting PZ Myers' summary of the eyes-in-the-Cambrian paper, the very same summary that Anonymous has been so industriously quote-mining.

PZ starts out saying this of the paper:

the metaphorical digital ink on it is barely metaphorically dry, and creationists are already busily mangling it.

I appears PZ got a letter about the paper from someone north of the border:

Where in this is the refutation of evolution? I don't know. But I did receive a letter from that Canadian idiot, David Buckna, crowing about it, and linking to his very silly creationist article describing it, in which you'll find the abstract for the paper with curious random spastic boldfacing added which supposedly highlight the parts of the story that contradict evolutionary theory, words like "complexity" and "Cambrian explosion" and "more complex" and "great evolutionary event".

Sound familiar? I wonder if "Anonymous" is spelled B-u-c-k-n-a.

PZ then lays out the reasons why The Other Jim's comments here are a correct summary of the paper's import for evolutionary theory, in paragraphs that Anonymous has deliberately quote-mined in a pathetic attempt (considering most of us have already read PZ's summary) to give the opposite impression:

The sudden appearance of complexity is no surprise, either. We know that the fundamental mechanisms of eye function evolved long before the Cambrian, from the molecular evidence; what happened here was not that, poof, eyes instantly evolved, but that the evolution of body armor gradually increased from the pre-Cambrian through the Cambrian, making the organization of eyes visible in the fossil record.

It is also the case that the measure of complexity here is determined by a simple meristic trait, the number of ommatidia. This is not radical. The hard part in the evolution of the compound eye was the development of the signal transduction mechanism, followed by the developmental rules that governed the formation of a regular, repeating structure of the eye.

Anonymous was foolish enough to quote this last bit, evidently not realizing that the 'signal transduction mechanism' referred to there is the earliest stage in eye evolution.

And finally, there's nothing in the data from this paper that implies sudden origins; there can't be. ... It's a logical error and a failure of the imagination to assume that these descriptions are of a population that spontaneously emerged nearly-instantaneously.

So, summarizing: What Anonymous has written here, in the words of the PZ Myers summary that Anonymous himself has repeatedly quoted, is "mangling" the scientific paper by "curious random spastic boldfacing," in ways that are a "logical error" and indicate a "failure of the imagination."

About sums it up, I think.

Anything to say for yourself, David?

The Other Jim said...

@ Jud, thanks for saving me the typing time ;-)

@ Anonymous,

Thanks for playing the shopkeeper in the ID/Evolution version of the dead parrot sketch.

http://www.youtube.com/watch?v=4vuW6tQ0218

Anonymous said...

I have quoted specifically THE FACTS as described in the referenced articles.
FACTS always interest me.
I am not as interested in the spin and speculation of evolutionists.

The FACTS lead to the conclusion of a saltation around 520 mya.

Evolutionists are very unwilling to accept the idea of saltations. They are unwilling, not because of the facts. They are unwilling, because they feel it may give support to "creationists" and evolutionists do not want that. So evolutionists overlook the actual facts and make up stories.

This is the unfortunate situation evolutionists have boxed themselves into.

I am interested in the FACTS. Not the politics.

Anonymous said...

Is there any actual physical evidence for eyes prior to the creatures in the Cambrian?

I am asking about physical evidence.

Anonymous said...

Concerning Parvancorina:
http://www.landesmuseum.at/pdf_frei_remote/ANNA_83_0083-0090.pdf
"There are no traces of sessile or stalked eyes ....".

Anonymous said...

This is a funny statement:
"It's a logical error and a failure of the imagination to assume that these descriptions are of a population that spontaneously emerged nearly-instantaneously."

It is an admission that evolution thinking is based on "imagination".

It is being said that those who rely just on the facts, are "failing" in "imagination".

Evolutionists imagine things. I rely on evidence.

But go ahead. Try to defend the foolish things that Myers has said.

The Other Jim said...

Anonymous said...

Is there any actual physical evidence for eyes prior to the creatures in the Cambrian?

I am asking about physical evidence.


Yes. Re-read my July 6 post, or google Spriggina.

The Other Jim said...

Anonymous said...

Concerning Parvancorina:
http://www.landesmuseum.at/pdf_frei_remote/ANNA_83_0083-0090.pdf
"There are no traces of sessile or stalked eyes ....".


You truly, and utterly missed the point of everything that has been said to you. Re-read it slowly. The light may go on yet.

Anonymous said...

I had posted:
"Is there any actual physical evidence for eyes prior to the creatures in the Cambrian?
I am asking about physical evidence."

The Other Jim replied:
"Yes. Re-read my July 6 post, or google Spriggina."

Here is some info on Spriginna:
http://en.wikipedia.org/wiki/Spriggina
"Spriggina's affinity is currently unknown; it has been classified as an annelid worm, a rangeomorph-like frond, Proarticulata, and an arthropod, perhaps related to the trilobites."
And "the front segment was the shape of a horseshoe, with a pair of depressions on its upper surface which may represent eyes."

I think The other Jim is making a joke. They can't even tell if this is a frond.
Imaginary eyes on fronds don't count.

Is there any real, credible evidence of eyes before the Cambrian?

Anonymous said...

The other Jim also mentioned Bomakellia.
http://en.wikipedia.org/wiki/Bomakellia
"Closer examination identified a tetraradial symmetry, and a frond-like morphology more reminiscent of Rangea – its current interpretation is as a rangeomorph frond, possibly closely related to the Chinese Paracharnia."

Perhaps The other Jim thinks that fronds actually do have eyes and count as eyes before the Cambrian.
No, he can't actually think that.
He must just be joking with us.

M. Dionis said...

Anonymous wrote:

We have seen saltations in the development of human beings [...]

There is no "we".
It is just you wishfuly "seeing" saltations in data leaving no room for such interpretations.
You are tremendously misrepresenting what we actually know.

You stated your point like this:
The article says two things:
1. only 1 in every 100 million letters of DNA is altered each generation.
AND
2. new mutations are the ultimate source from which new variation is drawn.


You should have read the rest of the review article as well: "The unexpected findings came from a careful study of two families consisting of both parents and one child".
Two cases constitute by no means a statistically significant sample. Even study coauthor Philip Awadalla says: "the mutation rate can be extraordinarily variable from individual to individual". The huge difference between 92% and 36% of father-originated inherited mutations speaks rather clearly: we've analysed deeply only two incidental points in a stochastic sea, it is obviously a nice step forward but it would be premature to assign a statistical meaning to the letter-mutation rate of 1 in every 85 million (this is a better value for this study results). In other words: given the high variance of the input, if the present day average on two families is 1 in 85 million letter changes, there is no enough data to conclude that the statistical average on the whole humanity (the meaningful quantity for evolutionary purposes) would be very close to this value (but the order of magnitude should be given correctly enough, unless we've been very unfortunate with these two cases). OTOH, the data refers to nowdays individuals who are less exposed to warm & UV light than naked tropical-ranged hominids for which the mutation rate should have been higher. Anyway, even if we accept (just for the sake of the argument) that the aforementioned mutation rate is essentially right , this wouldn't bother the theory, it would simply make a slight change of some parameter: The discrepancy could mean that chimps and humans shared a common ancestor longer ago than many had thought.

The study makes specifical mention to DNA letter alterations (called sometimes "point mutations", although some authors prefer to include more kinds of mutations in the definition, see e.g. J. Rafferty ed. - New Thinking about Evolution, Britannica Educational 2011: Mutations can be classified into two categories - gene, or point, mutations, which affect only a few nucleotides within a gene, and chromosomal mutations, which either change the number of chromosomes or change the number or arrangement of genes on a chromosome. A gene mutation occurs when the nucleotide sequence of the DNA is altered and a new sequence is passed on to the offspring. The change may be either a substitution of one or a few nucleotides for others or an insertion or deletion of one or a few pairs of nucleotides. or K. Ahluwalia - Genetics, New Age Intl. 2009: If the mutation involves cytologically visible changes in chromosomes we call them variations or aberrations in chromosomes. But if the change occurs in a gene, is cytologically invisible, [and] it is conventionally referred to as a gene or point mutation.). There is a reason to prefer them in the study: they are subjected to a simpler mathematical treatment and may be used as molecular clock. Nevertheless, at the very same small-scale, other kinds of mutations (such as insertions or deletions) do naturally occur. For instance, the inactivation of the CMAH gene has been triggered by a 92-bp deletion happened ~3 MYA BP on the human lineage.

Boojum said...

@Anon
If you actually read the paper you'd know that Abathochroal eyes predate the Emu bay shale eye by five million years. Now please shush!

M. Dionis said...

I did not say that "the author" (which is NATURE) used point mutation. Quite the opposite.

So?! Whether you want or not, base substitutions (as well as other small- and large-scale mutations) do occur naturally in any lineage and they do not disappear as you claimed. The most obvious example coming into mind is the sickle cell mutation which consists in only 1 base substitution (a GAG coding for glutamic acid becomes GTG which codes for valine) -> 1 different amino acid from a total of the 287 making up haemoglobin and has a very light deleterious effect in heterozygotes and causes a severe pathological condition in HbS homozygotes. Were it not for the increased resistence to malaria of the heterozygotes, such a mutation would have been wiped out by natural selection (as shown in population genetics and confirmed by absence of the mutant allele outside malarial African regions, with the noticeable and obvious exception of outside Africa people with African origins). The selective pressure of malaria in its area resulted in a balanced polymorphism which kept the mutant allele at a relatively high frequency; the selection process lasted at most 2000 years (since agricultural revolution in Africa; the mutation itself occured at some time around that historical moment).
This example shows that even an otherwise disadvantageuos base substitution can survive with a bit of selective pressure on its side; as population genetics taughts, favorable base substitutions will eventually go fixed while selection-neutral mutations can survive at least as different alleles in populations on a long term scale (and might also get fixed by chance).

Change is brought about by a package of related nucleotide changes.
And saltation is brought about by a package of related gene changes.


The first phrase concerns a frameshift mutation. The generating event is usually a very small change in the DNA: an unique base deletion (or insertion), there is little point in calling that a "package" (and the same holds even for longer deletions/insertions of base sequences leading to frameshift mutations). The consequences are huge because not only one amino acid gets changed but all amino acids coded by frameshifted bases (if there was generated no stop codon). The probability that an amino acid resulting from a frameshift mutation does a good job (from a selective point of view) is smaller than for base substitutions; actually the frameshift you were talking about produces inactivation of the gene, but among all deleterious/lethal gene inactivations naturally occuring, this one might have had collateral beneficial effects for the early hominids (that is: it might have got fixed by some selective pressure but also as a result of natural stochastic effects).
Phenotypical change is brought by all kind of mutation events, be them small or large: all of them occur naturally and all of them can get fixed in the genome with different probabilities (e.g. a large genomical event which got fixed in the human lineage is the reduction of chromosome pairs number).
Concerning your second phrase, I have to observe first that any mutation is a quantized discrete event and can be seen as a genomical micro-saltation (there is no continuum of states between GAG and GTG). Consequently, the phenotypical effects of most mutations should be quantizable too (as the difference between normal and anemic haemoglobin cells), but most physical traits (such as body length/height or skull size) have a huge amount of variance in any natural population which hides the eventual discrete character of the change. Some phenotypical "saltation" could thus have been triggered by a single (small/large) genetical event who got fixed and this possibility has to be dissociated from your meaning.
I hope that by "related gene changes" you don't mean a single frameshift mutation. Now, you should clear out what changes are you referring to, what was their timeframe and why on earth you consider them "related".

The Other Jim said...

ID Anonymous,

I'm done playing this merry-go-round game with you. Here is a nice summary of the argument I have been laying out the whole time.

http://www.fossilmuseum.net/Evolution/TrilobiteArmsRace.htm

Scroll down to "Trilobite Eyes"

Yes the page is a bit old, but that is irrelevant to the point.

I'll be away for the next month, and have better things to do in that time. If you actually have an intelligent point by mid-August, I'll respond when I get back.

The Other Jim said...

They can't even tell if this is a frond.
Imaginary eyes on fronds don't count.


Welcome to real science. Full of controversy. There is debate about the classification of many pre-cambrian organisms, based on their fossils. The lack of shelly parts makes fossilization rare, and what we do get are - surprise - sort of crosses between the current living phyla (that whole comment descent thing that you like to ignore).

But the leap from "some doubt the current classification" to "imaginary" is absurd.

Also, there are sessile orgasms with eye-spots, so is it really that inconceivable? Nature appear to be far more imaginative than you.
http://www.springerlink.com/content/n1w5622618332v50/

Anonymous said...

It looks like The other Jim has backed away from the creatures he had mentioned.
I guess he was just joking.

Looks like there is no physical evidence of eyes before the Cambrian and then exceptionally advanced eyes appeared in the Cambrian.

The Other Jim said...

How ever could I guess that you would try and get brave the day I'm leaving?

No, I did not abandon the organisms. I simply acknowledged that there is controversy in taxonomic classification of Precambrian fossils. I will avoid quote mining and dumpt the whole paragraph, controvercy and all.

Spriggina,
http://evolutionwiki.org/wiki/Spriggina
Spriggina was a 3 centimeter-long Edicaran organism found in Australian Precambrian strata dating from 555Ma. It has been identified at various times as being an annelid worm, a cnidarian-like "frond organism," and as a primitive arthropod.

Most experts now suggest that Spriggina was an arthropod, possibly related, or ancestral to trilobites."


So from your favorite scientific reference, Wikipedia, that leaves us with...

http://en.wikipedia.org/wiki/Spriggina
The front segment was the shape of a horseshoe, with a pair of depressions on its upper surface which may represent eyes.[2] The second segment may have borne antennae.

Hmmm. Sounds like Precambrian eyes to me.

M. Dionis said...

Anonymous quotes from an outdated article:

http://www.pnas.org/content/99/18/11736
"Taken together, these studies indicate that the CMAH gene was inactivated shortly before the time when brain expansion began in humankind's ancestry, ≈2.1–2.2 mya."


You didn't read carefully my Wednesday, June 15, 2011 12:19:00 PM post, did you?
"If we assume a 6-MY divergence time, our estimate of CMAH inactivation time (T) becomes 3.2 MY and that of TMRCA in the sample becomes 2.9 MY"
It is ridiculous to ignore a provided information and to keep claiming that "shortly before" refers to a little bit more than about 2.2 MYA BP. Actually, from 3.2 up to 2.2 MYA there is 1 MYA: plenty of time on evolutionary scale.

We could consider that that form of eye could well have existed 5 million years earlier, making it 520 mya.
That would make it the same time period as the rapid appearance of the creatures associated with the Cambrian Explosion (520 mya)
[...]
If anyone disagrees with this, please let us know specifically where your disagreement lies with what I have said.


According to your "method", we just could consider anything and then take it as granted. You may call that "science", I will be polite and call that "bad science" resulting from wishful thinking.

Quoting again:
"Sharp vision must therefore have evolved very rapidly, soon after the first predators appeared during the 'Cambrian Explosion' of life that began around 540 million years ago."

That is: some important functional improvement of the already-existing vision must have evolved very rapidly at a geological timescale (which is hardly surprising given the tremendous selection advantage of sharper-vision moving creatures). So?!
BTW, you could also read an interesting reference article, A Pessimistic Estimate of the Time Required for an Eye to Evolve (Proc. R. Soc. Lond. B 1994 256, 53-58) wrote by D.E. Nilsson & S. Pelger.

I have shown that this rapid evolution likely took place around 520 mya.

May I suggest you to reconsider your point?!

FACTS always interest me.
I am not as interested in the spin and speculation of evolutionists.
The FACTS lead to the conclusion of a saltation around 520 mya.


Well, that should read: "I am not interessed in scientifical deductions with method but only in my own speculations and misinterpretations which I take as ultimate factual truth".

Is there any actual physical evidence for eyes prior to the creatures in the Cambrian?
I am asking about physical evidence.


That's sneaky. Not enough though. Try to answer this: "is there any actual physical evidence that you breathed air yesterday? I am asking about physical evidence". When you will answer it, you might understand something.

Anonymous said...

M. Dionis posted:
"Some phenotypical "saltation" could thus have been triggered by a single (small/large) genetical event who [that] got fixed ...."

The saltation was triggered by activating the switch(es) that turned on the "logic" (the set of genes) that caused the "explosion" of the set of advanced creatures.

See the info about Pax 6.

Anonymous said...

http://en.wikipedia.org/wiki/Evolution_of_the_eye
"Complex eyes appear to have first evolved within a few million years, in the rapid burst of evolution known as the Cambrian explosion. There is no evidence of eyes before the Cambrian, but a wide range of diversity is evident in the Middle Cambrian Burgess shale, and the slightly older Emu Bay Shale[4]".

Jud said...

BTW, you could also read an interesting reference article, A Pessimistic Estimate of the Time Required for an Eye to Evolve (Proc. R. Soc. Lond. B 1994 256, 53-58) wrote by D.E. Nilsson & S. Pelger.

Actually, that's cited in the Nature article itself. It seems articles' authors are always disagreeing with Anonymous about what their articles mean.

Jud said...

M. Dionis writes:

BTW, you could also read an interesting reference article, A Pessimistic Estimate of the Time Required for an Eye to Evolve (Proc. R. Soc. Lond. B 1994 256, 53-58) wrote by D.E. Nilsson & S. Pelger.

Actually, that's cited in the Nature article itself. It seems articles' authors are always disagreeing with Anonymous about what their articles mean.

Anonymous said...

The saltation was triggered by activating the switch(es) that turned on the "logic" (the set of genes) that caused the "explosion" of the set of advanced creatures.
See the info about Pax 6."

More detail:
http://blogs.discovermagazine.com/notrocketscience/2010/07/27/jellyfish-eye-genes-suggest-a-common-origin-for-animal-eyes/
"Pax-6 is so important that it’s largely the same in very distantly related animals (the technical term is ‘conserved’). You can take the version of Pax-6 from a mouse and shove it into a fly, and it will still be able to trigger the development of an eye. Even though these misplaced eyes have been activated by a mouse gene, they have the compound structure of typical fly eyes. This underlies the role of Pax-6 as a conductor – its job is to coordinate an orchestra of other eye-producing genes."

Anonymous said...

http://en.wikipedia.org/wiki/Evolutionary_developmental_biology
"The developmental-genetic toolkit consists of a small fraction of the genes in an organism's genome whose products control its development. These genes are highly conserved among Phyla. Differences in deployment of toolkit genes affect the body plan and the number, identity, and pattern of body parts.
A paragon of a toolbox gene is Pax6/eyeless, which controls eye formation in all animals. It has been found to produce eyes in mice and Drosophila, even if mouse Pax6/eyeless was expressed in Drosophila.[18]"

Anonymous said...

As I have been pointing out, the development of the eye is controlled by Pax genes.
http://en.wikipedia.org/wiki/PAX6
"PAX6 is the most researched of the Pax genes and appears throughout the literature as a "master control" gene for the development of eyes and other sensory organs, certain neural and epidermal tissues as well as other homologous structures, usually derived from ectodermal tissues."

The Nilsson & S. Pelger article does not present a correct picture of the structure and formation of the eye. It does not incorporate the Pax genes control structure.

Nilsson & S. Pelger have presented a picture that bears no relationship to the actual structure and formation of the eye.















his is a very significant issue. But I expect people here will simply turn this into another argument

paleobarbie said...

Anonymous said...

"It looks like the folks here do not like where the evidence is leading us and they have just gone quiet."

Facepalm is usually unaccompanied by vocalisation

Anonymous said...

The Nilsson & S. Pelger article does not present a correct picture of the structure and formation of the eye. It does not incorporate the Pax genes control structure.

Nilsson & S. Pelger have presented a picture that bears no relationship to the actual structure and formation (forming) of the eye.


It would be very helpful if someone here could present us with a realistic picture of the purported evolution of the eye including the role of Pax control genes.

The presentation does not need to be at the detail level.

Jud said...

Anonymous writes:

As I have been pointing out, the development of the eye is controlled by Pax genes.

...which are found in both the phylum Cnidaria and the subregnum Bilateria, groups of animals that diverged ~700 million years ago. But this should not cause you to rethink your thesis that eyes "suddenly" (well, over millions of years) poofed into existence in the Cambrian.

M. Dionis said...

Anonymous wrote:

M. Dionis posted:
"Some phenotypical "saltation" could thus have been triggered by a single (small/large) genetical event who [that] got fixed ...."

The saltation was triggered by activating the switch(es) that turned on the "logic" (the set of genes) that caused the "explosion" of the set of advanced creatures.


If you refer to Cambrian further development of the sight, keep in mind that I was commenting rather your own statements concerning human lineage (see your message of Friday, June 24, 11:22:00 AM).
Anyway, what makes you think that development of Cambrian creatures has been triggered by sudden activation of a group of genes?! How do you think that inactive genetic material organized itself in the right order for "prospective purposes" without any selection pressure for many-many hundreds of MYA and then some fortunate mutation turned on the genes just at the right moment?! Your position makes very little sense.

Another wikiquote:
There is no evidence of eyes before the Cambrian, but a wide range of diversity is evident in the Middle Cambrian Burgess shale, and the slightly older Emu Bay Shale

As well as for languages evolution, a wide diversity range is a typical signature of a long-lasting divergence.

For which concerns your Pax6 blabla, I wonder how did you managed to misinterpret the facts to such an extent (OK, if you have already a Wells-like work schedule starting with the conclusion "evolutionism must be wrong" and backpropagating this conclusion through distorted reasoning up to any allegedly supporting facts, I understand it). Actually, this fact is another very strong sign of common ancestry, see e.g. M. Ridley - Evolution 3rd ed., Blackwell 2004:
"Two interpretations are possible. One is that the common ancestor of fruitflies and mice had eyes. The structure of insect and vertebrate eyes are still so different that they probably evolved independently, but perhaps from a common ancestor that had, rather than lacked, eyes. The eye in that common ancestor might have been a much simpler structure [...], but there would be an element of homology between the insect and vertebrate eyes. The evolution of eyes in the two taxa would have been easier if they already possessed the developmental genetic machinery for specifying something about eye development.
Alternatively the homology may be more abstract: ey/Pax6, or the ancestral gene from which they evolved, might have specified some activity only in a particular location in the body (the top front of the head). Then the use of the same gene in mice and fruitflies would reflect only the fact that the two animals grow eyes in a similar body region"

The most probable interpretation appears to be the first one:

"Light sensing is widely spread in non-metazoan species but the clustering of photoreceptor cells to form sensory organs was a major innovation in animal evolution. The question of a unique origin for all animal eyes or a repeatedly convergent evolution is a long-standing one (Nilsson and Arendt 2008). However several key components of the genetic circuitry driving eye specifi cation and phototransduction in bilaterians (Pax, Six, c-opsins) are already available and properly regulated in cnidarians, strongly supporting the hypothesis of a unique origin in the Cnidaria Bilateria ancestor." (B. Galliot - A Key Innovation in Animal Evolution, the Emergence of Neurogenesis [...] in Key Transitions In Animal Evolution, Taylor & Francis 2011).

Nilsson & S. Pelger have presented a picture that bears no relationship [...]
That's false; anyway, you should still read the Nilsson&Pelger article, it's crucial for your understanding.

Concerning your favorite "saltation" theory: yes, most biologists don't like it; the reasons are linked with the kind of arguments exposed e.g. by Dawkins in the chapter Puncturing Punctuationism from "The Blind Watchmaker"

Anonymous said...

http://en.wikipedia.org/wiki/Evolution_of_the_eye
"Complex eyes appear to have first evolved within a few million years, in the rapid burst of evolution known as the Cambrian explosion. There is no evidence of eyes before the Cambrian, but a wide range of diversity is evident in the Middle Cambrian Burgess shale, and the slightly older Emu Bay Shale[4]".

Anonymous said...

http://en.wikipedia.org/wiki/Evolution_of_the_eye
"Complex eyes appear to have first evolved within a few million years, in the rapid burst of evolution known as the Cambrian explosion. There is no evidence of eyes before the Cambrian, but a wide range of diversity is evident in the Middle Cambrian Burgess shale, and the slightly older Emu Bay Shale[4]".

We can begin with the fact that "there is no evidence of eyes before the Cambrian."

The interesting question is how did complex, powerful, advanced eyes begin to appear in the early Cambrian.

M. Dionis said...

Anonymous wrote:

We can begin with the fact that "there is no evidence of eyes before the Cambrian."

We can begin with you commenting on "there is no evidence of you having breathed air yesterday".

The interesting question is how did complex, powerful, advanced eyes begin to appear in the early Cambrian.

The interesting question is how you started breathing air only today, while browsing the web and reading spurious messages on this site.

It is strange that you keep quoting the wikipedia phrase without noticing the discourse emphasis on what follows after "but": as said, the high diversity observed at a moment t in divergent phyla is a standard indicator of their split a long time before t, this should give you a clue about the time-lines of the interesting vision-related evolutionary events, to be correlated with other clues coming from genetics.

And for the sake of precision:

"It's a logical error and a failure of the imagination to assume that these descriptions are of a population that spontaneously emerged nearly-instantaneously."

It is an admission that evolution thinking is based on "imagination".


No. It means you are using your imagination in a fallacious mode. In detail, IF you think those descriptions were of a spontaneously sudden emerged population, THEN:
1. you have used your imagination;
2. the way you used it was fallacious.
There is no implication about scientists using imagination, it's just about you (assuming you're the person PZ Myers was talking about, a claim already made and not denied by you).

Anonymous said...

http://en.wikipedia.org/wiki/Ocelli
"The structure of an animal's eye is determined by the environment in which it lives, and the behavioural tasks the animal must fulfill in order to survive. Arthropods differ widely in the habitats in which they live, as well as their visual requirements for finding food or conspecifics, and avoiding predators. Consequently, an enormous variety of eye designs are found in arthropods: nature has repeatedly developed novel solutions to overcome visual problems or limitations (for a review of arthropod visual systems see Warrant, 2006).

The bolded part is exactly what I have been saying. NATURE is an immense, living, intelligent organism and it "develops novel solutions".

Anonymous said...

http://en.wikipedia.org/wiki/Ocelli
"The structure of an animal's eye is determined by the environment in which it lives, and the behavioural tasks the animal must fulfill in order to survive. Arthropods differ widely in the habitats in which they live, as well as their visual requirements for finding food or conspecifics, and avoiding predators. Consequently, an enormous variety of eye designs are found in arthropods: nature has repeatedly developed novel solutions to overcome visual problems or limitations (for a review of arthropod visual systems see Warrant, 2006).

The bolded part is exactly what I have been saying. NATURE is an immense, living, intelligent organism and it "develops novel solutions".

Not only does NATURE "repeatedly develop novel solutions" facilitating adaptation, it also develops new types of creatures.
In the early Cambrian, NATURE exploded in a new set of creatures (and body plans). That is what all the evidence shows.

Anonymous said...

M. Dionis consider this:

"There is no evidence of eyes before the Cambrian, but a wide range of diversity is evident in the Middle Cambrian Burgess shale, and the slightly older Emu Bay Shale."

Since there is no evidence of eyes before the Cambrian, then the diversity arose within the Cambrian.
That is what the evidence indicates.

Jud said...

Anonymous writes:

NATURE is an immense, living, intelligent organism

Indeed, so immense that caps-lock is apparently necessary just to write its name.

and it "develops novel solutions".

...with ancient materials, as you've emphasized about the Pax6 gene.

But not novel all the time, as you've so helpfully reminded us by mentioning convergent evolution.

M. Dionis said...

Anonymous wrote:

Since there is no evidence of eyes before the Cambrian, then the diversity arose within the Cambrian.
That is what the evidence indicates.


The alleged nonexistence of evidence is debatable. Aside this, you got the picture wrong. Consider this: there is no evidence of the idioms spoken by ancestors of Archaic Latin, Ancient Greek, Avestan or Sanskrit written texts authors. The comparative study of the written idioms shows they're undoubtedly related (their common ancestor being usually labeled Proto-Indo-European - PIE), but the differences between them are considerable. Which one would you pick for most likely hypothesis?!
1. since there is no trace of what was before the first written IE text, we should assume that the differentiation between these languages from PIE occurred just before the first written texts ("just before" should be intended as a very short interval in terms of language evolution, say a couple of hundreds of years);
2. the considerable amount of differentiation displayed by first conserved texts in IE languages is the result of a long time separation between speakers of those ancient languages (of an order of magnitude comparable with usual timings for language divergence, say several thousands of years).
Just for the record, I mention that the first IE texts in Anatolian IE languages are attested around 1900 BC while the main branching of PIE is usually ranged by linguists at least 1500 years prior of this moment (aside the fact that the Anatolian branch split should have occurred earlier), but most theories propose longer diversification times issued from several millenia of separate evolution.
Getting back to the sight question bothering you, the genetic evidence indicates common ancestry for different phyla vision systems, but the first preserved sight systems exhibit already a noticeable diversity. Answer yourself to the breathing question, make a mental note on it, compare it with the situation of sight organs, then elaborate an educated inference from the existing evidence in the spirit of what I mentioned above (keeping in mind that for that mental note related reasons, the absence of evidence does not mean/imply evidence of absence).

NATURE is an immense, living, intelligent organism and it "develops novel solutions".

There's no need to shout. The word "living" is debatable (it depends on what you mean by "life"), the word "intelligent" is very unhappy since nature's picks are arguably a random mix of what one would call "intelligent" and "stupid" choices. I can cope with nature "developing novel solutions" if the expression is not meant literally but merely as "natural processes enhanced by various natural feedback mechanisms lead to new organization forms of the living world which could be described as if they were novel solutions were the nature have a plan". But the nature has no plan, no more than a particle who gets from the point A to the point B on that very specific path minimizing the action functional as if it could compute in advance the integral of the Lagrangian on every single possible path, compare them and choose the minimum (actually and obviously, the particle doesn't compute anything, it just obeys Newton's phenomenological laws which are rigorously equivalent to the variational principle).

In the early Cambrian, NATURE exploded in a new set of creatures (and body plans). That is what all the evidence shows.

The evidence shows that several phyla started to develop parts of the body more likely to be preserved as fossils in a short time with respect to the whole geological time. The time was still large enough for evolutionary purposes. The question is why organisms started to develop these parts then. The answer is given by strong selective pressure which acted on all of them (and sight improvement is a huge advantage leading to its own selective pressure).

Anonymous said...

Jud seems to be getting it a bit, but still falls back into Darwinian thinking.

"Convergence" has a completely different meaning when we see NATURE as the encompassing, intelligence driving the process.

Anonymous said...

Another interesting example of the intelligence of NATURE:
http://blogs.discovermagazine.com/notrocketscience/2011/07/11/fish-fins-and-mouse-feet-controlled-by-the-same-ancient-genetic-switch/
"The appendages of all four-limbed animals (tetrapods) are governed by a cluster of genes called HoxD. This group oversees the development of a whale’s flippers, a finch’s wings, and a chimp’s arms. They control how big a limb becomes, the number of the bones within it, and the shape of those bones.
"Igor Schneider from the University of Chicago has demonstrated the relationship between fins and feet by swapping the mouse and zebrafish versions of CsB. These species have inordinately different limbs, and they’ve been separated by 400 million years of evolution. Nonetheless, their swapped versions of CsB work perfectly well in each others’ bodies, driving the activity of each others’ HoxD genes."

Anonymous said...

M. Dionis posted:
"Getting back to the sight question bothering you..."

It is not bothering me - it intrigues me, it interests me. Seeing how the intelligence of NATURE operates is fascinating!


Also I have learned from experience that discussing analogies (such as you have given) is of no value.

Jud said...

Anonymous writes:

Another interesting example of the intelligence of NATURE:

So now that you've cited common descent of Hox genes as examples of the wonders of Nature, and also, previously in this thread, disputed that there is such a thing as common descent, I guess we'll just wait for you to argue with yourself and let us know when you've arrived at a conclusion.

Anonymous said...

M.Dionis posted:
"The word "living" is debatable (it depends on what you mean by "life")."

NATURE is alive.
Are you in doubt about that?


You have posted that you "can cope with nature "developing novel solutions" if the expression is not meant literally"

I mean it literally. All the evidence supports that.

Anonymous said...

M. Dionis posted:
The evidence shows that several phyla started to develop parts of the body more likely to be preserved as fossils

Perhaps you can help me with something.
The article talks about fossil eyes (with no attached body).
Eyes are soft parts are they not? Why would these soft parts appear in the Cambrian but not earlier?

Anonymous said...

M. Dionis posted:
"..the word "intelligent" is very unhappy since nature's picks are arguably a random mix of what one would call "intelligent" and "stupid" choices."

The key word you have used is "arguably".
You can argue for or against that proposition. That is what you are saying. It is not a fact. It is arguable.

It is ridiculous to say that "the word "intelligent" is very unhappy". (Whatever in the world that means).

Anonymous said...

I thought Jud had started to get it but apparently not.

Jud said...

Anonymous writes:

Eyes are soft parts are they not?

Not. Try to actually read for comprehension the articles you keep quoting and citing. The information saying the early Cambrian eye fossils are not from soft parts is there, if you will only use the eyes and brain NATURE gave you.

Why would these soft parts appear in the Cambrian but not earlier?

Not soft parts. That's why they appear in the fossil record. Earlier, when they were soft parts, they didn't appear.

Easy to understand if you just read and comprehend what's right there in front of you. If you can't find the information, I'll be happy to quote the relevant portions.

It is ridiculous to say that "the word 'intelligent' is very unhappy."

Trouble with comprehension again? Happy to help. He means it's wrong to say nature is an intelligent entity. You are committing the teleological fallacy (or as I like to call it, the "Thermos fallacy," after an old joke that illustrates just what the fallacy is).

Anonymous said...

What people do not understand is that what we see in the fossil record and the genome is the working of the intelligence of NATURE.
Any observation that you explain by mindless, random forces is more plausibly and credibly explained by the intelligence of NATURE.

Seeing and analyzing the handiwork of NATURE is exhilarating.

Anonymous said...

As I have said, it is a waste of time trying to talk to Jud.

Jud said...

Any observation that you explain by mindless, random forces is more plausibly and credibly explained by the intelligence of NATURE.

Those observations are explained non-teleologically through equations. The equations need no input from "the intelligence of NATURE" to make them turn out correctly, any more than 2+2 needs some sort of innate intelligence to help it sum up to 4.

Saying something is due to "the intelligence of NATURE" is no more an explanation than saying it is due to God, voodoo, or black magic. It took Darwin to achieve the insight needed to synthesize the central organizing principle uniting all of the disparate kinds of life we see around us. Before that, those who (like you) didn't understand what they were seeing and needed a teleological explanation said each of the millions of diverse creatures was put here by an act of "special creation," for which your "intelligence of NATURE" is no more or less than an exact substitute.

Anonymous said...

We see the operation of NATURE in the fossil record, the creatures that are alive today, all we (increasingly) know about the genome and the functions at the cellular and molecular levels.
NATURE is quite impressive.

We can put forward some thoughts about what NATURE's purposes might be.
What we see through time is increasing complexity and diversity. We see a drive to take advantage of opportunities offered by climate and habitat.
We see the appearance of new families of creatures and extensive elaboration within those families.

We can conclude that those are NATURE's purposes.

Why NATURE has those purposes is another, separate (and fascinating) question. But we do not need to go to that level first.
First we can observe and analyze NATURE and actually see with our own eyes what NATURE is doing in terms of increasing complexity and diversity.

Anonymous said...

Jud is like all the other evolutionists I have ever dealt with.
He thinks that evolution theory explains it all.
But there is a flaw at the heart of evolution theory that evolutionists do not acknowledge.
The flaw is that evolution theory is based on the desire to survive. But evolution theory has absolutely nothing to say about where that desire to survive comes from. If evolution theory begins to try to explain where the survival extinct itself comes from then we can have an apple to apples discussion. Till then evolution theory has not actually explained anything.
Ultimately, evolution theory simply has no answer.
Evolution theory pretends that that question does not need to be answered.

But evolution theory at the same time wants to pretend that it has answered all the questions.
As if Darwin and those who follow him have answered all the questions.

Evolution theory pretends that questions of purpose do not need to be addressed. But obviously they do.
I do not expect evolutionists here to acknowledge the point I am making.

And there is no point arguing about it because people will pretend not to get it.

But if someone would like to tell us where the desire to survive comes from, please do.

Anonymous said...

Jud had posted:
"..for which your "intelligence of NATURE" is no more or less than an exact substitute."

Anyone who has been reading my posts knows that is a completely incorrect understanding of what I have been saying.
That is why I say it is a waste of time to talk with Jud. He does not follow the discussion and posts absurdities.

Jud said...

Anonymous writes:

As I have said, it is a waste of time trying to talk to Jud.

This was in response to my post that Anonymous was mistaken in thinking Cambrian eyes were "soft parts," and offering to get the information for him if he couldn't figure it out for himself. So we can assume Anonymous couldn't find the information for himself, or didn't like what he found. Thus, since Anonymous either wasn't competent enough to find and understand the information, or wasn't honest enough to acknowledge it if he did find it, I'll provide it here.

From Wikipedia on trilobites, possessing the oldest known Cambrian complex eyes prior to the recent discovery:

Even the earliest trilobites had complex, compound eyes with lenses made of calcite (a characteristic of all trilobite eyes), confirming that the eyes of arthropods and probably other animals could have developed before the Cambrian.

Calcite. Its hardness is roughly equivalent to that of a penny. Not a "soft part."

Now regarding the latest find, PZ's summary, which Anonymous quoted from here liberally, has this to say:

What was found was a collection of arthropod eye impressions, probably from cast-off molts. No sign of the bodies of these animals was found, suggesting that perhaps they were not fully sclerotized, or as the authors suggest, that disarticulated eyes were more prone to rapid phosphatization than eyes attached to a decaying body.

Now this has a few big words, so maybe Anonymous just wasn't up for trying to understand it all, or quote with "curious random spastic boldfacing" as PZ has aptly described it. But what it means is the following:

- The body parts to which these eye molts had been attached may not have been sclerotized, but the eye molts themselves were (see also the photo captions with the article, referring to "a sclerotized pedestal"). This is a hardening process using organic proteins, which would result in something like the hardness of plastic - not soft at all. Then the eye molts, according to the article authors, were phosphatized, meaning the organic stuff was rapidly replaced with calcium phosphate in a process taking as little as two to six days. This is a process responsible, according to Wikipedia, for "some of the most spectacular cellular-level preservation known from the geologic record."

Calcium phosphate. Again, not "soft parts."

See, Anonymous, if you'd only ask us to help explain these articles and their big words for you, you could save yourself raving on in public over half-baked ideas like complex Cambrian eyes being "soft parts." As PZ and others have mentioned, it's the hard parts of those complex eyes from the Cambrian that have been preserved, and "soft parts" from all eras, including the Cambrian and prior, whose preservation in the fossil record is so surpassingly rare.

Anonymous said...

It is a marvel to see how confused Jud is.
As I have said, trying to straighten him out is a waste of time.

I am interested in how the intelligence of NATURE operates.
Does anyone have anything to contribute to the posts I have made on that?

Jud said...

Anonymous writes:

Evolution theory pretends that questions of purpose do not need to be addressed. But obviously they do.

Ah yes, the "2+2 has to want to equal 4" argument. Why oh why will no one discuss the purpose and motivation of those two sets of 2?

How very scientific of you.

Jud said...

Anonymous writes:

What we see through time is increasing complexity and diversity.

Diversity yes, complexity no. Are you truly determined to go through every single item in the list of fundamental ID-creationist misunderstandings of evolution?

What we see is life branching out in all directions from its simplest origins. If it got more simple than its simplest origins, it wouldn't be life, so that's a barrier. (Think of a tree growing against a north-facing wall. It will branch out to the north, east and west, because it is blocked from branching out to the south.)

Life has been most successful at its simplest. There are overwhelmingly more bacteria in a thimbleful of dirt than there are humans on the planet. Thus life simply takes hold where it can, primarily in its very simplest forms, the exact opposite of a tendency toward complexity.

Anonymous said...

It looks like there is nobody else contributing except Jud. That is fine if that is the case.

Perhaps at some point in the future someone might be interested in considering the idea that NATURE is a living, intelligent being.
It is a very clarifying and exciting idea.

Anonymous said...

In another thread:
http://sandwalk.blogspot.com/2011/07/evolution-according-to-canadian-society.html
Atheistoclast brought our attention to the following study:
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000037

This demonstrates again the intelligence of NATURE.

Intelligence is involved in Nature.
Some people attribute this to "God" (which rubs evolutionists the wrong way). I attribute the intelligence to NATURE.
NATURE manifests its intelligence at the level of the biosphere and at the level of the cell.

Anonymous said...

This is interesting:
http://www.genomesize.com/rgregory/reprints/Macroevol.pdf
"Species and Biological Individuality. In what he viewed as a ‘‘radical solution to the species
problem,’’ Ghiselin (1974) proposed that species are not mere arbitrary snapshots of a constantly changing morphological continuum, as Darwin and other strict anageneticists had
believed, but rather ‘individuals’’ in their own right, with properties akin to those of organisms.
The link between this conceptual
shift and the ‘‘levels of selection’’ debate was made a short time later by Hull (1976, 1980),
who pointed out that, as individuals, species could potentially undergo their own process of higher-level natural selection."


Within NATURE which is an "individual" onto itself, we see other "individuals".

Anonymous said...

Would someone please tell us where the desire to survive comes from?
That would be very helpful.

M. Dionis said...

Anonymous wrote:

Also I have learned from experience that discussing analogies (such as you have given) is of no value.

Translated into normal language: "I prefer being learn-resistant than open-minded". Had you a minimal scientific educational background, these examples would have provided clear phenomenological insights.

NATURE is alive. Are you in doubt about that?

No. Were you to attach an affirmative meaning to this phrase, the word "alive" would became devoid of meaning.
Within usual definitions, nature as a whole is not alive, parts of it (i.e. organisms) are.

Eyes are soft parts are they not? Why would these soft parts appear in the Cambrian but not earlier?

Jud already hinted you the answer: in Cambrian we have hard fossilized parts of the eye.

It is ridiculous to say that "the word "intelligent" is very unhappy". (Whatever in the world that means).

Jud answered also to this. I have been nice with you, but it's obvious you don't get the point. Since the nature as a whole is not a living entity but a huge set of related and non-coordinated parts, it is ridiculous to speak about its' intelligence.

Any observation that you explain by mindless, random forces is more plausibly and credibly explained by the intelligence of NATURE

Certainly not in science, where Ockham's razor cuts off any useless assumptions of this kind. Why don't you try to read some science basics before lancing senseless attacks on it?!

What we see through time is increasing complexity and diversity.

(Jud answers: Diversity yes, complexity no.)
I complete: not even diversity increase has to be taken as granted. The Cambrian "explosion" displays an unprecedented and also never repeated diversity of body plans of which only a few survived. To quote S.J. Gould: "The sweep of anatomical variety reached a maximum right after the initial diversification of multicellular animals. The later history of life proceeded by elimination, not expansion. The current earth may hold more species than ever before, but most are iterations upon a few basic anatomical designs." (Wonderful life - W.W. Norton 1990)

The flaw is that evolution theory is based on the desire to survive.

Nope. There is no such finalist basic assumption in evolution theory. The flaw is in you knowledge.
OTOH, the "desire to survive" is a trivial byproduct of natural selection and has very little to do (if any) with conceptual issues in evolutionism.

But evolution theory has absolutely nothing to say about where that desire to survive comes from.

Try this: two otherwise similar organisms differ in that one has no "desire to survive" while the other has a minimal amount of self-protective behavior triggered by some genetic difference (natural variability). The first organism has fewer chances to survive and produce offspring, while the second can actively influence its' fate by living longer and producing more offspring (which will exhibit the same slightly enhanced behavior). The rest is mathematics and the predictable most probable result is survival of the second kind of organism. The self-protective behavior have the natural tendency to increase over time not because of some hypothetical background purpose but because of mathematics (and one cannot fight with mathematics).

I am interested in how the intelligence of NATURE operates.

You should read more about how mutations occur, then understand their effects on populations. This is how nature operates, there is no higher intelligence involved.

someone might be interested in considering the idea that NATURE is a living, intelligent being.
It is a very clarifying and exciting idea.


It's a nice idea having only a major drawback: its falsity.

Anonymous said...

Evolutionists think they can avoid the subject of purpose. They deride those who look for purposes in Nature.
BUT evolutionists are faced with the exact same question, but they just ignore it.
Evolutionists acknowledge the desire to survive - they accept the idea that the purpose of Nature is to survive,
But they do not explain where that purpose came from.

M. Dionis said...

Anonymous wrote:

Evolutionists acknowledge the desire to survive - they accept the idea that the purpose of Nature is to survive

Repeating nonsense doesn't make it true.
Natural selection points the time arrow to survival enhancement without any particular purpose: it happens so for all kinds of organisms which we observe in practice (otherwise, they wouldn't be observed).

FYI, here's a nice illuminating quote:
Without going into the details of biological processes, we can observe in all living organisms the following three properties:
(1) Every living system is characterized by metabolism. The presence of metabolism is therefore a necessary condition for a system to be alive. As we shall see, the fundamental reason for this is the complexity of the material structure of every organism. The fact that organisms metabolize means also that they are, in the thermodynamic sense, open systems, that is, they exchange matter and energy with their environment.
(2) A second property which we observe in all living beings is the faculty of self-replication. This too is ultimately a consequence of biological complexity. Organisms are constructed so intricately that they could never arise de novo in each generation. if this were possible then there would be no need for self-reproduction.
(3) The third and last property which we will see in all living organisms is mutability. If organisms only ever made exact copies of themselves there would be no evolutionary progress. It is only the continual variation of organisms, through mutation, which provides Nature with the assortment from which she selects those types best fitted to survive and further reproduce in their milieu.
These considerations lead us to the central postulate that the following properties are necessary for a system to be called "alive"
(1) metabolism,
(2) self-reproduction,
(3) mutability.
These criteria were first set up in 1924 by the Russian biologist A. Oparin, in order to demarcate living from non-living systems. They have sometimes been augmented by a fourth, that of natural selection. We shall not include this in our definition of a living being, since it is in fact not an independent criterion. Firstly, the phenomenon of natural selection is a property of a system composed of a population of organisms, and secondly, as we shall see, in particular circumstances where metabolism, self-reproduction and mutability all appear, selection in the Darwinian sense takes place automatically.
The three criteria of Oparin are necessary but not sufficient conditions for a system to be called "alive". However they provide a suitable working definition of a primitive organism. [...]

(B-O. Kueppers - Molecular Theory of Evolution - Springer Verlag, 1985)

Anonymous said...

M. Dionis could you please tell us where the desire to survive comes from?

Anonymous said...

Would someone please tell us where the desire to survive comes from?
That would be very helpful.


Even more helpful would be if someone could explain why so many organisms (ants, bees, naked mole rats, mothers in mammals, etc, etc, etc) seem to be able to suppress that desire to survive and die in the protection of their offspring... Oh wait, evolutionary theory can explain this.

Stop cherry-picking your "facts".

/SverigeSkeptiker

Anonymous said...

Hello SverigeSkeptiker.
My question is where did that desire to survive come from in the first place.
Can you answer that question?
Can anyone answer that question?

Larry Moran said...

anonymous the IDiot asks,

My question is where did that desire to survive come from in the first place.
Can you answer that question?
Can anyone answer that question?


I think it came from France.

Anonymous said...

By making a joke Moran reveals that in fact he cannot answer the question.
Perhaps someone could be honest and simply admit that evolution theory cannot answer the question.
That would be a good place to start.

Then we could truly deal with reality and undertake a search for the truth.

M. Dionis said...

Anonymous wrote:

M. Dionis could you please tell us where the desire to survive comes from?

Now, that is really boring.
I don't know on which basis are updated the comments on this blog. I suppose the most rational approach would be to look at them in simple chronological order (since moderation is turned on) and release them online as soon as one realizes they bear no inappropriate content. One could think to deal at first with all comments on a specific article then go to the next. One could also think to profiling, for some users might have a higher rate of garbage production & proposal.
Yet none of these approaches applies to my previous two comments on this thread since right now (as well as several hours ago) I can see the second (labeled Monday, July 18, 2011 2:34:00 PM) but still not the first (which was posted some tens of minutes before it). That is very odd because the second comment is to be understood in the context of the first one. Incidentally, the first comment contained also the answer to the raised question. As the time goes by, other comments are popping-up but my first yesterday intervention seems lost in the cyberspace. Maybe the owner of this blog could do something about since the dialog cannot flow normally like that.

[A Swedish ?] Anonymous wrote:
why so many organisms [...] seem to be able to suppress that desire to survive and die in the protection of their offspring... Oh wait, evolutionary theory can explain this.

There is no innate "desire to survive" (at least for the most part of the animal realm) but as explained, self-conservation behavior possibly supported by various mechanisms (e.g. pain) and enhanced by natural selection. Natural selection enhances through numerical positive feedback also offspring-defense behavior. More generally, the evolutionary success of a gene can be increased by any individual supporting survival and reproduction of its' relatives / similar individuals. For more information, you should start by reading W.D. Hamilton's fundamental papers (The genetical evolution of social behaviour I and II, Journal of
Theoretical Biology 7, 1964, pp. 1-16 and 17-32) on kin selection and inclusive fitness and see why altruism is a valid evolutionary behavior under certain numerical assumptions (from the abstract: "Species following the model should tend to evolve behaviour such that each organism appears to be attempting to maximize its inclusive fitness. This implies a limited restraint on selfish competitive behaviour and possibility of limited self-sacrifices.")

Anonymous said...

Give the correct answer:
where did that desire to survive come from?
Multiple choice:
a from outer space
b from the elan vital
c no desire to survive exists
d from the genes
e from the second law of thermodynamics

Jud said...

Anonymous writes:

My question is where did that desire to survive come from in the first place.

Once again the Thermos Fallacy (needless invocation of teleology to explain an apparent complexity that doesn't actually exist). This is a sign of a childish, anthropomorphic view of the world and a correspondingly childish level of analysis.

Non-living molecules replicate and continue to exist. Is that because they have a "desire" to reproduce and survive? Must water droplets "desire" to replicate and form clouds? Do water molecules in the form of liquid water fail to evaporate because they "desire" to survive as liquid?

No teleology - no desire to survive - is necessary to explain the fact of replication or continued existence of molecules, virii, bacteria, or other living things.

Boojum said...

Um could it be that things that don't survive, don't survive.
Lets say there were two populations of animals one were suicidal, one had a survival instinct. Which population do you think will last longer.....

Anonymous said...

Evolution theory does not indicate where the desire to survive comes from.
And yet evolutionists expect us to accept evolution theory.

Anonymous said...

Boojum, that does not explain where the desire to survive came from in the first place.

Jud said...

Anonymous writes:

Evolution theory does not indicate where the desire to survive comes from.

And yet evolutionists expect us to accept evolution theory.

So let's say, for the sake of argument, that a "desire to survive" exists in all living things, and that this is critical to survival.

So bacteria and viruses want to live more than all the rest? This will also have to account for great changes, like the Cambrian explosion and the Permian extinction. Apparently, whole groups of animals wanted very much to live for hundreds of millions of years, then suddenly lost all motivation. But you've said, Anonymous, that thinking in terms of "the intelligence of Nature" lends great clarity to your perspective. So you should not have any problem making this all clear to us.

Using exactly the same criteria you've specified for evolution, if you can't tell us where this desire to survive comes from and why it goes away, there's no reason to accept what you're saying. So come on, we're waiting for your revelation.

Anonymous said...

Anonymous said...

Boojum, that does not explain where the desire to survive came from in the first place.

And I am embarrassed of my ability to understand English.

It has clearly been pointed out that this desire is in your mind. It is something you imaging to explain your world. Do bacteria have desires? Viruses? Funguses? You are looking only at animals and implying your thoughts on them.

/SverigeSkeptiker

heleen said...

Boojum did not spell it out clearly enough for Anonymous to grasp. The utmost simplicity is required to reach Anonymous's brain.

Things that don't survive, don't survive.
That's it. All of it. Nothing else.

Anonymous said...

People are doing their utmost to avoid the question:
Where does the desire to survive come from?
This is question evolutionists cannot answer. Most do not even understand the question.

But if someone were to actually ponder this question, a whole new avenue of thought would open up.
But that requires opening up the mind.

Jud said...

heleen writes:

Things that don't survive, don't survive.
That's it. All of it. Nothing else.


Anonymous contends there is something more. He says thinking in terms of the "intelligence of Nature" gives him great clarity. So with this great clarity, he certainly should be able to explain to all of us just how this "desire to survive" works - how the great explosions and extinctions happened, how it is that the very simplest forms of life have a greater amount of this desire, since they are by far the most successful at surviving.

If he cannot, then by Anonymous' own standards there is no reason for us to believe what he says.

We continue to wait for Anonymous' revelation.

Jud said...

Anonymous writes:

But if someone were to actually ponder this question, a whole new avenue of thought would open up.

But that requires opening up the mind.

You've obviously pondered the question, so now you've had new a new avenue of thought open up to you, as well as obtaining great clarity by seeing things from the viewpoint of the "intelligence of Nature." So tell us how this desire to survive results in the differences in survival success we see in Nature, and how it created the historical record of explosions and extinctions. Otherwise, by the standards you yourself have set, we shouldn't believe what you're saying.

We continue to wait for your revelation....

M. Dionis said...

Anonymous wrote:

But if someone would like to tell us where the desire to survive comes from, please do.
Friday, July 15, 2011 11:15:00 AM

Would someone please tell us where the desire to survive comes from?
Sunday, July 17, 2011 1:17:00 PM

Evolutionists acknowledge the desire to survive - they accept the idea that the purpose of Nature is to survive,
But they do not explain where that purpose came from.

Monday, July 18, 2011 9:12:00 AM

M. Dionis could you please tell us where the desire to survive comes from?
Monday, July 18, 2011 6:08:00 PM

My question is where did that desire to survive come from in the first place.
Can you answer that question?
Can anyone answer that question?

Tuesday, July 19, 2011 9:36:00 AM

Evolution theory does not indicate where the desire to survive comes from.
And yet evolutionists expect us to accept evolution theory.

Tuesday, July 19, 2011 3:53:00 PM

Boojum, that does not explain where the desire to survive came from in the first place.
Tuesday, July 19, 2011 5:26:00 PM

People are doing their utmost to avoid the question:
Where does the desire to survive come from?

Wednesday, July 20, 2011 9:21:00 AM

Man, you've got an obsession.
Read my lips (and precedent comments):
1. There is no "desire to survive" (excepting humans and maybe a few animal species which might exhibit a fair amount of self-consciousness). There is self-protective behavior (SPB from now on) of individuals (and also "altruistic" behavioral patterns in several species).
2. There is no need to explain a non-existing concept. In humans, the desire of survival is the conscious reflection of the genetical hardwired SPB (the same should hold for other species having eventually reached a high degree of self-consciousness).
3. If there is something to be explained in evolutionary terms it's the SPB. The explanation is straightforward and has nothing to do with purpose. The individuals who exhibit more SPB than others (and this always happens due to inherent variability) are positively discriminated in terms of survival, which leads to increased evolutionary fitness with which natural selection operates. More complex are the organisms, more possibilities to improve SPB they have (e.g. if you have better eyes, you can improve your SPB by avoiding predators you see in your neighborhood; if you have a more performant brain, you may recognize easier the characteristics of a potential danger). Over the eons, the natural selection highly rewarded SPB assumes very elaborate forms, remaining yet a blind by-product of simple survival/reproduction mathematics.
4. It's about time for you to start reading something serious about natural selection mechanism and population biology, otherwise you will produce nothing else but garbage.

Anonymous said...

M. Dionis posted:
"The individuals who exhibit more SPB than others (and this always happens due to inherent variability) are positively discriminated in terms of survival, which leads to increased evolutionary fitness with which natural selection operates."

And my question is - where did that original SPB (survival instinct) come from? Please explain in evolution terms where it came from originally.
Use terms like random mutation, genetic drift, selection etc.

heleen said...

Anonymous wrote;
Evolutionists acknowledge the desire to survive - they accept the idea that the purpose of Nature is to survive,
But they do not explain where that purpose came from.
Monday, July 18, 2011 9:12:00 AM

Evolutionists don't acknowledge the desire to survive - they don't accept the idea that the purpose of Nature is to survive.

Things that don't survive, don't survive.
That's it. All of it. Nothing else. Very difficult to grasp, for Anonymous.

It's about time for Anonymous to start reading something serious about natural selection mechanism and population biology, otherwise you will produce nothing else but garbage.

Sorry for the repetition, but it takes extraordinary effort to get through to Anonymous.

Anonymous said...

People are doing their utmost to avoid the question:
Where does the desire to survive come from?
This is a question evolutionists cannot answer. Most do not even understand the question.

People here can't answer the question. In fact they can't even understand the question.
Nobody here has tried to explain where it came from originally in evolution terms, like random mutation, genetic drift, selection etc.

Here is a kind of answer.
The survival instinct came as the result of random arrangements of genes.
I am not saying that this is a good answer. But it is a kind of answer that an evolutionists might give.
Can someone come up with a better explanation?

Anonymous said...

Anonymous said,

The survival instinct came as the result of random arrangements of genes.

Here is your problem. Those who accept evolutionary theory do not believe that it is due to a roandom arrangment of genes. It is a set of behaviors that have been selected for. It is by definition, not random.

Ever played Yahtzee? Getting a Yahtzee (all 5 dice the same) in a single roll has a probability of about 0.00077. But, if you get 3 turns, and selection is applied to determine which dice to re-roll, the odds get much better. One person had estimated that to be about 0.04603 (http://mathforum.org/library/drmath/view/52174.html).

So behaviors that increase survival (and therefore reproductive success) increase in a population by selection. No need to invoke Gaia.

BUT evolution can also explain behavioirs that do not look like "desire to survive", and may actually look like suicide (die-after-mating, which is observed in many phyla). As long as the behavior increases reproductive success, it is also a valid solution, and will be selected for in those populations.

heleen said...

Anonymous said...

Where does the desire to survive come from?
The question assumes a desire to survive exists. No such desire exists. What can be explained is how animals (plants etc) come to survive, but a non-existent desire has no origin. Seems too difficult to grasp.
Especially, as Anonymous has not even shown a desire to survive exist. Note the DESIRE.

Jud said...

Anonymous writes:

Where does the desire to survive come from?

This is a question evolutionists cannot answer.

Anonymous cannot answer this question, despite being asked repeatedly. Thus, by his very own criterion, Anonymous has failed miserably.

Anonymous said...

Anonymous posted:
"So behaviors that increase survival (and therefore reproductive success) increase in a population by selection. No need to invoke Gaia."

These behaviors are determined by the genes are they not? Or are you thinking of behaviors that spring out of the blue without connection to genes?

By the way I am not invoking Gaia. I am invoking (your word) the intelligence of NATURE.
But if others want to relate it to the intelligence of Gaia - that is also an interesting idea. And certainly has a scientific pedigree. But I do not want to debate that. I am content to simply "invoke" the intelligence of NATURE.

Anonymous said...

In order to move this analysis along consider the following:
Either the survival instinct was there right from the very beginning or it evolved.

If it evolved, then there was a time when the survival instinct was not in effect. But at that time, on what basis was selection acting? On the basis of survival? No, that could not be, because our premise is that this was before the evolution of the survival instinct.
So we are led to the conclusion that the survival instinct was there right from the beginning.
In that case where did it come from?

Larry Moran said...

anonymous the IDiot asks,

So we are led to the conclusion that the survival instinct was there right from the beginning.
In that case where did it come from?


You're asking the wrong people. Why don't you jump into a cesspool and ask some bacteria?

Or trees. You do talk to plants, don't you?

Seriously, the way humans are behaving these days I'm beginning to think we got our survival instinct from lemmings.

Or dodos.

Anonymous said...

It looks like Moran is acknowledging that evolution theory and evolutionists cannot explain where the survival instinct comes from.
And yet the entire edifice of evolution theory is built upon it.

It seems to be okay to Moran not to have a clue about the fundamental aspect of evolution theory.

Anonymous said...

Anonymous said,
t looks like Moran is acknowledging that evolution theory and evolutionists cannot explain where the survival instinct comes from.
And yet the entire edifice of evolution theory is built upon it.


How many times must we repeat that this fictitious desire you speak of is nonsense? It is not a property. It is not even reliably observed in animals. You dodged someone's question above about bees. Why do bees kill themselves to defend a hive?

Anonymous said...

Simply calling something "nonsense" is not an answer.
Can anyone actually understand the issue and say something constructive?

Jud said...

Anonymous writes:

And yet the entire edifice of evolution theory is built upon it.

Ah, did everyone see that? Anonymous was loudly crowing about the "desire to survive" as something real, until he was asked to give any sort of explanation of it. Now he's making sure that he's only bringing it up as something *un*real that the "edifice of evolution theory" is built on.

O, brave Sir Anonymous! Once again you turn your back toward us and run!

Still waiting for any use of "the intelligence of Nature" in an actual explanation, rather than as some slogan you wave about.

Anonymous said...

Anonymous said...
Simply calling something "nonsense" is not an answer.

In this case is really is.

It is like me asking how your Gaia world explains the tooth fairy. I mean, those kids always get money under their pillows, right? And wikipedia tells me the parents do not put the money there, so how do you explain the tooth fairy?

And calling this nonsense is not an answer

/stupid

heleen said...

Anonymous said..
Wednesday, July 13, 2011 5:49:00 PM

NATURE is an immense, living, intelligent organism and it "develops novel solutions".
Not only does NATURE "repeatedly develop novel solutions" facilitating adaptation, it also develops new types of creatures.


Saturday, July 16, 2011 11:29:00 AM
Intelligence is involved in Nature.
… I attribute the intelligence to NATURE.
NATURE manifests its intelligence at the level of the biosphere and at the level of the cell.


Anonymous said...
Friday, July 22, 2011 10:22:00 AM
I am invoking (your word) the intelligence of NATURE.
... I am content to simply "invoke" the intelligence of NATURE.


Still waiting for any use of "the intelligence of Nature" in an actual explanation, rather than as some slogan you wave about. Explain NATURE, and the intelligence of NATURE, and tell everyone how it works, and why you seem to suppose ‘the intelligence of NATURE’ is anything different from evolution.


Anonymous said...
Wednesday, July 20, 2011 9:21:00 AM
Where does the desire to survive come from?
No such DESIRE exist. Anonymous should explain why he thinks such a DESIRE exists. As to Can anyone actually understand the issue and say something constructive? : there is no issue apart from Anonymous misunderstanding of life, and the constructive thing has been said: there is no desire to survive, organisms survive or not.

heleen said...

Anonymous said... Saturday, June 25, 2011 11:10:00 AM

What happens when a creature with a particular single letter mutation mates with another creature? That other creature does not have the same particular single letter change. After mating, the offspring will have a 50% chance of having that mutated single letter. Similarly with the next mating and each one afterwards.
The original single letter mutation will fade way. The chances of it continuing are astronomically low.
So not only do we have very few single letter mutations to begin with, but they fade away over the generations.


Anonymous thinks that mating itself change allele frequencies. Anonymous thinks that mating itself a probability ½ after one generation, ¼ after two generations and so on. Anonymous has never heard of the Hardy-Weinberg law.
Anonymous was talking as if mating itself has a frequency effect, he was not talking about the probabilities of drift.
Larry Moran in his answer credited Anonymous with to much intelligence.

Anonymous said...

Anonymous posted:
"And calling this nonsense is not an answer."

So anonymous reserves the right to label other people's thoughts "nonsense" but demands that nobody label his/her thoughts that way. (I have never done that of course).

At least he/she acknowledges that simply throwing out an insult of "nonsense" is not an answer.

Anonymous said...

If people are interested in the intelligence of NATURE I recommend the work of Dr. James A. Shapiro.
http://shapiro.bsd.uchicago.edu/

His work is about "Natural Genetic Engineering".
Or in other words - NATURE's genetic engineering.

His work is primarily about the intelligence involved in what we call adaptation. But he has stopped short of following this line of thinking and research into the intelligence that must be involved in macroevolution.

Even so he has met with hostility from the evolution establishment.

But note that what Dr. Shapiro has shown conclusively is that there is intelligence in Nature.

heleen said...

Anonymous said... Saturday, July 23, 2011 10:59:00 AM

If people are interested in the intelligence of NATURE I recommend the work of
The work of somebody else?
I'm not interested (at least here) in what somebody else is doing, so don't hide behind that. Anonymous should do his/her/its own explanation of what he/she/it has written on this blog.
So, still waiting for any use of ‘the intelligence of Nature’ in an actual explanation, rather than as some slogan you wave about. Explain NATURE, and the intelligence of NATURE, and tell everyone how it works, and why you seem to suppose ‘the intelligence of NATURE’ is anything different from evolution.
Still waiting for an explanation about that ‘desire to survive’ too.

Anonymous said...

Some background info:

http://en.wikipedia.org/wiki/Miacoidea
"The Miacidae (miacids) evolved into the modern Caniformes (dogs, bears, raccoons and weasels), while the Viverravidae evolved into the Feliformes (cats, hyaenas and mongooses), both of the order Carnivora."


http://en.wikipedia.org/wiki/Carnivora
"Carnivorans evolved out of members of the paraphyletic family Miacidae (miacids). The transition from Miacidae to Carnivora was a general trend in the middle and late Eocene, with taxa from both North America and Eurasia involved. The divergence of carnivorans from other miacids, as well as the divergence of the two clades within Carnivora, Caniformia and Feliformia, is now inferred to have happened in the middle Eocene, about 42 million years ago (mya). Traditionally, the extinct family Viverravidae (viverravids) had been thought to be the earliest carnivorans, with fossil records first appearing in the Paleocene of North America about 60 mya, but recently described evidence from cranial morphology now places them outside the order Carnivora.[1] Traditionally, some paleontologists considered the viverravids to be ancestral to the aeluroid carnivorans (felids, hyaenids, herpestids and viverrids), but this is now doubted."

Anonymous said...

heleen is not interested in the extensive, scientific research of Dr. Shapiro on natural genetic engineering. So be it.

Anonymous said...

heleen posted:
"Anonymous should do his/her/its own explanation of what he/she/it has written on this blog."

heleen has referred to me as "it".
In the face of such rudeness, it is only common sense for me to stop responding to him/her.

M. Dionis said...

Anonymous wrote:

And my question is - where did that original SPB (survival instinct) come from? Please explain in evolution terms where it came from originally.

You should still keep on reading some modern biology basics, otherwise my meaningful words will always look incomprehensible to your eyes. Here you have a condensed relevant extract from Futuyma's Evolution (Sinauer Associates, 2005):

The principal claims of the evolutionary synthesis are the foundations of modern evolutionary biology. Although some of these principles have been extended, clarified, or modified since the 1940s, most evolutionary biologists today accept them as fundamentally valid. These, then, are the fundamental principles of evolution [...]

1. The phenotype (observed characteristic) is different from the genotype (the set of genes in an individual's DNA); phenotypic differences among individual organisms may be due partly to genetic differences and partly to direct effects of the environment.

2. Environmental effects on an individual's phenotype do not affect the genes passed on to its offspring. In other words, acquired characteristics are not inherited.

3. Hereditary variations are based on particles - genes - that retail their identity as they pass through the generations; they do not blend with other genes. [...]

4. Genes mutate, usually at a fairly low rate, to equally stable alternative forms, knolwn as alleles. The phenotypic effect of such mutations can range from undetectable to very great. The variation that arises by mutation is amplified by recombination among alleles at different loci.

5. Evolutionary change is a populational process: it entails, in its most basic form, a change in the relative abundances (proportions or frequencies) of individual organisms with different genotypes (hence, often, with different phenotypes) within a population. [...]

6. The rate of mutation is too low for mutation by itself to shift a population from one genotype to another. Instead, the change in genotype proportions within a population can occur by either of two principal processes: random fluctuations in proportions (genetic drift), or nonrandom changes due to the superior survival and/or reproduction of some genotypes compared with others (i.e., natural selection).
Natural selection and random genetic drift can operate simultaneously.

7. Even a slight intensity of natural selection can (under certain circumstances) bring about substantial evolutionary change in a realistic amount of time. [...]

8. Natural selection can alter populations beyond the original range of variation by increasing the frequency of alleles that, by recombination with other genes that affect the saine trait, give rise to new phenotypes.
[...]
11. The differences between different species, and between different populations of the same species, are often based on differences at several or many genes, many of which have a small phenotypic effect. This pattern supports the hypothesis that the differences between species evolve by rather small steps.
[...]
13. Phenotypically different genotypes are often found in a single interbreeding population. Species are not defined simply by phenotypic differences. Rather, different species represent distinct "gene pools"; that is, species are groups of interbreeding or potentially interbreeding individuals that do not exchange genes with other such groups.
[...]


A good exercise for you would be to connect my keywords "inherent variability", "positively discriminated", "increased evolutionary fitness" and "natural selection" with the concepts expressed by Futuyma (of course, this exercise won't exempt you from the fundamental homework of reading something ).

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