Comment on Gary Gilbert, Spectrum, and Pseudogenes by Sean Pitman.
You will not at all find any scientist in the field in consternation over ENCODE. Rather they are joyfully incorporating these new observations into models of genomic structure and gene regulation that have existed based on simpler and less complete data for some years now.
Yes, and not bothering to note how many creationists predictions are being confirmed these days by the genome project in the face of long-held neo-Darwinian predictions. Evolutionists are very flexible. They are very good at ignoring the various predictions that used to be “key arguments” once they are shown to be false and incorporating confirmed creationist predictions into neo-Darwinism. It’s easy to do when your dealing with just-so story telling instead of a falsifiable scientific theory…
Sean Pitman Also Commented
Gary Gilbert, Spectrum, and Pseudogenes
Don’t be so obtuse here. We’re not talking about publishing just anything in mainstream journals. I’ve published several articles myself. We’re talking about publishing the conclusion that intelligent design was clearly involved with the origin of various artifactual features of living things on this planet. Try getting a paper that mentions such a conclusion published…
Gary Gilbert, Spectrum, and Pseudogenes
That’s not what I said – and you know it. What I said was that science can detect design – even very high-level intelligent design.
Most, even among secular scientists, would agree that it is an obvious truism that if God did actually exist and if God decided to act in a manner detectable as “intelligent” by science, that science could in fact detect those particular actions as requiring deliberate intelligence.
God, if He exists, is most certainly is no less capable of producing a radio signal or a highly symmetrical granite cube or a space craft than is some alien or even human-level intelligence.
As another hypothetical example, say you had one of the loaves of bread that Jesus miraculously made to feed a large crowd. Would you be able to tell that your loaf of bread was in fact produced by a Divine miracle just by looking at it and examining it carefully? Of course not. However, you would most certainly be able to tell that it was the product of intelligent design.
The same is true of various artifacts found within living things – to include higher level functional information stored within the DNA of all living things.
Your repeated requirement for absolute demonstrations to support such conclusions simply isn’t part of science – as you should known since you claim to be a scientist.
4] Why are there different gene copy numbers between the different species but very similar pattern of pseudogenes and structure in higher primates?
Humans; 7 alpha 2 pseudogenes, 6 beta 2 pseudogenes
Chimp; 8 alpha genes 1 pseudgene, 6 beta 1 pseudogene
Because, as I’ve already pointed out, non-coding DNA is more important than coding DNA. Proteins are like the basic bricks and mortar for building a house. Non-coding DNA is the blueprint that dictates how the basic bricks and mortar are to be used – what type of house to build.
5] If the function of pseudogenes are at all important why are there none in platypus or bat that have 6 alpha/4 beta and 6 alpha/2 beta respectively.
Again, as I’ve already explained, just because every creature doesn’t share the same functionality doesn’t mean that functional sequences aren’t beneficial in the creatures they’re in. Just because you can live without your legs or arms doesn’t mean that they’re not important to you.
6] Across the species examined almost all the homologs have pseudogenes in some species of other.
So what? Lots of systems have homolog components. That has nothing to do with explaining the novel functional differences beyond very low levels of functional complexity. In human design it has more to do with conservation of design when building similar systems with similar structural and functional needs.
7] If you look at figure 4 you will see that the progression of beta gene expression through life is seen with greatest complexity in primates and humans but is not a feature of marsupials or monotremes where only embyronic and fetal/adult forms of the beta and alpha components of haemoglobin is produced.
Again, so what? This says nothing about the enhanced functionality of the primate system and does not speak speak against the argument that only intelligent design could have produced these enhancements – unless you can actually come up with a statistically viable mechanism. Of course, you haven’t done this. You admittedly have no idea how RM/NS can produce much of anything beyond very low levels of functional complexity. You just have faith, blind faith, that somehow someway, it must have happened. It’s not testable in a falsifiable manner and it is not demonstrable either. Again, that’s not science. That’s blind faith philosophy – a form of blind faith religion.
8] If you look at figure 5 the complexity of regulation in an erythroid cell line is evident and shows that the encode data for transcriptional factor binding sites and DNase hypersensitivity sites really does not show significant activity at the site of the beta pseudogenes (figure 5c). It is hard to argue that it has importance compare to to the LCR region
You’re completely ignoring the other reasons for its importance and overall functionality and the reason why it is so heavily conserved by natural selection. The beta pseudogenes appear to have only a limited job for a very limited time. This does not mean, however, that their function is therefore non-beneficial or unimportant.
Recent Comments by Sean Pitman
Science and Methodological Naturalism
Very interesting passage. After all, if scientists are honest with themselves, scientific methodologies are well-able to detect the existence of intelligent design behind various artifacts found in nature. It’s just the personal philosophy of scientists that makes them put living things and the origin of the fine-tuned universe “out of bounds” when it comes to the detection of intelligent design. This conclusion simply isn’t dictated by science itself, but by a philosophical position, a type of religion actually, that strives to block the Divine Foot from getting into the door…
Why is it that creationists are afraid to acknowledge the validity of Darwinism in these settings? I don’t see that these threaten a belief in God in any way whatsoever.
The threat is when you see no limitations to natural mindless mechanisms – where you attribute everything to the creative power of nature instead of to the God of nature.
God has created natural laws that can do some pretty amazing things. However, these natural laws are not infinite in creative potential. Their abilities are finite while only God is truly infinite.
The detection of these limitations allows us to recognize the need for the input of higher-level intelligence and creative power that goes well beyond what nature alone can achieve. It is here that the Signature of God is detectable.
For those who only hold a naturalistic view of the universe, everything is attributed to the mindless laws of nature… so that the Signature of God is obscured. Nothing is left that tells them, “Only God or some God-like intelligent mind could have done this.”
That’s the problem when you do not recognize any specific limitations to the tools that God has created – when you do not recognize the limits of nature and what natural laws can achieve all by themselves.
Since the fall of Adam, Sean, all babies are born in sin and they are sinners. God created them. Even if it was by way of cooperation of natural law as human beings also participated in the creation process.
God did not create the broken condition of any human baby – neither the physical or moral brokenness of any human being. God is responsible for every good thing, to include the spark or breath of life within each one of us. However, He did not and does not create those things within us that are broken or bad.
“The owner’s servants came to him and said, ‘Sir, didn’t you sow good seed in your field? Where then did the weeds come from?’ ‘An enemy did this,’ he replied. “The servants asked him, ‘Do you want us to go and pull them up?'” Matthew 13:27-28
Of course, all humans are indeed born broken and are in a natural state of rebellion against God. However, God is not the one who created this condition nor is God responsible for any baby being born with any kind of defect in character, personality, moral tendency, or physical or genetic abnormality. God did not create anyone with such brokenness. Such were the natural result of rebellion against God and heading the temptations of the “enemy”… the natural result of a separation from God with the inevitable decay in physical, mental, and moral strength.
Of course, the ones who are born broken are not responsible for their broken condition either. However, all of us are morally responsible for choosing to reject the gift of Divine Grace once it is appreciated… and for choosing to go against what we all have been given to know, internally, of moral truth. In other words, we are responsible for rebelling against the Royal Law written on the hearts of all mankind.
This is because God has maintained in us the power to be truly free moral agents in that we maintain the Power to choose, as a gift of God (Genesis 3:15). We can choose to accept or reject the call of the Royal Law, as the Holy Spirit speaks to all of our hearts…
Remember the statement by Mrs. White that God is in no wise responsible for sin in anyone at any time. God is working to fix our broken condition. He did not and does not create our broken condition. Just as He does not cause Babies to be born with painful and lethal genetic defects, such as those that result in childhood leukemia, He does not cause Babies to be born with defects of moral character either. God is only directly responsible for the good, never the evil, of this life.
Again, your all-or-nothing approach to the claims of scientists isn’t very scientific. Even the best and most famous of scientists has had numerous hair-brained ideas that were completely off base. This fact does not undermine the good discoveries and inventions that were produced.
Scientific credibility isn’t based on the person making the argument, but upon the merits of the argument itself – the ability of the hypothesis to gain predictive value when tested. That’s it.
I agree with Prof Kent. I think you have a few problems
1] You have used an arbitrary statistical limit to define a universal limits of evolutionary development and speciation
The limitation is not arbitrary. It is both observed in real time and can be calculated to show that it (a minimum requirement of 1000 specifically arranged residue positions) is the most likely limitation this side of trillions of years of time – from the perspective of RM/NS.
2] You have conceded that 80-90% of the genetic variation between species has been acquired over 4000 years. (I am surprised that you feel able to extend this to 5000 years given EG White’s writings.
It depends upon what type of variation you’re talking about. Certainly all variation at lower levels of functional complexity could easily be realized in this period of time.
3] You allow for rapid development of phenotype and novel repurposing of proteins in the development of evenomation
DNA can and does rapidly mutate – true.
4] You claim some value for a limit of 1000fsaar but do not seem able to identify concrete examples of this during speciation.
Speciation is not based on producing novel functional complexity beyond very low levels of functional complexity. In fact, speciation can be based on functionally neutral genetic changes. Also, there are no examples of evolving beyond the level of 1000 specifically arranged amino acid residues because it is statistically impossible to do so. Only variations at low levels of functional complexity can be or ever have been demonstrated.
5] Indeed comparative genomics between man and apes suggests that the differences between these species is mostly at the single nucleotide level and in gene duplications
and that there seems to be none of the barriers of 1000fsaar complexity that Sean suggests to limit evolution of homo sapiens from an hominid ancestor common with great apes.
Humans and apes are quite different in various respects, to include brain structure and function – which is thought to be based on numerous differences in genetic regions that code for miRNAs (around 8% of which are human specific).
“miRNAs recently have been implicated in synaptic development and in memory formation. As the species specific miRNAs described here are expressed in the brain, which is the most complex tissue in the human body, with an estimated 10,000 different cell types, these miRNAs could have a role in establishing or maintaining cellular diversity and could thereby contribute to the differences in human and chimpanzee brain … function.”
Eugene Berezikov, Fritz Thuemmler, Linda W van Laake, Ivanela Kondova, Ronald Bontrop4, Edwin Cuppen & Ronald H A Plasterk, “Diversity of microRNAs in human and chimpanzee brain”, Nature Genetics, Vol 38 | Number 12 | December 2006 pp. 1375-1377.
The Y-chromosome is even more unique. A study published by Nature in early 2010 showed many striking differences between human and chimp chromosome structure, gene content, and even qualitatively unique genes between the two species. As far as looking at specific genes, the chimp and human Y-chromosomes seem to have a dramatic difference in gene content of up to 53 percent. In other words, the chimp is lacking approximately half of the genes found on a human Y-chromosome. Because genes occur in families or similarity categories, the researchers also sought to determine if there was any difference in actual gene categories. They found a shocking 33 percent difference. The human Y-chromosome contains a third more gene categories, entirely different classes of genes, compared to chimps.
Hughes, J.F. et al. 2010. Chimpanzee and human Y chromosomes are remarkably divergent in structure gene content. Nature. 463 (7280): 536-539.
For further discussion see:
6] You define species classification as being arbritary but have some nebulous concept of a barrier of complexity for potential changes induced by the acquired changes which you concedes occurs rapidly and frequently.
This limit to complexity you relate to some theoretic 1000fsaar limit.
Again, this limit is both observable and calculable based on known distributions and densities of viable sequences in sequence spaces at various levels of functional complexity.
You seem to support models of rapid evolution by Darwinian mechanism inside a 1000fsaar limit; if you think them scientific they must be tested by reference to reality and real data. I suggest you look at the genomic data and point out the genetic differences that correspond to your 1000 FSAAR limit.
I’ve given you numerous examples already of systems that require a minimum of far more than 1000 specifically arranged residues. How many more examples do you need?
You might like to also comment on you model of evolution of all Y chromosome variation that exists today from a single Y chromosome 4000 years ago at the time of flood.
In case anyone suggests there were 4 males on the boat and therefore there were 4 Y chromosomes, Noah and his 3 sons would all have the one identical Y chromosome because of transmission from Noah to his sons. Humans in terms of Y chromosomes are equivalent to a breeding pair.
The variation in the Y chromosome in humans today, like all other unclean animals must therefore date to mutations in the last 4000 years.
All this genomic sequence is now freely available so there is no excuse for not testing it except the paucity of value you see in your arguments.
What testing would you want? Low level genetic changes can and do take place very fast – especially in larger populations. There are no examples of higher level changes because, statistically, they are impossible this side of a practical eternity of time.
Both Jeff Kent and I have both offered advice in publication of these experiments in the peer reviewed literature.
Until you give me some real evidence based on experimental data you seem to be simply doing what Bob Ryan abhors; telling just so stories.
Sit down. Do the math for yourself. Then, come back and talk to me about who is telling the just-so stories regarding the creative potential of random mutations and natural selection (RM/NS).