You are absolutely right Sean. I do not at all …

Comment on The Basis of Biblical Credibility by Sean Pitman.

You are absolutely right Sean. I do not at all understand the mathematics of sequence space even in Wiki and certainly could not understand the maths. That is why I accept expertise of others and rest easy in the understanding that I have access to such expertise should it impact my life.

The basic math regarding sequence space is relatively simple. For instance, it is very easy to calculate the sizes of sequence space at various levels by simply taking the number of characters in the alphabet and raising that number by the power of the minimum size requirement for the sequence (i.e., the sequence space size needed to hold a 100aa protein is 20^100 = 1e130 sequences). It is also relatively easy to calculate the number of potentially beneficial sequences within sequence space. And, it isn’t that much harder to determine that the distribution of these beneficial sequences is essentially uniform throughout sequence space (although beneficial sequences are clustered into island groups). This information is enough to understand that exponentially greater amounts of time are required for random mutations of any kind to achieve anything beneficial within a higher level of functional complexity.

Sean Pitman: how random mutations must randomly search through many junk sequences in sequence space before natural selection can do anything…

But I do know enough biology to know that what you say may not really be true? Particularly when modern concept of evolution include models of evolution involving IAD innovation amplification and divergence

http://www.ncbi.nlm.nih.gov/pubmed/23087246

and MNR or multinucleotide replacement.

http://www.ncbi.nlm.nih.gov/pubmed/23447710

What do these articles have to do with finding novel beneficial islands within sequence space at various levels of functional complexity? Nothing. Nothing at all. They simply discuss various types of mutations and the differences between genes, but say nothing about the odds of finding a qualitatively novel island of beneficial sequences within a given level of sequence space at a particular level of functional complexity.

For example, here is the abstract of your NCBI paper:

Gene duplications allow evolution of genes with new functions. Here, we describe the innovation-amplification-divergence (IAD) model in which the new function appears before duplication and functionally distinct new genes evolve under continuous selection. One example fitting this model is a preexisting parental gene in Salmonella enterica that has low levels of two distinct activities. This gene is amplified to a high copy number, and the amplified gene copies accumulate mutations that provide enzymatic specialization of different copies and faster growth. Selection maintains the initial amplification and beneficial mutant alleles but is relaxed for other less improved gene copies, allowing their loss. This rapid process, completed in fewer than 3000 generations, shows the efficacy of the IAD model and allows the study of gene evolution in real time.

First off, the function in question already existed in the gene pool to begin with, just at “low levels” of activity. Second, a simple increase in the copy number of the gene enhanced the very same type of function – easy. Nothing qualitatively new evolved here. Third, the function in question is an enzymatic function that doesn’t require more than a few hundred specifically arranged residues for minimum selectable activity.

No wonder this process is very rapid! Of course it would be since it is about as low-level as you can get. This is nothing like what it would take to actually find the minimum structural requirement needed to get a qualitatively novel function to work to at least some minimal selectable level of activity. And, this doesn’t even come close to the minimum requirement of 1000 specifically arranged amino acid residues.

Again, you continue to list off these very very low level examples of evolution in action like they mean something when it comes to explaining higher levels of evolution. That is simply a false assumption due to a lack of understanding of the basic math involved with the problem of sequence space…

Sean Pitman
www.DetectingDesign.com

Sean Pitman Also Commented

The Basis of Biblical Credibility

Your argument that evolution cannot work because Paul Cameron or anyone else lacks a precise mechanism to overcome your declared barrier (1000 fairly specified amino acid residues) is based on the fallacy of ignorance.

Then I suppose SETI science, forensic science, and anthropology are all based on the “fallacy of ignorance” as well? – since these scientists can’t think of any mindless natural mechanism to explain certain types of radio signals, murder victims with certain unnatural features, or pieces of rock with artefactual features?

I’m sorry, but there is no fallacy with the argument for the detection of intelligent design behind various kinds of artefacts – like the origin of a highly symmetrical polished granite cube. It isn’t that these scientists are ignorant of how the phenomenon in question could have been produced by intelligent design. They know how the features they’re considering could have been produced by many different intelligently designed methods. What they don’t know is how the artefact in question could have been produced by any known mindless mechanism of nature. That, my friend, is the very basis of all sciences dealing with the detection of true artefacts of intelligent design.

The very same thing is true of the biomachines within living things that I’m presenting. Clearly, these machines very closely resemble machines that we know were produced by intelligent design. We known and understand how such machines could be produced by various means by intelligent design. What we don’t know is how they could be produced by any mindless natural mechanism this side of a practical eternity of time (i.e., trillions upon trillions of years). This means, of course, that the very best scientific conclusion, the theory with the best predictive power, is that any such biomachine was almost certainly produced by intelligent design.

Now, does the intelligent designer of these biomachines have to be God? No. Not at all. Omnipotence is not required to explain something like a bacterial flagellar motility system. However, even though omnipotence is not required to explain the origin of such machines (to include things like a wrist watch or a granite cube), intelligence of some kind is required.

Does this therefore mean that God did not make something just because God-like power is not required? No. God can make simple stuff just as easily as you and I can make simple stuff. If it just that a God-like creative power is not required to explain everything that God can make. For example, is it possible for God to make a loaf of bread? – the same type of loaf of bread that your mother can make? Sure it is.

It’s funny, don’t you think, that you don’t argue against SETI radio signals or highly symmetrical granite cubes as being anything other than obvious artefacts of intelligent design. Why then the double standard for biological machines that are even farther beyond any known mindless mechanism while being at least closely approximated the creative powers of known intelligent agents?

Sean Pitman
www.DetectingDesign.com


The Basis of Biblical Credibility

You obviously can declare anything you want in terms mutation rates and how many SNP indels and genes were present in the 2 mythical pigs but how many can really be present in the original haplotypes. You have said before that copy number variation was not at all the basis for the genetic richness of the original 2.

I see no reason to argue for a significant difference in past mutation rates as compared to today’s rates. Consider that the pig genome is similar in size to the human genome, ~3 billion bases (haploid). The two pigs on the Ark could easily have had a 0.3% difference in genome sequences to start with (with regard to SNPs). Also, in each family line novel SNPs are produced in each generation for each individual at a fairly high rate (up to 100 per individual per generation). And, the generation time for pigs is ~1 year. A comparison between hundreds of pigs from different family lines, even within the same breeding population of average size, would yield a huge number of SNPs in very short order. So, I don’t see why this is an appeal to “magic”?

As far as “unique genes” are concerned, much of this can be explained by a loss of genetic information by one population vs. the other after the split. This is one of the reasons for the “hybrid vitality” already mentioned. Producing such hybrids gives the hybrid offspring access to genes that are missing from each separate gene pool, but were originally available in the ancestral gene pool.

Of course, the production of novel alleles is also a factor. And, in an average population, any beneficial allelic variation would become fixed in relatively short order.

The differences in indels is interesting, but I see no need to invoke magic to explain a few hundred thousand indels in a comparison of hundreds of pigs – especially since muticharacter mutations are quite common as well and would already have existed within the first pair on the Ark to begin with. For example, there are thought to be thousands of conversion mutations per individual in each generation. Combine this with what is generally assumed to be a high rate of inversions/translocations, ~10 duplications/insertions/deletions (changing up to 20 times the number bases that point mutations change per generation), and >100 satellite mutations, and you have yourself a very high overall mutation rate that adds up to many thousands of nucleotide changes per individual per generation.


The Basis of Biblical Credibility

“The discovery of the Cit + mutants in Lenski’s experiment has been a mote in the eye for those suggesting that major phenotypic innovations cannot be explained by micro-evolutionary (gradual) processes…

Do you know anything about the experiment where Lenski’s produced Cit+ E. coli bacteria?

What Lenski did was to grow E. coli under oxic conditions in citrate-rich media. E. coli bacteria are generally unable to use citrate under oxic conditions as a source of energy. However, they can use it under anoxic conditions. In other words, they already have the gene for citrase in their genome. It is just that it is normally turned off under oxic conditions. How is it turned off? Well, the promoter for the gene that transports citrate into the bacterium is not active under oxic conditions. So, all that needs to happen is to move the citrate transport gene close to a promoter that is actually active under oxic conditions. Once this is done, citrate will enter the bacterium and be used for energy.

And, this is exactly what happened. Nothing structurally new needed to be evolved. After about 31,000 generations, in a large population of bacteria, there was a single genetic mutation in a bacterium that ended up moving the citT gene and placing it under the control of a promoter (rnk) that is active under oxic conditions. The fact that just this single translocation mutation took so long to achieve should clue you in to how difficult it is to achieve even such low-level changes in function via random mutations. The protein product, however, remained the same – i.e., <500aa with no required amino acid changes to achieve a selectable effect. All that was required was to move a pre-existing gene close to a promoter to turn it on during oxic conditions. That's it. The protein itself didn't need to be changed for a useful advantage. Now, at this point, multiple copies of the gene were rapidly produced in some colonies. However, having just one copy was enough to produce a selectable advantage in the citrate-rich environment. It doesn't matter if there are 1 - 9 copies of the gene - the same function is realized to different levels - i.e., the cit+ function can exist, to a selectable degree, with just one copy of the gene producing the the very same protein. Additional "refinements" are easy once at least a minimum useful level of a particular type of function is realized - not a problem at all. Again, this "unicorn" of yours is a very low-level example of evolution in action where nothing structurally new was produced to achieve the function in question. The only thing that happened was a mutational move from one location to another within the genome. That's not a statistical problem for Darwinism at all...

Pubmed still does not have any reference to novel structure composed of 1000 amino acid residues. But indeed there is refence to uinicorns so your 100FSAAR is rarer than unicorns in the biomedical literature. Perhaps you should publish your obvservations.

Tell me, what is the minimum number of specifically arranged amino acids required to produce a rotary bacterial falgellar motility system? Is it possible to reduce it to less than 1000 specifically arranged residues? – without a complete loss of the motility function?

Again, the concept of functional complexity has been published and is well defined in literature, to include the minimum size requirement. I’ve already given you the references a couple times now.

Sean Pitman
www.DetectingDesign.com


Recent Comments by Sean Pitman

Pacific Union College Encouraging Homosexual Marriage?

“Essentially all the administrators, staff and faculty on our campus, including the pastors on our campus already know where I stand. I have never kept any secrets. I have to laugh when I see you say that I am upset because you ‘blew my cover.’ There was no cover to blow.” – Bryan Ness

You’re not the main problem here. I’d have no problem with you personally and what you personally believe at all except that you are a professor in an Adventist school – Pacific Union College.

It’s this school who presents itself as being in line with the primary goals and ideals of the Adventist Church, when it really isn’t. I have friends of mine who have gone to PUC and talked to the leadership about sending their children to PUC. They’ve specifically asked about the situation at La Sierra University and asked the PUC leadership and heads of departments what their position is on teaching the theory of evolution as “the truth” – and if the teachers at PUC support the SDA position on origins and other issues? They were told that PUC does not condone what happened at LSU and that the professors at PUC are fully in line with the SDA position on origins and all of the other fundamental positions of the church.

Of course, you know and I know that this just isn’t true. You, for one, publically speak and teach against the church’s position on origins as well as human sexuality. This reality is not being presented by the leadership of PUC to the parents of potential PUC students. This reality simply isn’t being advertised to the general church membership at all. What PUC should be advertizing to parents and the church membership at large is,

    “Yes, we do maintain professors who teach our students that the church’s position on various fundamental doctrinal issues is in fact wrong and should be changed to reflect the more popular secular position on these topics.”

That’s what it should be telling everyone, but this just isn’t what is being done.

I am attacking no one… Since when is a difference of views an attack on the church?

Since it was placed as one of the church’s “fundamental beliefs” by the church (Link). When you publically publish an article stating that the Church’s position is clearly mistaken and should be changed, that’s an attack on the church’s position.

And of all the issues facing the church, same-sex marriage hardly rises to the level of a “primary goal and ideal.”

The SDA Church has chosen to describe the definition of marriage as being between one man and one woman as one of the “fundamental” messages to spread to the world – as one of the fundamental reasons for its very existence…

Now, you call what you’re doing, not an “attack”, but a “plea for compassion”. However, your plea for compassion is presented as a clear statement that the church’s position is absolutely mistaken – that the church’s position is not at all “compassionate” or even biblical. Now, you may be very honest and sincere in your views here, but that doesn’t mean that you’re not attacking the church’s position in a very real and fundamental way. The fact is that you are making a very clear attack on the church’s position while accepting money from the church as a representative who is supposed to be supporting the church as a paid employee.

Why do you want to cause such people so much pain?

That’s not my goal. However, if a person wants to know what the Bible has to say about what they are doing, I’m not going to pretend that the Bible has nothing to say when the Bible does in fact have something to say. If what the Bible says “causes pain” to a person living in what the Bible says is a “sinful” lifestyle, that’s between them and God. The very same thing is true of me and my own sinful tendencies. If what the Bible says about what I’m doing causes me pain, I can either respond to that by ignoring what the Bible has to say, or I can ask God for help in changing my ways.

Jesus himself said that He did not come to bring peace to those who are living in rebellion against God’s ideals for humanity, but a “sword” (Matthew 10:34). The denial of self and what we naturally want to do given our fallen condition, in order to follow God and what He calls us to do, is often quite painful indeed. That doesn’t mean it’s not the best path to follow. There simply can be no peace between God and those who wish to hang onto what God has said to give up. God does not condemn the sinner for being born broken, but He does warn those who refuse to accept His offer of help to escape their broken condition that, eventually, such refusals of help will not end well for those who are determined to follow their own way.


Pacific Union College Encouraging Homosexual Marriage?
Response from Bryan Ness:

Yet, these professors get very upset when their actions are made public – when they can no longer hide what they are doing from the church at large. – Sean Pitman

Uh, I have never hidden my support and affirmation for LGBTQ+ individuals, and any parent who wanted to know my views on the subject could easily look up what I’ve written, or they could just plain ask me. I openly acknowledge where I stand on these issues on social media too. Essentially all the administrators, staff and faculty on our campus, including the pastors on our campus already know where I stand. I have never kept any secrets. I have to laugh when I see you say that I am upset because you “blew my cover.” There was no cover to blow.

You have not simply let people know what I advocate, you have attacked me personally and impugned my motives and personal spiritual path. You are causing pain not just to me, but to the very people I am trying to comfort and encourage. Your words are not just being seen by the legalistic and judgmental people like yourself, but by parents of LGBTQ+ children and those LGBTQ+ individuals themselves, many of whom are likely already heavily weighed down with self revulsion and depression. And you are doing this for who’s good?

And you wonder why I might be angry and upset? As hard as it is for me to do, I have daily decided to pray for you and those like you that God would soften your heart and show you the grave wounds you are inflicting on God’s beloved. I pray God will help you find compassion and clearer spiritual insight.

Do you really think it’s a “little thing” when our own professors are attacking the primary goals and ideals of the church from the inside? – Sean Pitman

I am attacking no one. You act as if you have not even read my article. I did suggest in there that I think it is time for the church to change and affirm same-sex marriage, but that is not an attack, that is a plea for compassion, a plea that the church return and study this topic again, and I laid out the reasons I think it is fully warranted that we do so. Since when is a difference of views an attack on the church? And of all the issues facing the church, same-sex marriage hardly rises to the level of a “primary goal and ideal.” You are inflating the importance of this topic. the only place where same-sex marriage really rises to a high level of importance is when you are an LGBTQ+ person contemplating marriage, or are the parent, relative or friend of an LGBTQ+ person. Why do you want to cause such people so much pain?


Pacific Union College Encouraging Homosexual Marriage?
Posted by ArkDrey:

The purpose of the H.E. is not to wall people off by modifying curriculum of every subject to fit dogma. The dogma itself has to be enhanced with broader understanding of how to relate various perspectives to these fields of human enterprise.

Certainly, Adventist schools should by no means isolate students from popular ideas that are prevalent within secular culture. If anything, students educated in our schools should have a much better understanding of ideas like neoDarwinism or homosexuality than students educated in secular institutions. However, the education of students within Adventist schools shouldn’t stop here. Adventist education should also give students a reasonable explanation as to why the Adventist perspective on these ideas is actually supported by the Church – by professors who actually personally hold to the Church’s positions on these topics (like the topics of origins or homosexuality, etc).

Again, it is simply counterproductive to have a church school if professors in that school teach that the church’s position is not only wrong, but downright ludicrous, outdated, and completely opposed to the overwhelming weight of “scientific evidence”. Such teaching, by professors that are respected by the students, will strongly influence most students to be naturally opposed to the church’s position on these topics. Clearly then, this would not be in the church’s best interest. It would be far better, from the church’s perspective, not to form church schools at all than to have professors within their own schools attack the church organization from the inside.

But there is world of difference between presenting it as fact that the teacher believes, and a theory with problems. – @ajshep (Allen Shepherd)

I’m in total agreement here. Again, it is one thing to teach about a particular concept that opposes the teachings of the church. It is a far far different thing to then support this particular concept as “true” as compared to showing the students why you, as their teacher, don’t find it convincing.

That is why a teacher, employed by the church, is actually stealing from the church when they attack the church’s position on a given topic from within their own classroom or via a public forum. Such activity simply goes against what a teacher is being paid to do by his/her employer.


Pacific Union College Encouraging Homosexual Marriage?
From David1:

Your presumption and hubris are exactly what Jesus pointed out to those who brought the women caught in adultery. Have you learned nothing from the examples of what it means to be a Christian that you would indulge in such harshness and judgemental words and pronouncements.

Consider that while Jesus most certainly was very kind and gentle and forgiving to the woman caught in adultery (certainly one of the most beautiful stories in the Bible), that He did in fact tell her to “go and sin no more”.

I would say that the very same action and recommendation should be given to all who find themselves part of the LBGTQ+ community. God loves sinners and came to save all of us who find ourselves caught in the web of fallen and sinful lives. He doesn’t condemn us for being broken, but He does offer us a way out and tells us to “go and sin no more”.

In light of this, my problem with the efforts of Dr. Ness is that he is making the claim that there is no brokenness or moral problem with committed monogamous homosexual lifestyles – that the Bible says absolutely nothing in this regard and therefore there is nothing for God to forgive here. There is simply no need to say, “I love you, now go and sin no more”.

I’m also not quite sure why Dr. Ness draws the line with monogamy since he doesn’t accept the Biblical statements, often within the same passages as those discussing monogamy, that speak against homosexual activities? This seems inconsistent to me since it seems quite reasonable, given the arguments presented by Dr. Ness, that polygamy could also be argued as being even more consistent with God’s will and natural genetic mutations that God Himself designed. Upon what “scientific” or “religious” or “philosophical” basis does Dr. Ness draw the line at monogamy as being the clear Biblical standard where God draws the line? – when many have very strong and very “natural” polygamous tendencies?

Of course, I also have a problem with a paid representative of the Seventh-day Adventist Church, who is responsible for teaching our youth in support of the primary goals and ideals of the Church, publicly arguing that these goals and ideals are completely wrong – on the church’s dime. Such activity, even if one is totally convinced as to the error of one’s employer, is unethical since it is a form of stealing from one’s employer.

At the very least, parents who are paying a great deal of money to send their children to one of our church schools should be very well informed as to what they can expect their children to be taught at our schools and what positions the teachers at the school are publicly promoting. Providing this information to such parents is my primary purpose in responding to Dr. Ness’s publicly published article in public forum.


Pacific Union College Encouraging Homosexual Marriage?
Response from Dr. Ness:

Do you not understand what it is like in academia? Differences of opinion among scholars is not only tolerated, it is valued. I have nothing more to say concerning your accusations. Our church has no “official” stand on this issue, if by that you mean I am disavowing my membership in the church by simply believing that gays should allow ro get married to one another. That is not even how our church operates. I can point to many other church employees who openly disagree about certain issues of belief, including this one, and congregations that are fully affirming of same-sex marriage. They are a part of the SDA church just as I am.

My concern still is more about the tone and stance of your attacks. You are attacking fellow SDAs, some of them being the most vulnerable members of our church, and you seem to have no sense of the damage you are potentially doing to these individuals. By attacking me in the fashion you are you are also attacking all those for whom I am standing up. You may want to take Jesus’ words to heart:

But whoso shall cause one of these little ones that believe on me to stumble, it is profitable for him that a great millstone should be hanged about his neck, and that he should be sunk in the depth of the sea. Matt. 18:6

I know very well what it’s like to be involved in leadership positions within the church and within academia. My own father is a retired pastor and teacher. It’s one thing to publicly present and even promote various opinions that do not directly undermine the church or school one is working for. However, it is another thing entirely to directly attack the fundamental positions of the church while being a paid representative of the church. Such activity is not at all encouraged and is, in fact, unethical – a form of theft from your employer. Sure, there are many pastors and teachers who think to do such things anyway. That doesn’t make such activities morally right. It’s still wrong to do what you are doing.