Here are some thoughts I’ve been having recently that surely touches the interface of science and faith, but is not one I’ve seen discussed much as the usual favourites (evolution, . . . → Read More: Thoughts about Psychopathy and the Moral Law]]> Hi, everyone, I’m back after a long gap.  Hopefully in this new format the waters will be calmer than they were at the end of last year.

Here are some thoughts I’ve been having recently that surely touches the interface of science and faith, but is not one I’ve seen discussed much as the usual favourites (evolution, climate change, the environment etc).

C.S. Lewis writes in “Mere Christianity” of what he calls the “Moral Law” – the innate sense of right and wrong that we seem to have instilled in us – which gives us a conscience.  Francis Collins, in his book “The Language of God” writes that it was the existence of this Moral Law, and indeed our awareness that we often break this law wantonly, that shattered his atheism and ultimately brought him to faith in Christ.  He argues that it is a pointer towards the existence of God, but warns about falling for the “God of the Gaps” analogy.

I think Paul is writing about the same thing in Romans 2:14-15 thus:

(Indeed, when Gentiles, who do not have the law, do by nature things required by the law, they are a law for themselves, even though they do not have the law, since they show that the requirements of the law are written on their hearts, their consciences also bearing witness, and their thoughts now accusing, now even defending them.)

(I find it wonderful that such a large grain of wisdom is contained in a parenthetical comment!)

However my thoughts have been stretched recently into thinking about psychopathy, and how this fits into the picture.  Psychopathy is characterized as an inability to feel remorse, guilt, conscience, empathy towards victims, and also severe emotional detachment.  Many psychopaths are of course in jail – and it is common to hear a judge condemning a serial killer or rapist as not showing any remorse for their crimes, as if this somehow makes them more evil.  Such people are often condemned as “evil” especially by the press, and of course the acts they commit are indeed evil.

But is this all just a symptom of an illness, which they can’t help?  Dr. Kent Kiehl is a cognitive neuroscientist who is researching into psychopathy using fMRI scanning techniques, on prison inmates, to see if one can find specific brain abnormalities that lead to psychopathic behaviour.  It  is hoped eventually that this might lead to possible treatments to reduce psychopathic tendencies.  The work is described in this New Yorker Article.

I am wondering where all this leaves the moral law argument?  If psychopaths are people without a functioning conscience this is a kind of disability – and it points to the idea that not all of us have an innate sense of right and wrong as Lewis suggests.  The problem is perhaps wider than just prison inmates – prisons contain  ”failed psychopaths”, but it is believed there are many more successful psychopaths out there who have succeeded by manipulating and exploiting other people without the normal pangs of conscience and the constraining aspect that most of us feel guilty when we do something wrong.

I don’t have any real answers to this, or indeed any firm conclusion, but I’d be interested to see if anyone else has some interesting insights into this.

Audio files of talks are being posted at http://www.asa3.org/ASAradio/ASA2008podcast.xml

Attendees and ASA members . . . → Read More: Science, Faith, and Public Policy]]> The 2010 ASA annual meeting is set to begin on Friday July 30. The first plenary talk will feature Congressman Venon Ehlers, an ASA member for many years. Other plenary speakers and contributed papers can be seen in the final program and the abstract book.

Audio files of talks are being posted at
http://www.asa3.org/ASAradio/ASA2008podcast.xml

Attendees and ASA members are encouraged to use the comment feature of this post to submit comments and questions pertaining to any aspect of this meeting. Speakers will be encouraged to respond to any question directed to them.

The goal of our organization is to facilitate dialog among Christians in a context of Christian love, without fear of unjust condemnation. We do not shy from controversial topics but encourage respectful discussion of any topic related to science and faith, within the context of our statement of faith and our commitment to integrity in the practice of science.

Let the discussion begin.

Randy

1. 73% of Christian professionals in the sciences affirmed the following: “Plants and animals developed through evolutionary processes” (with natural and/or non-natural causes from ancestral forms) 2. 60% affirmed “Plants and animals developed through evolutionary processes with natural causes from ancestral forms.” 3. 61% affirmed “Biologically, Homo Sapiens evolved . . . → Read More: Hamilton’s Rule]]> A recent poll of ASA members showed some interesting results.

1. 73% of Christian professionals in the sciences affirmed the following: “Plants and animals developed through evolutionary processes” (with natural and/or non-natural causes from ancestral forms)
2. 60% affirmed “Plants and animals developed through evolutionary processes with natural causes from ancestral forms.”
3. 61% affirmed “Biologically, Homo Sapiens evolved through natural processes from ancestral forms in common with primates.”

There was one key area where the support dropped that I want to explore. Only 27% affirmed “Human behaviors, like kindness, care for children, competition, or desire for revenge, developed through evolutionary processes with natural causes.” Note that this is less than the 40% that affirmed “Living organisms on earth developed through evolutionary processes with natural causes from non-living material more than 3 billion years ago.”

The reason for this in my opinion is that while the theory of evolution has great explanatory power there are areas where to date it hasn’t. One such area is cooperation or altruism. Furthermore, the implications of “nature red in tooth and claw” goes against our Christian beliefs. This kind of ambivalence to evolutionary theory by Christians goes all the way back to Darwin’s “Origin of Species”.

Darwin added the following quote of Charles Kingsley to his second edition:

A celebrated author and divine has written to me that “he has gradually learnt to see that it is just as noble a conception of the Deity to believe that He created a few original forms capable of self-development into other and needful forms, as to believe that He required a fresh act of creation to supply the voids caused by the action of His laws.”

On the other hand, fellow evolutionist Alfred R. Wallace advocated to Darwin to use Spencer’s term “survival of the fittest” as a synonym for natural selection. Darwin did do this starting in his fifth edition.

From the use of this term, many Christians inferred social darwinism. (Whether social darwinism really is implied is historically dubious.) It is the social darwinism of laissez faire economics more than anything else that motivated William Jennings Bryan during the Scopes trial. He said the following on the age of the earth question: “It is better to trust in the Rock of Ages than to know the ages of rock.”

Since Darwin, evolutionary theory has struggled to explain cooperative or altruistic behavior in humans and eusocial creatures. One such attempt is known as Hamilton’s Rule.

Formally Hamilton’s Rule is genes should increase in frequency when

rB > C

where
r = the genetic relatedness of the recipient to the actor, often defined as the probability that a gene picked randomly from each at the same locus is identical by descent.
B = the additional reproductive benefit gained by the recipient of the altruistic act,
C = the reproductive cost to the individual of performing the act.

This is known more informally as kin selection. Since this only explains sacrifice for related creatures the self-sacrifice for the “unrelated” is still unexplained. That was until an apparently little-noticed paper two weeks ago in Science.

Hamilton’s rule states that cooperation will evolve if the fitness cost to actors is less than the benefit to recipients multiplied by their genetic relatedness. This rule makes many simplifying assumptions, however, and does not accurately describe social evolution in organisms such as microbes where selection is both strong and nonadditive. We derived a generalization of Hamilton’s rule and measured its parameters in Myxococcus xanthus bacteria. Nonadditivity made cooperative sporulation remarkably resistant to exploitation by cheater strains. Selection was driven by higher-order moments of population structure, not relatedness. These results provide an empirically testable cooperation principle applicable to both microbes and multicellular organisms and show how nonlinear interactions among cells insulate bacteria against cheaters. [Emphasis mine.]

Here’s how Smith et al generalized the rule:

To bridge the gap between theory and data, we derived a generalization of Hamilton’s rule that does not assume additivity or weak selection and whose parameters are empirically measurable (21). We found that cooperators increase in frequency if

r . b – c + m . d > 0 (1)

Distributions can be described by their moments: parameters that measure their shape and location. The relatedness vector r = {r1, r2, …} measures how the distributions of social environments encountered by cooperators and noncooperators differ in each of these moments (fig. S2). r1 is equivalent to r in Hamilton’s rule (5). The other terms are higher-order relatedness coefficients (22, 23). Any smooth function can be expanded into a Taylor polynomial series whose coefficients measure its linear, quadratic, and higher-order components. The benefit vector b describes noncooperator fitness as a function of social environment (red lines in Fig. 1) in terms of its Taylor coefficients. c is the cost of cooperation when all neighbors are noncooperators. m d is nonzero when benefits depend on recipient genotype (Fig. 1C). m is the moments vector for cooperators. d is the difference between the Taylor series of cooperators and noncooperators. Unlike Hamilton’s rule, Eq. (1) disentangles fitness effects from population structure and is valid for arbitrarily complex forms of social selection. When fitness effects are additive, Eq. (1) reduces to rb – c > 0.

Fig. 1. Measuring the costs and benefits of cooperation in microbes. Blue, cooperator fitness; red, noncooperator fitness. (A) In Hamilton’s rule, b is the slope of fitness against the frequency of cooperators among social neighbors; c is the fitness difference between cooperators and noncooperators for a given social environment. Fitness effects are nonadditive when benefits are (B) nonlinear or (C) depend on recipient genotype.

Putting this into English, it was the population structure rather than kinship that selected for cooperators of M. xanthus over cheaters, aka Richard Dawkin’s “selfish gene”. Furthermore, this work takes Hamilton’s rule from a heuristic to an empirically useful structure to look at other social structures. So, I suspect we will see a lot of followup on this in the coming years. It also challenges our intuitive concept of what constitutes the “fittest” which survives.

One thing that those of us who are critical of intelligent design are fond of saying is that it promotes a God of the gaps. The study above shows that we should be careful of our own gaps. Whether it’s research like this or the RNA World concerning origin of life or even multi-verses we should be careful that our apologetics doesn’t lean too heavily upon a lack of a natural explanation. History has shown that such an explanation often does come along even if it takes a long time. I’ll close re-quoting Kingsley’s warning to us about gaps — this time as he wrote Darwin in 1859:

I have gradually learnt to see that it is just as noble a conception of Deity, to believe that he created primal forms capable of self development into all forms needful pro tempore & pro loco, as to believe that He required a fresh act of inter-vention to supply the lacunas wh. he himself had made. I question whether the former be not the loftier thought.

Now about me: I’m making good progress. I am in my third cycle of . . . → Read More: Book review:”Fire, ice and paradise” & My progress]]> I’d like to call your attention to the above titled book by H. Leighton Steward, which is reviewed on my blog at
http://bricolagia.blogspot.com/2010/05/more-satisfying-view-of-anthropogenic.html. It seems that many geologists take a different view of AGW than climatologists, and their views should be taken into account.

Now about me: I’m making good progress. I am in my third cycle of chemotherapy and the bad proteins have come down by about 66%. When they get down near zero I will have a stem cell transplant at M. D. Anderson Cancer Center in Houston. Your prayers will be appreciated.

I’ve been debating global warming here for years because I believe that evangelicals have been manipulated by the energy companies and their political and . . . → Read More: Where’s the Outrage?]]> Since I’m revisiting the BP spill disaster, you might assume from my title I’m talking about the President. I’m not. Rather, I’m talking about evangelicals in general and global warming skeptics in particular.

I’ve been debating global warming here for years because I believe that evangelicals have been manipulated by the energy companies and their political and ideological allies. The energy companies want two things. The first is less regulation and the second is to limit their exposure to legal liability. In the case of the latter, this has been done since the 70s when current global warming skeptics such as Richard Lindzen were hired to claim that cigarettes did not cause cancer. As a Brown and Williamson memo put it:

Doubt is our product since it is the best means of competing with the ‘body of fact’ that exists in the mind of the general public. It is also the means of establishing a controversy.

Energy companies such as BP latched onto this strategy. They also sought to promote offshore drilling in the last presidential campaign and gained the support of conservative evangelicals. I received a flier from the political arm of Focus on the Family concerning the Senate race in Colorado. In it they listed offshore oil drilling as a family-related issue!

Just before this blog was formed I was asked why I was not commenting on the so-called ClimateGate. My response then was since this was the result of a crime that it was inappropriate to make comments on it. Since then, official investigations have largely exonerated the participants and some are ongoing. What I find ironic is the accusations made then and how they apply to the current situation:

1. The scientists manipulated research to make things fit their preconceived notions.
2. The scientists blocked independent researchers from accessing their data.

First of all, BP and other oil companies created an illusion that oil was simply not running out in the U.S. and thus more oil production in environmentally sensitive areas would give us more “energy independence”.

Look at this ASA e-mail post from August 2004, entitled Funny Numbers and note from where the “funny numbers” came:

Looking at the 2004 BP Statistical Review of energy shows up lots of funny
numbers. Here are a couple I found interesting
With respect to tables listing “Proven Reserves” of Oil:

1. of 53 geographical regions covered in the review, the proven reserves of 39
   of them were exactly unchanged from the previous year. For example the US is
   reported to have 30.7 billion barrels (Bbbl) of proven reserves at the end of
   2002 and again at the end of 2003, this despite the fact that domestic
   production amounted to 2.7 Bbbl during 2003. Similarly 10 out of 11 of the
   Middle Eastern country’s reserves are unchanged from the previous year despite
   production of some 8.25 Bbbl of oil in 2003 from these nations.
2. eight producing regions listed small declines in oil reserves; 6 listed
   small increases in reserves; overall, according to the BP report, world proven
   reserves of oil grew from 1146.3 Bbbl in 2002 to 1147.7 Bbbl in 2003; this
   despite world production of more than 28 Bbbl of oil in 2003. Remarkably, most
   nations, including the US, must be discovering new reserves at exactly the same
   rate that we are producing oil.

And note this post by ASA member and oil industry expert Glenn Morton from February 2005:

“The Gulf of Mexico shelf has a serious problem–declining production that is not being arrested. Production from shelf wells has dropped from above 333 MMbbl and 4.8 tcf in 2000 to a projected 186 MMbbl and 2.5 tcf in 2004. The 244 MMbbl of produced oil in 2003 is down 27% from 2000. Oil production for 2004 is expected to drop 44% from 2000. Gas production in 2003 at 3.3 tcf is down 1.5 tcf, 31% off the 4.8 tcf produced in 2000.” James Dodson, Ted Dodson, Victor Schmidt, “GoM deep Shelf Incentive Fails to Overcome Decline,” Offshore, Jan 2005, p. 35

And the situation has not gotten any better since then. The EIA has noted that OCS production will only decrease gasoline prices by pennies a gallon in the 2020s. The oil industry has misrepresented the amount of so-called energy independence these risky wells will produce.

Second of all, that’s not the worst of it. BP low-balled the spill rate from the beginning. Why? Because it reduces their exposure in court. The same M.O. that was used in global warming denial was done by one of their executives on Anderson Cooper called the larger — read more and more accurate with every passing day — estimates “alarmist”. They also said estimates of the flow could not be done like what was claimed with respect to the computer models for global warming.

Furthermore, independent scientists have been blocked from measuring the flow or have access to injured wildlife. Employees and contractors of BP have been required to sign onerous non-disclosure agreements. Media cameras have been blocked from sensitive areas.

But so what? Because of the low estimates there is now insufficient production capacity to remove the oil from the cap BP installed. This is why it’s important to have the best estimates. Even if the blowout could not have been avoided and this is the best mitigation that could be done, the bad estimates are causing oil to go into the Gulf that could have been avoided with sufficient production resources in place. The same holds true for the low-ball estimates of the global warming skeptics. The same people are telling us that anthropogenic global warming is under control and we can fix whatever problems are caused by it. Fool me once…

BP is doing the exact same thing that got all the people incensed about ClimateGate. Where’s the outrage? So far I’ve heard crickets.

Venter’s achievement is remarkable and embodies two critical accomplishments–first, the use of a chemically (vs. biologically) synthesized chromosome. Venter’s chromosome had never . . . → Read More: Thoughts on Craig Venter’s Synthetic Cell]]> On May 10 ScienceExpress published on-line Craig Venter’s Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. A talk by Venter given last year at TED.com is a good introduction to the work.

Venter’s achievement is remarkable and embodies two critical accomplishments–first, the use of a chemically (vs. biologically) synthesized chromosome. Venter’s chromosome had never seen a cell prior to its “booting up” in the new host. Of course, the sequence was based on a known bacterial chromosome, but contained modified genes to distinguish it from the host cell and with “watermarks” (more on that later).

The second accomplishment is that the synthesized chromosome was inserted into a host cell (with different DNA from a different species). The system was engineered so that the original host cell DNA would be destroyed and that the new chemically synthesized chromosome would be preserved. This happened and the cell was transformed to function according to the new “program”, the new synthesized chromosome.

This is a remarkable achievement and paves the way to all sorts of future experiments. In principle, however, this is merely a large-scale and chromosome level version of already existing recombinant DNA technology. Venter calls this a “synthetic cell” and at this point I consider this to be mostly hype. Future experiments may result in something that could be called a “synthetic cell”, but for now this is an already existing cell transformed by a chromosome replacement. Thus, the ethical implications of this seem minimal to me.

The ScienceExpress paper notes:

Phenotypic effects of the recipient cytoplasm are diluted with protein turnover and as cells carrying only the transplanted genome replicate. Following transplantation and replication on a plate to form a colony (>30 divisions or >109 fold dilution), progeny will not contain any protein molecules that were present in the original recipient cell. This was previously demonstrated when we first described genome transplantation. The properties of the cells controlled by the assembled genome are expected to be the same as if the whole cell had been produced synthetically (the DNA software builds its own hardware).

Thus within 30 generations, the proteins of the bacterium have been completely determined by the new chromosome. Presumably this would eventually be true of cellular components synthesized by these proteins.

Starting off with a living bacterial cell (even if the DNA has been destroyed) limits the claim of “synthetic cell.” Again, I’m not in the least trying to minimize Venter’s accomplishment, but he started with a living system and synthesized a chromosome that used the same genetic code as the starting living system. I will wait for “booting” the DNA without a starting living system before I apply the moniker “synthetic cell.” That seems a bit more difficult. Since the entire chromosome is synthesized, why not alter the genetic code, i.e. change the aminoacyl-tRNA synthetases so that there is a completely novel relationship between the DNA and amino acid sequences. At first glance this would require booting from scratch, without the presence of the pre-existing living cell, but accomplishing this would be a convincing proof of concept.

Questions have arisen about such experiments in eukaryotes. Could we regenerate a Neanderthal, or a woolly mammoth, or a Tasmanian wolf (organisms for which the code exists “digitally”)? Epigenetic factors in the fertilized egg into which the synthesized chromosome was “booted” would influence development at first. (Think about the chimp with human DNA in Michael Crichton’s Next). But, if it is true that the original epigenetic factors are diluted after a number of generations as in the bacterial case, then perhaps we would end up with something very close to the organism originally coded for by the synthesized DNA. No control exists, however, so we will never know if we have the real Neanderthal or just something very close.

In the TED video Venter comments on the success of this project as showing that via genome acquisition and incorporation, fast and large-scale evolution is demonstrated. Indeed, Mycoplasma capricolum evolved into Mycoplasma mycoides in one generation (or at most 30 generations).

Venter’s watermark is fascinating, and I think somewhat relevant to the intelligent design debate. Venter’s synthetic chromosome spells out the following “words” in some sections of the coded proteins using the one-letter codes of the amino acids coded for by the synthesized gene:

VENTERINSTITVTE
CRAIGVENTER
HAMSMITH
CINDIANDCLYDE
GLASSANDCLYDE

Without overly simplifying the ID argument, it has often struck me that if God wanted to give us a definitive proof of His hand in Creation he could have done such a thing by writing out a message in English (or whatever language you like) using the one letter amino acid codes. (Think about Sagan’s Contact and the message encoded in the digits of pi.) How does the ID argument fare even here? Are these “watermarks,” which we know are intelligently designed, detectable?