Doubting Didymus

Welcome back.

Well, I confess that I am not all that familiar with the intelligent design movement. That study is a luxury I can not afford to fit alongside my study of actual biology. I didn't think that IDists were primarily concerned with the ability of darwinian mechanisms to increase information. I thought that was more a YEC thing, and IDists were more concerned with things like detecting supposedly reliable indicators of design, pointing to irreducible complexity, and so on. However, you are probably more up to date with that area, so I will defer to your knowledge.

Hold it right there! First of all, 'purposeful breeding' wasn't neccesarily involved in laboratory examples. There are many cases where speciation has occured by accident, as a side effect of two populations being kept separated from each other for a long time in the course of running expermiments with unrelated goals. Secondly, we've seen it happen outside the laboratory without any sort of human involvement. So I hope we can settle that matter.

Ahh bugger. This is one of the trickiest ideas to get across. You know how to make things hard on us, don't you?

If I were a cruel man, I'd be asking you to give a robust and consistent definition of genetic information that we can work with, but I know that that is a bit too hard even for the leaders of the ID movement. Evolutionary scientists, on the other hand, have an easier time: the genome is spoken of, NOT in terms of "information", but in terms of net fitness. It doesn't matter what information is in it, really. Natural selection makes modifications to genomes that increase net fitness in the enviromental context the organism finds itself in. Losing a negative feature is as good for the organism as gaining a positive one.

I know that's not going to satisfy your point, however. I'm just pointing out that IDists and evolutionary scientists are looking at the effect of natural selection in two different contexts. I do know what you are really looking for. You want evidence of a beneficial mutation that is actually adding something to the genome, right? You want to see a novel protein or other polypeptide appear that wasn't there before. If so, I think your standards are too high. The best you will get is the modification of an existing gene that improves or otherwise modifies its function. That is how evolution works. You can't go from nothing at all to something as complex as a protein with selectable effects in a single step. What you CAN do is more subtle: you are aware of gene duplications, right? Well, what if a gene were duplicated in such a way that it makes effectively no difference? You end up with two functional genes doing the same job. Natural selection is then free to pick out mutations in ONE of the two that actually stop it doing its job, and make it do something slightly different. The other gene is still doing its job, but the new gene can end up doing something slightly new. I can not imagine how that could not be considered an increase in information. Where you had one function, you now have two. The point is, you should not be expecting wild new features springing from nowhere under the eyes of watchful observers. What we expect to see if we are seeking increases in genome information are small subtle modifications to existing genes.

I give you three known phenomena with much empirical support:

1) mutations exist, and can make modifications to genes that benifit the organism.
2) Natural selection is easily capable of spreading such mutations through a population.
3) Copying errors can add genetic material to the genome in many ways, one of which is the duplication of existing functional genes.

Given these, what problems to you see with the origin of bacteria, or with anything else for that matter?

Lets not. Lets stick with what the actual topic was, and bring that to a satisfactory conclusion first.

The topic was that there is: "no way, in principle, that an eye can be formed in incremental steps"

A photocell is NOT an eye. It performs none of the functions we attribute to eyes, and is essentially worthless as an organ for seeing. For now you may imagine the origin of the photocell in any way you like. Lets imagine an organism feels its way around using very sensitive touch sensors. Imagine a change in the sensory phospholipid membrane protein receptors (that are directly coded for by genes), that makes it stimulated by photons. Thats not too difficult to imagine, as there are a number of such proteins in non-vision related receptors. Chlorophyll on the photosystems of plant cells is one (though certianly not related to animal eyes of course).

Thats just an imaginary hypothetical I pulled out of my imagination. We probably dont know exactly how it happened and never will. But its not the point, and its not the immediate topic. I have provided you a series of transitionals, each one no different from the last than two siblings might be. So, what problem is it that you see with the formation of an eye in incremental steps? Is it really just the first photocell? Are you okay with an entire eye forming from natural selection, if only a photocell was possible?

See, you can't just seek out the dark spots in our knowledge, like the origin of the first photoreceptor or the bacterial flagella, point to them, and demand a robust theory with supporting evidence that accounts for its existance. It is telling that the things ID are most fond of talking about just happen to be things that occured in the deepest darkest past, from which no evidence is reaching us and probably never will, and say "There!, there in that invisible patch, is the thing that disproves darwinism. We demand that evidence from that specific place be brought to us."

Vorkosigan

Was it philsophy proceeding from science or science proceeding from philosophy. He obviously argues the latter, and I find it hard to disagree with him.

Look...after the end of the 18th century naturalists were in a ferment. On one hand it was overwhelmingly obvious that organisms had changed over time. On the other, nobody could specify how. In 1756 Linnaeus had attempted to lay the problem to hybridization, for he had noticed that while it was easy to classify animals into groups with a common ancestor, it was difficult to identify which one was the original kind. Unfortunately for him, hybridization as the source of diversity was annihilated by the primitive evidence scientists could muster even back then.

There then came a long, long period of throwing out ideas to explain the origin of this diversity, along with using the word "evolution" in this context as early as 1826. Lamarck's was only one such theory. What Darwin did was not identify change -- that was a solid fact for more than a century before him -- but explained why such change occurred.

This idea that Darwinism emerged and was adopted everywhere is triumphalist mythology, I suspect a deliberate creation of Creationists working with heroic histories of another day. The reality is that in some places Darwin retained influence, in others it nearly disappeared. In the US a form of neo-lamarckism became extremely popular for a period in the late 19th century (Darwin saw a limited role use-inheritance a la Mendel) and in Germany as well. Darwin faced a seriously problem in that he did not have a mechanism for transmission of genetic information. Ironically, Mendel's revolutionary thesis sat on his shelf, unread.

What happened was that different fields adopted different paradigms. In experimental biology Lamarckism was abandoned as Mendel was rediscovered and modern genetics was born. Suddenly Darwin was vindicated completely, in that field. At he same time, many paleontologists subscribed to some form of Lamarckism and the various fields did not develop one view until the emergence of neo-Darwinian synthesis in the 1930s and 1940s.

I hope this little sketch has helped. First, Darwin's ideas were subjected to searching, even vicious attacks by other scientists and non-scientists (popular writers such as Shaw and Samuel Butler were staunchly Lamarckian). Second, far from capturing the world immediately, a diversity of ideas on origins existed in many fields, and were only adumbrated by the emerging synthesis of natural selection and genetics in the 1930s and '40s. In Russia Lamarckism remained strong until the 1950s. Lots of people think Lysenko was an aberration, but in fact he was simply the continuance of a long line of Lamarckians. Before he shot himself over the midwife toad fraud, Austrian biologist Paul Kammerer was heading to Russia to take up the position Lysenko would eventually be given. Periodically forms of Lamarckism appear even today.

Vorkosigan

pz

Yes, they do. With a bit of patience, you would have been auotomatically redirected to the ncseweb page that has the information.

More directly, you can find the review by Scott here.

MrDarwin

Please define "information". Then tell me the mechanism (if not the cause) of that information. It's not a trivial question.

But in the meantime, look at the differences between a chihuahua and a great dane. Do you believe the differences between them are the result of different "information"? If so, where did that information come from? And before you point out that they are the result of artificial selection by humans, I would point out that the genetic differences between chihuahuas and great danes were generated by random genetic mutation. In other words, humans did not cause the genetic change because until very, very recently, humans did not have the potential to cause genetic change in other organisms, they only had the potential to recognize and select it (often quite unconsciously). All the variation in all the domesticated plants and animals, until very recently, resulted from natural, spontaneous genetic change. We know this because such genetic changes still happen today.

Now, I might also add that Darwin knew precious little (actually I think the key word is nothing) about genetics so when we're talking about genetic change, technically we're not talking about Darwinian mechanisms. Darwin didn't know how differences between organisms were generated. But he did propose a mechanism for manipulating those changes, once they occurred.

MrDarwin

luvluv, early in the discussion you asked:

I can think of many things that would falsify evolution (at least as evolutionary theory now stands). But it's probably fair to say that evolution is a theory based upon many separate but interrelated hypotheses, which have been vigorously tested and potentially (but not) falsified. Some of these key hypotheses of evolutionary theory are (1) the continuity of life, (2) variation within populations, (3) the ability to pass on that variation from one generation to the next, (4) natural selection acting on that variation to change its pattern from one generation to the next, (5) the splitting of lineages into separate populations that go on to change in different ways. There are others, but these are some of the basic ones, and these are the things that scientists test and confirm every day.

But let me turn your question around. What would convincingly falsify evolution for you? Or, if you prefer, what evidence would you find compelling for evolution?

Principia

luvs,
I have spent a good deal of time in the last couple of years with the Intelligent Design movement. And I can state unequivocably that if an ID proponent knows what he is "mostly disputing," he'd be the first.

But since you asked, let me give my take on what ID is about. It is about promoting anything and everything that is non-Darwinian and non-scientific, for the sake of defeating everything that is Darwinian and scientific. It is about blurring the lines between scientific causal explanations and non-scientific, supernatural mumbo-jumbo. It is about making political inroads towards teaching children a concept that has no theoretical or evidentiary substance. It is about fighting a perceived cultural war directed against religious elements.

A number of people have already taken you to task on the vague "genetic information" nonsense. I'll add to this commentary. There are two ways to view this claim. One is to wait for someone to define concretely what genetic information actually entails and then perform experiments to determine if selection and heritable variation can "create" that information. This is the all too familiar Definitions Game. And ID people have played this game for ages. I'll have to disappoint you, however, that the track record is abysmally poor for the ID proponents -- there isn't a single biologically relevant definition that has withstood scrutiny. And last I checked, they're still working on it.

The second way to look at this claim is on a philosophical level. How does one scientifically investigate what ultimately creates "genetic information" (whatever it may be)? Say we identify one cause of this phenomenon. An ID proponent then comes alone and says "No, no. That cause must have a cause, too." And the researcher goes to look for a cause to the proximal cause. He returns to the ID proponent, only to hear him say "No, no. Common sense says that cause is too improbable. What is the ultimate cause?" Well, you know where this is going... The ID game is set up so that there is no adequate response to the question "what creates genetic information (whatever it may be)" -- save the scientifically untestable. For every additional causal link, the ID proponents simply claim it is an inadequate cause. The problem for the poor researcher playing this game is that he's too devoted to doing science that he forgets why he ought to be playing the ID game anyways. Hell, he didn't even notice that the ID proponents aren't playing the game themselves. When was the last time they tried looking for how "genetic information" is created? What is their model for how "genetic information" is created?

This is the very essence of the problem from arguing a negative thesis -- e.g. "Darwinian mechanisms cannot produce X". It is pratically impossible to verify. But it makes for great rhetorics. Of course, this is why we're here discussing a lawyer's take on science.

RBH

<Post whacked because of it duplicates one earlier that I neglected to read. Oh, well.>

Albion

Actually, I think it IS true. Not necessarily a literal reading of Genesis but a perception that if God isn't specifically included as an explanation, he's specifically excluded. Things like problems of stasis in the fossil record and other genuine problems don't tend to make scientists refuse to accept evolution, they tend to make scientists think that they have an incomplete explanation and that they should do experiments or fieldwork to try to expand the explanation. It tends to be creationists who are ready to discard the entire theory at the first sign of a bit of a problem. On the other hand, things like information creation and irreducible complexity are creationist fabrications whose entire purpose is to undermine the theory of evolution. They don't arise from actual research because the ID people don't DO actual research. They exist simply to give ID creationists an excuse to proclaim that natural processes are insufficient to explain obwerved phenomena.

To say that the ID people are looking for anything other than evidence of non-natural processes is to be disingenuous in the extreme. How come so much of the ID literature consists of philosophical attacks on secular society and philosophical naturalism if we're really dealing with genuine science?

RufusAtticus

luvluv,

Here is my take on linking information with biology.

INFORMATION
Individuals don't evolve. Populations do. So in linking information theory to evolution, one must consider the information in the population, which creationists do not do. Biologically, information can refer to different things. Pseudogenes, contain information about evolutionary history but not information that can be selected upon. In the context of this discussion, it would be best right now to consider the genetic information underlying traits, with an interest in adaptable traits. It is difficult to determine a way to measure the amount of this information, but one possibility is the size of the proteome. This is the number of unique proteins produced in the population and includes all loci and alleles. Whenever a mutation produces a novel allele, it adds information to the population. In other words, there is a new trait for selection to act upon. Here are two examples of the effects of information in a population.

Jeff knows something about Gina: "Gina is neat." Thus he has information about Gina. Before he leaves town, Jeff replicates this information by telling it to two people, Nick and Randy. Because neither of them pays attention, they don’t replicate the information exactly. Nick thinks "Gina is sweat," and Randy thinks "Gina is near." We can measure the about of information about Gina by the number of non-redundant attributes people ascribe to her. Here, the amount of information about Gina has doubled: from "neat" to "sweat and near." Clearly when we remember that it is the population that’s important to evolution, it is obvious how mutations can add information for selection to act upon.

Take this example retrieved from LocusLink [1], the only difference occurs in the 7th codon (6th amino acid because the first one, 'm,' gets cut off). The letters refer to amino acids [2].
Each allele does not encode the exact same information since each one produces a distinctly different product. A single point mutation has enough effect on the information contained in the genome that it can determine whether an individual dies from malaria or not. In the presence of malaria, HBB-S is maintained because of heterozygote advantage. However, HBB-C also offers resistance to malaria, but the most fit genotype is the homozygote.[3] It is expected to become the most common allele in parts of Africa if the environment stays the same. These mutations have clearly added new information to the population. Selection then acts on this new information, changing the make up of the population. Thus, evolution happens.

It is important to realize that evolution occurs even if information is lost. It also occurs when information is gained or without any change in the amount of information at all. Thus no-new-information arguments do not actually address evolutionary theory. By focusing on individuals and not populations, no-new-information claims never even get close to disproving evolution. In fact, the actual claim, when applied to biology, is that the information capacity of an individual's genome cannot increase. However, this claim is false because there are known types of mutations that can increase the length of the genome and thus its capacity to hold information. Ernst Mayr discusses this origin of new genes in his latest book:

1. http://www.ncbi.nlm.nih.gov/LocusLink/
2. http://www.chem.qmul.ac.uk/iupac/AminoAcid/AA1n2.html
3. Modiano D. et al. (2001) Haemoglobin C protects against clinical plasmodium falciparum malaria. Nature: 414 pp 305-308
4. Mayr E. (2001) What Evolution Is. Basic Books.

Secular Pinoy

I would say I've rarely met these people. A lot of liberal-minded people I know deny evolution because of its implication that we are descended from monkey-like ancestors. No amount of argument and evidence will disabuse them of this fear. All it takes is a reminder that if evolution is true, then we are nothing more than glorifed apes.

Another common and related reason for disbelief is the idea that if evolution is true, then as animals, we have no inclination to be moral (note the naturalistic fallacy). If animals live "red in tooth and claw," then why should we humans be different. This scares them, and they refute evolution with all their might.

And these same people are the first to criticize organized religion and fundamentalism.