Saturday, 21 February 2009

Life in the lab

Another way to determine what alternative life might look like is to try to invent it ourselves.

If we can create new molecules which can behave in life-like way, we may then go out and look for these in the environment, says Professor Steven Benner, of the University of Florida.

His team have created perhaps the closest yet to a man-made alternative form of life.

"We are announcing the first example of an artificial synthetic chemical system capable of Darwinian evolution," he told the conference.

"Is it alive? Well, I can tell you that it is not self-sustaining.

"You have to have a graduate student stand there and feed it from time to time, but it is evolving."

The molecule is essentially a modified version of our own DNA double helix - but with six "letters" in its genetic alphabet, instead of four.

These nucleotides pair up in strands, which can replicate, though only with the help of polymerase enzymes and heat.

"Sometimes mistakes are made in pairing and these mistakes are maintained in the next generation - it is evolving," said Prof Brenner.

"The next step is to apply natural selection to it, to see if it can evolve under selective pressure.

"The accepted definition of life is a molecule capable of Darwinian evolution, so we are trying to put together molecules that are capable of doing it."

But he questioned whether our definition of "living" is perhaps too "Earth-centric".

"Remember - just because you are a chemical system which is self-sustaining and capable of Darwinian evolution, that doesn't mean that is the universal definition of life," he said.

...fine...but what other definitions might we apply. According to my latest reading, life is defined not just as being capable of Darwinian evolution (i.e. hereditary descent with modifications), but is required to consume energy and...something else which I've forgotten right now (D'oh - will look it up and update this).

What caught my eye was the ability to create something life-like with a different DNA coding. Would be interesting to see if you could go the other way and reduce it to two letters - essentially a binary code!

The Legacy of Darwin's Discoveries

(This is my attempt at answering the question posed in section 1.4 of the OU course S170 - Darwin and Evolution. While I have no qualms about anyone using the material (this is the net, after all), it is my own, original work and I would appreciate citation - there are almost certainly errors below, too, so caveat copier!)

[1] Why is there a 'struggle for existence' in nature and how can it result in evolution by natural selection and the adaptation of organisms to the circumstances in which they live?

The 'struggle for existence' is the natural outcome of many organisms reproducing and filling their environment - there is limited space, and there are limited resources.

If we consider just a single species, there is a limited set of materials it requires to reproduce - the chemicals required to create and maintain its own body and those required to create its offspring. This includes the food it requires to generate the energy to power this creation. These can only come from its environment, which only has them in a finite supply. The more organisms that are usig the supply, the smaller share each has - and hence the more efficient an organism is at using them, the more likely it is to leave offspring. [It can produce more with the same amount of resources]. And the more likely it is to leave offspring, the more of those attributes that lead it to be able to leave offspring will exist in the population [because they are copies of their parents].

The flip side to this is that the more likely you are to die - either naturally or y being eaten - before you have a chance to leave any offspring, the fewer of those attributes will survive in the remaining population.

While the common summary of evolution by natural selection is 'survival of the fittest', perhaps a more apt phrasing would be 'extinction of the least-fit'. For even if there are no super-efficient users of resources, or super-efficient reproducers in the population, those that are least fit will - by pure virtue of this fact - be culled from the population, leaving those that were able to survive to populate the next generation. [Repeated iterations of this process will obviously tend to select for the better fit, by removing those least fit, and reducing the available variation]

This is the process of natural selection: those that do not not survive. Those that do, do.

How does this lead to adaptation? Any individual that has a slightly better reproduction rate or a slightly more efficient method of using the available reources wil tend to, over time, represent a higher proportion of the population.

If there is a change to the environment - for example, resource A becomes scarcer and resource B becomes more prevalent, then those that are able to use resource B will gain an advantage, and tend to become more prevalent because there is much less of A to go around. [Nylonase example]

[2] How does the breeding of domesticated animals and plants serve as a model for the way that evolution by natural selection operates?

Human selection of which plants or which animals breed mirrors natural selection by culling of those which are unfit. Only certain animals "make it" - whether it be because of human precociousness and whim or nature's brutal and harsh removal of those that do not fit their environment.

It is much easier, of course, to study the way traits are inherited when humans are involved in the selection process, and this was one of the key ideas that Darwin noted - and then made the parallel with the way that nature works.

[3] What kinds of evidence support the idea of a branching pattern of evolution through time, and how can natural selection help to explain that pattern?

There are many instances in nature of very similar organisms - which would generally be classed as a single species except for a particular difference. This often is seen in places where a population has reached an extreme in its environment. Where one group has developed the ability to survive at the extreme. This may lead to morphological changes or not, but especially if it does, it often leads to the two varieties - the original population and the population adapted to the 'extreme' condition - which no longer mate, perhaps because they are not 'alike', because they tend not to come into contact with each other, or because they become physically unable to. This defines them as distinct species.
Natural selection works at such extremes - because those organisms that cannot cope at one extreme will die off, leaving those more suited to that environment to reproduce, the population will tend to become more geared towards coping in that environment. Thus two separate groups evolve.

[4] What kinds of evidence indicate the great antiquity of the Earth?

Dondrochronology, carbon dating, radio-isotope dating, fossil evidence, geophysical evidence (e.g. erosion - as shown in DG2)....and much more [TBC!]

Saturday, 31 January 2009

Survey on evolution

These are supposed to be True/False questions, but the wording is perhaps in need of a little improvement - feel free to add comments!

  1. Evolution is a scientific fact.
  2. Evolution is something you should either believe in, or not believe in.
  3. Evolution is a process that involved the origin of life.
  4. Evolution is primarily concerned with the origin of humans.
  5. According to evolution, people came from monkeys a long time ago.
  6. Evolution was first proposed and explained by Charles Darwin.
  7. Evolution is the same as "Natural Selection."
  8. Evolution is something that happened only in the past; it is not happening now.
  9. Evolution is something that happens to individual organisms.
  10. Evolution is a totally random process, or a series of "accidents."
  11. Evolution was developed in order to destroy or undermine religion.
  12. Evolution tells us that there is no God.
  13. Evolution can be compatible with all the world's major religions.
  14. Evolution simply means "change."
  15. "Evolution is only a theory."
  16. There is actually very little evidence for evolution.
  17. One indication that evolution has not occurred is the total absence of "transitional organisms" (those with traits intermediate between two different groups).
  18. Fossils provide many problems which evolution cannot explain.
  19. Most biological and medical and agricultural research assumes evolution is real.
  20. Evolution theory has been tested many times, and has always been supported by the evidence.
  21. Dinosaurs lived during the time of early humans.
  22. Evolution involves individuals changing in order to adapt to their environment.
  23. There is actually considerable observable evidence against evolution.
  24. Science can properly infer what has happened in the past, based on evidence.
  25. The formation of complex structures, like the eye, can be readily explained by evolution.

Please email your responses to: mnjones (plus) wonder (at) gmail (dot) com
(That (plus) is a "+", in case you are confused!)

More on Neanderthals

I was pointed at this account of a refutation of the commonly held view amongst the scientific community that Neanderthals are a separate species of hominid (indeed, of the genus Homo). I have many issues with both the premises as presented and the conclusions drawn. In fact, every paragraph seems to have at least one thing I feel is wrong or misunderstood. Below each paragraph I have tried to show which items I believe are fallacious premises, which are non-sequiturs as conclusions, and which are misrepresentations of facts.

Neanderthal Men Were Modern Men
by Brian Thomas, M.S.*

A set of fossilized human remains has been discovered in Iberia that shows partial Neanderthal characteristics, proving again that Neanderthals interbred with anatomically modern men.1 This adds to a growing list of evidence, consistent with biblical history, that demonstrates Neanderthal to have been fully human, rather than an evolutionary transition.2

Ref[1] indicates that this is the Sima de las Palomas find. Apparently this is dated to 40,000 years. Also seems like the site has only Neanderthal remains, unless it's not stated in the abstract that there are also 'modern' humans (i.e. Homo sapiens). “The human fossils from the upper levels of the Sima de las Palomas are anatomically clearly Neanderthals, and they are now securely dated to 40,000 years ago.”[ref] From the reports on this find[ref][ref][ref], none other than this one mention “partial” Neanderthal characteristics.

After writing the above paragraph I went and did some more digging, and found this which does say that the PNAS article mentions characteristics similar to modern humans. One of the two explanations it says are put forward in the article is that there was hybridisation. However, Antonio Rosas, an expert on Neanderthals, says that he does not believe the find demonstrates this hypothesis, saying "The variation seen in the Neanderthals they have found can be explained without hybridisation. Genetically, there is no data that exists to affirm this hybridisation, and the genetic separation between modern humans and Neanderthals is very large."

What I understand from the abstract of Ref[2] (that does indicate a “mosaic of European early modern human and Neandertal features”) is that this is suggesting that the two groups lived alongside each other rather than the Homo sapiens population overrunning (and hence replacing) the Neanderthal populations in the Late Pleistocene (which it implies was the prevalent current conjecture). Nor, as the author of the article appears to (erroneously) believe evolution claims, that the Neanderthals died out, and modern man replaced them with no overlap.

Why does commonality of features prove them to have been “fully human”? What does “fully human” mean? They are fully human in the sense that they are within the genus Homo… In exactly the same way that both they and ourselves are hominids (in the family Hominidae or "Great Apes"), along with the genera Pan, Pongo and Gorilla.

Though evolution models once held that Neanderthal man was one of the “missing links” between an ape-like ancestor and modern man, the repeated discoveries of Neanderthal remains right next to those of modern humans—instead of in separate, lower, older strata—have forced him out of the pool of “pre-human” evolutionary ancestor candidates. In contrast to ever-evolving naturalistic interpretations, the biblical creation model has consistently maintained that Neanderthal man was just that—man.

Evolution also claims that Neanderthal is a form of man, and that Homo neandertalensis and Homo sapiens split off the same branch of human ancestors. Evolution does not describe a ladder, but a tree.

Ancestors can still co-exist with descendant species. Think of mud-hoppers – fish that have changed very little from those fossils of trasitional forms such as Tiktaalik. Also think of a great-grandfather living at the same time as his great-grandson. They are related, but one is several generations younger. Think also that there are many branches from the great-grandfather, and some of his offspring may look more like him than others. And of course, even more appropriate, a man's granddaughter and grandson will be alive at the same time. While my examples cover a very small time-period, the principles are still the same - two separate lines will be alive at the same time. The Neanderthals died out - but that does not mean they were not around at the same time as Homo sapiens. Indeed, they *must* have been at the start of the divergence of the two species.

In fact, it is the data that tell us that some forms of man followed on in a somewhat sequential manner, because one appears to have died out shortly after the inception of the other. The theory of evolution does not predicate any such sequence.

Neanderthal did have distinct characteristics that are apparently now either extinct or diffused, but his family line was fully human for several hundred years after Noah’s Flood, when humans repopulated the earth about 4,300 years ago.

The Iberian find is dated to 40,000 years. Most Neanderthal fossils are in the order of 50-60 thousand years old. How does this statement reconcile itself with the evidence that the author has already presented?

The mounting evidence for Neanderthal and modern man’s coexistence calls into question whether the Neanderthal and other human varieties even lived in separate times, as the evolutionary story still maintains. Both the Bible and science indicate that this was not the case. Biblical history has no place for such a separate, distant time of evolutionary development, but it does allow for variations within the human kind in its 6,000-year history.

"The mounting evidence" presented here appears to be one reference, or perhaps two. And I don't think that even these really debunk anything in the theory of evolution or common descent.

The "evolutionary story" maintains that "human varieties" lived at separate times? See above. This is at best a dubious statement, if not completely fallacious.

Anthropologist Marvin L. Lubenow has shown that Neanderthal, other than having a larger cranial capacity, was anatomically the same as Homo erectus.3 Their fossils do not fit into the depiction of a linear evolutionary ape-to-man transition that is iconic today, but were simply comingling variations of humankind. Furthermore, a fossil elbow (KP 271) and the Laetoli footprints of Neanderthal man are indistinguishable from modern man, and both have been dated by evolutionary scientists at 4 million years or older—predating the earliest Neanderthals!4 Thus, within the published evolutionary dates, “anatomically modern Homo sapiens, Neandertal, archaic Homo sapiens, and Homo erectus [as well as Lucy-like Australopithecinces] all lived as contemporaries.”3

Again, see above – evolution does not claim a linear transition. It claims common descent - i.e. a common ancestor.

"Comingling variations of mankind". Indeed. There is a possibility that contemporaneous varieties and species within the Homo genus might have interbred, although the further apart they are, the less likely that is. One of the common lines in the various definitions of species is that they cannot (or do not…) interbreed, or that if they can, they produce infertile offspring. HGT may also account for some intermingling of DNA; I have not looked at how much influence this is thought to have. If the evidence does point to both Homo sapiens and Homo neandertalensis co-existing (I don't think the references here cited do, but I don't think it's impossible or unlikely), that would not mean that the evolutionary theory was incorrect.

As for the Laetoli footprints are not believed to have been made by H. neandertalensis. The wikipedia entry suggests that they were made by Australopithecus afarensis. Encarta agrees with it being A. Afarensis. Another opinion is presented by William E. H. Harcourt-Smith, who doesn't actually say what species made the footprints, but does point out reasons for it not necessarily being A Afarensis as nearby remains might suggest. The one tentative alternative is A. anamensis ( The reason the footprints look similar to those made by modern man is because they are made by hominids which walked in a similar, upright, bipedal stance. This does not mean that they are H. sapiens. Or indeed even within the genus Homo, as A. afarensis appears to be main contender. That there is contention about them suggests that they certainly are different in some respects to modern humans' footprints. The similarities - which are what prove that they belong to a bipedal animal - are the arched foot and the forward-pointing big toe.

The overlap of species appears is depicted here. Yes, there are overlaps - exactly as to be expected, as explained above.. (see also this talkorigins page)

As seen in the fossil remains from Iberia, the more that is discovered about Neanderthal, the more evolutionary models morph to accommodate the data. In contrast to this ambiguity, both the Bible and science confirm that man and apes—though many small differences can be discerned within each kind—nevertheless remain totally separate, untransitioned created kinds.

"The more evolutionary models morph to accomodate the data". Well, that is how science works. The more data you get, the better your theories become. If there is something that doesn't fit, then you have to change your ideas. However, if the rest of the data can be accounted for by the existing theory, and there is some slight deviation in this data, then only a small change is needed. If the deviation is huge, then perhaps a different theory is needed. Everything so far seems to fit the theory, or the former example. None of it has so far so catastrophically refuted the existing theory that it needs major revamping. Even things like relativity didn't change Newton's theory of gravity, as it described the existing data perfectly well.

Friday, 30 January 2009

99% Ape - ch1: 99% Ape

Mutations in HIV

A diagram showing the tree of mutations in a strain of HIV in a dentist and four patients is given on p.9. The text says that patients A, B, and C were shown to have received the virus from the dentist, but that patient D was not.

The diagram, however, shows that the mutation that lead to patient B's virus strain occurred 'before' that of the dentist (or, at least, that the differences between it and the dentist's strain suggest an earlier divergence). What was the conclusion wrt patient B?

Evolutionary Trees

Q: Where did HIV come from?

A: HIV and SIV (Simian Immuno Virus) are closely related [[M] by examining their genomes?]

Q: Where and how did SIV develop? Since when is it known to exist?

Darwin, Apes and Victorians

Biblical account of Genesis
  • Humans created in God's likeness.
  • Species separately created ("Special Creation")
  • Each 'type' of animal is fixed
    • Similarities show design plan commonalities

    Darwin saw similarities as a consequence of evolution.

    Alfred Russel Wallace in 1859 was going to publish his theory. Darwin said it was "an excellent short abstract" of "On the Origin of Species".

    Evolution - the idea - was not invented by Darwin. Many others before him believed that species changed (such as Erasmus Darwin 1731-1802)

    Joseph Dalton Hooker - friend of Darwin's to whom he wrote about his initial thoughts on evolution.

    Darwin's contribution was to discover a method by which evolution works.

    While Darwin knew nothing of viruses, his theory perfectly descries how they change over time - one major piece of evidence for evolution by natural selection.

    Darwin's Insights

    The third point on page 14 states that the idea that evolution occurs gradually has stood the test of time. There does, as far as I am aware, appear to be evidence that, given the right environment (e.g. a new, unpopulated territory, or niche), organisms will evolve (diversify) rapidly to fill that niche, and then slows down once the 'hole' has been populated.

    What's in 1%?

    What are the counter claims against "99% similar"?
    They are based on other ways of measuring difference.
    Q: What are these, and how relevant are they?

    Many of the differences are likely switches which turn genes on or off - this allows a much greater effect than would be suggested by a small change.
  • Thursday, 29 January 2009

    On Reading Breaking the Spell - Ch1.2

    Dennett puts forward his initial stab at a definition of religion as:

    Social systems whose participants avow belief in a supernatural agent or agents whose approval is to be sought.
    As he points out, this excludes some things that are generally considered to be religions (or at least, religious), and includes others that perhaps should not be:

    What apparent grounds the widespread respect in which religions of all kinds are held is the sense that those who are religious are well intentioned, trying to lead morally good lives, earnest in their desire not to do evil, and to make amends for their transgressions.
    He had just mentioned things such as satan worship and groups who feel they can summon and control supernatural beings (such as demons) for their own personal ends. These are the sorts of things he feels deserve to be left out of his definition of religion - presumably because he wants to try and capture what most people think of when they think 'religion', and also wants to analyse those that, as he states above, are based on trying to conform to some moral code of conduct.

    There are, in contrast, a few 'congregations of one' which he feels fall outside his definition, but deserve to be included as 'honorary' religions.

    I could hardly deny the existence of individuals who very sincerely and devoutly take themselves to be the lone communicants of what we might call private religions. Typically these people have considerable experience with one or more world religions and have chosen not to be joiners.
    So, we have an initial cut at a definition of what he will talk about in the book, and already he's tearing it apart, trying to find where it doesn't fit. Indeed, even before he makes his first stab at it, he has said that nothing he defines will truly fit the bill. This dissection is a good thing, imho - it means that while he is going to talk about "religion" it isn't necessarily some fuzzy term meaning different things to different people - but he *is* allowing it to be a bit fuzzy sometimes and encompass some of those things that the rigorous definition does not explicitly include or exclude.

    What other definitions of religion are there? Is even defining religion an exercise in futility because so many people think it has so many different meanings? Or is it good to put a stake in the ground, and use this to point out wha

    Monday, 26 January 2009

    How many Neanderthal fossils have been unearthed?

    A friend made a quip about there only having been (about) 5 Neanderthal fossils found (and most looked like 'old men with arthritis', apparently)... So I thought I'd do a bit of digging, and the first hit I found on googling 'how many neanderthal fossils' gives:
    2 from Belgium and Gibralter from before "Neanderthals" were identified as not being H. sapiens
    7 from the Neanderthal "type site" in Germany
    2 from Grotto of Spy d'Orneau in Belgium
    between 24 - 36 individuals from Croatia (remains are fragmentary)
    1 near-complete skeleton from La-Chapelle-aux-Saints in France
    1 from Saint-Cesaire in France
    1 from Arcy-sur-Cure, France
    6 from the Moula-Guercy cave, above the modern Rhone River, France
    9 from the Shanidar cave in Iraq
    *at least* 13 from sites at Tabun, Qafzeh, and Skhul near Mount Carmel, Israel
    ...there were more paper references turned up in my search, but I did not track them all down.

    While exact numbers don't seem to be available from this, simple summing of the ones above yield a minimum number of 66 individuals. I remember seeing somewhere that we actually have remains of almost 200 Neanderthal individuals, but I cannot substantiate that at the moment.
    (from here)

    And while this:
    Neanderthal fossils have previously been found over a large area, stretching from the Mediterranean as far east as Uzbekistan. Most remains are fragmentary, however, so it can be difficult to determine whether a fossil is of Neanderthal or of modern human origin.

    (from here) doesn't actually mention specific numbers, it does imply a few more than 5. It does mention two specific sets of fossils, one of a child from Teshik-Tash in Uzbekistan, and one set of adult fossils from Okladnikov in southern Siberia.

    And this article says "Thousands of Neanderthal fossils and artifacts are known", though does not give any specific list.

    This one gives: "In 1887, two complete skeletons were found in a cave near Spy in Belgium, and more from sites in France in 1887, 1908 and 1911." which seems to match a few from the first quote.

    Talk Origins lists around five 'prominent' fossils, again, most listed in the first link. "...there are now thousands of hominid fossils. They are however mostly fragmentary, often consisting of single bones or isolated teeth. Complete skulls and skeletons are rare."

    Britannica says:
    Neanderthal skeletons have been found in caves and shelters across Europe, in southwest Asia, and eastward to Uzbekistan in Central Asia, providing abundant skeletal remains and associated archaeological material for understanding these prehistoric humans. The Neanderthals are now known from several hundred individuals, represented by remains varying from isolated teeth to virtually complete skeletons.
    And here's a timeline. Note that not all entries are Neanderthal finds, but the majority appear to be.

    Apologetics press points out that there have been mis-datings made, though, and I haven't gone in to check all the dates of the articles above against the date of the 'dating disaster', but I think they might be overreacting to one incident against much other information. As does Panda's Thumb.

    ...and as for the arthritis comment, the following is from a review of the book "Buried Alive: The Startling Truth about Neanderthal Man" by Jack Cuozzo, who is a creationist.
    In four and a half pages (pp.274-279) he [Cuozzo] demolishes the notion that the distinctive Neandertal morphology is entirely due to disease, taking apart the three proposed hypotheses - arthritis, syphilis, rickets - one by one; he even chastises a fellow creationist, Lubenow, for getting caught up in the rickets hypothesis.

    Ontological argument parallel

    In "God is Not Great" by Hitchens:

    "Are there dragons?" she asked. I said that there were not. "Have there ever been?" I said all the evidence was to the contrary. "But if there is a word dragon," she said, "then once there must have been dragons."
    He points out that this passage is a fairly parallel argument to that made by Augustine in his argument for god:

    1. God is the greatest imaginable being.
    2. All else being equal, a being or entity that exists is greater than one that doesn't.
    3. Therefore, God exists.
    (from Iron Chariots wiki)

    Saturday, 24 January 2009

    Horizontal Gene Transfer

    A recent article in New Scientist talks about how Horizontal Gene Transfer (HGT) may well be a turning point in the Darwinian view of how life has evolved. It is pointing out that, from recent research, much of the genetic material in the eukaryotic and archaean organisms is transferred, not 'vertically' - by sexual reproduction - but 'horizontally', by swapping genetic material or by hybridisation.

    It further suggests that this also happens in the prokaryotic branch of the tree - that which includes the majority of multicellular organisms, including ourselves. It points out that methods of horizontal gene transfer might occur through mediating viruses which cut and paste genetic material between hosts. It can also occur via hybridisation, where two separate species cross. This, according to Loren Riesberg, is the case for about 14% of plant species. There is also some evidence that this may have happened in early humans, between our ancestors and concurrent species, such as Homo erecutus and Neanderthals.

    Personally I feel that some of this is a bit fuzzy. Firstly, the article suggests that DNA is subject to vertical transfer, but HGT can be seen in RNA. While perhaps that is just poor wording in the article, it feels from the first that the article is trying a bit too hard to make a point - and starts out almost hostile to the tree-of-life view, and so I wonder if it's trying to hide something there in order to prove a point. The article does ease up towards the end, describing the different viewpoints of scientists who feel that the tree of life needs to be 'uprooted' and those who feel that HGT just adds a new dimension to the data.

    As far as the hybridisation comments, it would seem odd that where speciating groups overlapped they did not hybridise to some extent if they were able to. In fact, I am fairly sure this is what Darwin talked about in Ch. 4 or 5.

    In the article it asks whether the tree-of-life view does not still apply to multicellular organisms. And replies - almost, at least - "Well, they aren't the majority, so we shouldn't bother with that view anymore". If the tree is still the way in which some genetic material is transferred, then, whatever other methods are available for its transfer, it is still a valid view.

    I kept thinking "Newton...Einstein" throughout reading this, and, sure enough, right at the end he says:

    If he [Michael Rose] is right, the tree concept could become biology's equivalent of Newtonian mechanics: revolutionary and hugely successful in its time, but ultimately too simplistic to deal with the messy real world.
    Some of the things mentioned in the article gel with my feelings about early life - knowing that single-celled organisms can only reproduce by copying made me wonder about how genetic variety worked before sexual reproduction occurred.

    I guess we live in interesting times - and I am sure the Discovery Institute is going to have a field day with this. It will be interesting to watch how it all develops.

    Thursday, 22 January 2009

    On reading The Origin of Species: Ch. 6 - Difficulties on Theory

    Here Darwin points out the main attacks on the theory of natural selection. He lists four main arguments - and they are arguments that creationists, and indeed some others, still use today.

    1. "Why, if species have descended from other species by insensibly fine gradations, do we not everywhere see transitional forms?"
    2. "Is it possible that an animal [with one set of habits] ... can be formed by modification of some animal with wholly different habits?"
    3. "Can instincts be acquired and modified through natural selection?" For instance those of bees to make honeycomb.
    4. "How can we account for species, when crossed, being sterile and producing sterile offspring, whereas, when varieties are crossed, their fertility is unimparied?"
    He deals with 1) and 2) in this chapter, and devotes a chapter each to 3) and 4).

    For 1) he basically suggests two methods of isolation, and notes that both methods will tend to favour those animals more suited to the particular environments...and thus the parent species, which tend to be less well suited become less numerous and die out. The two methods are by geological change - e.g. islands being formed where once there was continuous land, and by habitat specialisation - where a species extends over a large area, and where that are covers two distinct types of habitat - while the animal is expanding over the two habitats it might remain fairly homogeneous, but once specialisations for the two habitats begin to emerge, the original, more generic variety will dwindle in numbers, and because it dwindles in numbers is less likely to produce variations that make it more successful than the more numerous, already-specialised varieties.

    It is also here that he makes his oft-misquoted comment about the eye "I freely confess that it is absurd in the highest degree to suppose that the eye was formed by natural selection". He then goes on to list the possibilities.

    He also makes a couple of interesting statements:
    He who will go thus far, if he find on finishing this treatise that large bodies of facts, otherwise inexplicable, can be explained by the theory of descent, ouht not to hesitate to go further, and to admit that a structure even as perfect as the eye of an eagle might be formed by natural selection, although in this case he does not know any of the transitional grades. His reason ought to conquer his imagination; though I have felt the difficulty far too keenly to be surprised at any degree of hesitation in extending the principle of natural selection to such startling lengths.


    We should be extremely cautious in concluding that an organ could not have been formed by transitional gradations of some kind. Numerous cases could be given amongst the lower animals of the same organ performing at the same time wholly distinct functions [...or...] Two distinct organs sometimes perform the same function in the same individual.

    Whereby he shows the folly of letting the limits of your imagination be the limits of your reasoning. "Because I can't imagine it is so, it must not be so."

    Wednesday, 21 January 2009

    On reading The Origin of Species: Ch. 5 - Laws of Variation

    When we see any part or organ developed in a remarkable degree or manner in any species, the fair presumption is that it is of high importance to the species; nevertheless the part in this case is eminently liable to variation. Why should this be so? On the view that each species has been independently created, with all its parts as we now see them, I can see no explanation. But on the view that groups of species have descended from other species, and have been modified through natural selection, I think we can obtain some light.
    Darwin points out that creationism doesn't provide any answers.

    And again, later in the chapter:

    He who believes that each equine species was independenly created, will, I presume, assert that each species has been created with a tendency to vary, both under nature and under domestication, in this particular manner, so as often to become striped like other species of the genus; and that each has been created with a strong tendency, when crossed with species inhabiting distant quarters of the world, to produce hybrids resembling in their stripes, not their own parents, but other species of the genus. To admit this view is, as it seems to me, to reject a real for an unreal, or at least for an unknown, cause. It makes the works of God a mere mocker and deception; I would almost as soon believe with the old and ignorant cosmogonists, that fossil shells had never lived, but had been created in stone so as to mock the shells now living on the sea-shore.

    Tuesday, 20 January 2009

    How to be Organized(sic) in Spite of Yourself

    I picked this book up because (I think) it appeared on I've just started it, and, as per the subtitle - "Time and space management that fits your personal style" - it is suggesting that anyone can get organised; you just need to know how to adapt organisation to how you work, not the other way round.

    So - the first step is trying to find out where you fit into the 'types of person' profiles. "There are ten operational styles", it says. And goes on to list them, broken into two categories: Time and Space.

    Under "Time" it has:
    They like to have lots of irons in the fire and work on several tasks simultaneously, but they constantly jump from task to task without ever completing any of them

    Perfectionist Plus
    They think they can do anything, but they get so involved in trying to do everything right that they often can't get projects done on time. Even when they finish a job, they're seldom really satisfied with the results.

    Allergic to Detail
    They'd much rather formulate plans than carry them out, so after they start a project they're weak on follow-through.

    Fence Sitter
    They leave everything to chance because they have trouble making decisions and worry whether or not they will make the right one.

    Cliff Hanger
    They thrive on excitement, delay everything to the last minute, and usually need outside time pressure to complete a task.

    OK. I nodded my head at each of these...but that then made me wonder if I was just being pulled in by some well-contrived wording of the kind fortune-tellers use - something that could apply to anyone. And some of them sound mutually exclusive - 'Perfectionist Plus' and 'Allergic to Detail', for example.

    How do I see myself fitting into each category?

    Am I a 'Hopper'? Well, yes - I love having lots of little projects on the go at once, and yes, I often - usually in fact - never get round to completing any of them.

    Am I a 'Perfectionist Plus'? I believe I can turn my hand to most things - within reason. And when I try to do something, I do often try to do it 'right'; usually with the effect that I never get it completed because I'm always trying to tidy it up. Or, as it says, I am very seldom happy with what I've completed because i think I could have done a better job of it.

    Am I 'Allergic to Detail'? I once described myself (from having been provided with a list of 'types of people to have in a team') as a "starter" - someone who can get the ball rolling on things, but one they've got it going expects or needs someone else to complete it. I think that "weak on follow-through" fits that quite well.

    Am I a 'Fence Sitter'? I wouldn't say I leave everything to chance, but I do often find it difficult to make a decision. I guess this is the one where I feel the weakest match to the description.

    Am I a 'Cliff Hanger'? 'Thrive on excitement' certainly doesn't quite fit (not that I don't like a little excitement, of course). I do generally delay until the last minute. And, yes, being told I have a deadline does give me a boost - especially when it's close.

    The other thing I notice is that out of these five 'operational types' not a single one of them actually appears to be organised. Well, OK...I guess maybe they're aiming at the target market - those that are habitually disorganised and want to get better. But surely there should be some positives along with the negatives!

    Carrying on, the five types listed under 'Space' are:

    Everything Out
    They work best when everything they need is out in front of them and feel it's a waste of time to put things away in drawers and closets when they're going to use them again.

    Nothing Out
    They hate to see clutter, so having a clear desk and hiding things from sight makes them feel as though they're in control.

    Right Angler
    They confuse neatness with organisation and believe they're getting organised when they straighten things up and arrange piles with perfectly straight edges

    Pack Rat
    They have a compulsion to save because something might come in handy someday, someone else might have a use for it, or they don't know what else to do with it.

    Total Slob
    They are totally disorganised and believe that they have more important and creative things to do with their lives than stay neat.

    Well, I feel less inclined to categorise myself quite so readily in any of these. I do sometimes work "Everything Out" (oo-er), but can also work "Nothing Out" - although it's not for disliking seeing clutter, but that it's easier to find things if there is only what I'm working on out. I have in the past done some "Right Angling". I am most certainly a "Pack Rat" - I keep things that I invariably never want again. And as for "Total Slob" - it's more a feeling of lack of desire or time to do the tidying than that I "have more creative or important" things to do. I just procrastinate!

    So where does that leave me? I guess I'll find out when I keep reading. It has also reminded me that I never finished The Now Habit; some of the ideas are reminiscent...

    Monday, 19 January 2009

    On reading The Origin of Species: Ch. 4 - Divergence of Character (2)

    A lot is said in this section, and Darwin tries to put forth a solid basis for his reasoning that variation leads to speciation by giving a conceptual example.

    He suggests that if we look at a given point in time, we may have eleven different species within a single genus, "large within its own country" - i.e. there are many different species and much variation within each species of this genus in a given area.

    If we imagine that two of these species vary a lot, and produce, after many generations several varieties each, and these in turn produce multiple varieties, and so on up the ages. While at the same time most of the other species in that genus die off - possibly because the two which are varying a lot are doing so because they have some advantage, and start to occupy the niches that the other species were. And because they have this advantage, they perform much better than the other species that are not varying quite so much, and not producing offspring that can survive quite as well. But still these two species' offspring are also competing amongst themselves, and of course some of the varieties die off...

    After many thousands of generations, we might have eight variants of the first species, and six of the second species, and perhaps one of the original 11 species manages to survive through that many generations, also, but relatively unchanged. From Darwin's diagram on pp. 160-1 we can see that from the one species (A), out of the eight variants that have made it through, one group of three is fairly closely related, another group of two is also closely related, and a further group of three is closely related. We can also see that the latter group of three is more distantly related, and hence more distinctly different to either of the first two groups.

    A similar situation exists in the second species' (I's) progeny. We have two groups, each consisting of three very closely related varieties each.

    We can also see that these two groups will be quite distinct from each other, for not only were the ancestors whose progeny they are somewhat distinct, they have also accumulated differences as the ages pass.

    What's more, they are each somewhat closer to the species that descended from the other species, F, than they are to each other, by the fact that species A was more distinct from I than it was from F, and the accumulated variations are less likely to have brought them closer together than further apart.(*)

    He then goes on to point out that a naturalist looking today at the varieties would most likely lump the three groups descended from A into three separate sub-genera or genera, and likewise those of the descendants of I....In other words, they are separate species.

    (*) At least - I think this is what he is trying to say. I am not 100% convinced on this front, although I can see an argument for saying that the number of ways of diverging are greater than the number of ways of converging, thus statistically they are more likely to diverge than converge.

    After reading this chapter, I can still see how a creationist might claim that Darwin has not proven that speciation does actually occur. My other thought is that he is relying on variation which he has stated stems from sexual reproduction on which natural selection can then work. If we start with a single single-celled organism produced by abiogenesis, where does the variation come from? I guess we are relying on imperfect copying creating sufficient distinct entities quickly enough that natural selection eventually has something to work on.

    Thursday, 15 January 2009

    John Whitfield has a blog on the Origin of Species - a post per chapter as he goes.

    In chapter 2's entry he covers some of the ground I did in one of my earlier posts - about how Darwin views the definition of species. I particularly noted his comment:

    Here's some advice for anyone agonizing over creating a perfect, all-encompassing species concept: chill out. Pretty much any biological category you care to think of has fuzzy boundaries. Genomics is making the concept of the gene more problematic. Colonial, clonal and modular organisms, such as slime moulds, aspen, and the vast underground mycelia of some fungi, make the concept of the individual tricky to pin down. The giant mimivirus blurs the line between viruses and cellular life. There's been a long debate over whether viruses themselves should be classed as living things. And it's proved impossible to come up with a list of properties that unambiguously define life.

    This does not mean that terms such as species, gene, individual or life are useless. In many or most cases it'll be obvious whether the thing or group of things you're looking at belongs in a particular category or not.
    I shall post, asking for comments on thoughts about the utility of the terms...will at least enlighten me!

    Monday, 12 January 2009

    On reading The Origin of Species (ch 4)

    Darwin postulates that there may be a 'law of nature' that "a cross with another individual is occasionally - perhaps at very long intervals - indispensable [to increasing 'vigour and fertility']" as I mentioned in my last post.

    He goes on to talk about the methods by which flowers may be pollinated - pollination by bees and insects, either by them carrying pollen from the anthers of one flower to the stigma of another, or by triggering some mechanism that causes the flower to self-pollinate - for example by pushing its anthers against its own stigma as the bee or insect crawls into the flower to get at the nectar.

    He then goes on to note that in many flowers, such as Lobelia fulgens:

    ...either the anthers burst before the stigma is ready for fertilisation, or the stigma is ready before the pollen of that flower is ready, so that these plants have in fact separated sexes, and must habitually be crossed. How strange are these facts! How strange that the pollen and stigmatic surface of the same flower, though placed so close together, as if for the very purpose of self-fertilisation, should in so many cases be butually useless to each other! How simply are these facts explained on the view of an occasional cross with a distinct individual being advantageous or indispensable!
    He also says two things that seem somewhat at odds - and he hints at further coverage of the points later on. First off:
    ...if you bring on the same brush a plant's own pollen and pollen from another species, the former will have such a prepotent effect, that it will invariably and completely destroy, as has been shown by Gartner, any influence from the foreign pollen.
    Then a few paragraphs later:
    Yet the pistil of each cabbage-flower is surrounded not only by its own six stamens, but by those of the many other flowers on the same plant. How, then, comes it that such a vast number of the seedlings are mongrelised? I suspect that it must arise from the pollen of a distinct variety having a prepotent effect over a flower's own pollen... appears to me that the principle is acting one way in one case and in another way in a different case - almost as if nature knows which organisms are distinct species, and which are distinct varieties....

    Saturday, 10 January 2009

    What would make you convert to a religion?

    Now here's an interesting question.

    Especially if you already subscribe to one religion, what are the sorts of things that another religion might profess that would make you want to convert to it?

    Would miracles be part of it?
    A moral code?
    A set of laws for governing societal behaviour?
    A 'better' deity? (And what would make one deity better than another?)

    Equally, are there any religions could you adopt that would not require you to renounce your current one?

    Are there any that would mean that, if you did not already profess a religious belief, you would not have to change any of your ideological outlooks? i.e. are there any religions around that would not require you to change your mind about some currently held idea or ideal? (Perhaps with the exclusion of the fact that a deity actually exists!)

    On reading The Origin of Species (ch 4)

    ...a cross between different varieties, or between individuals of the same variety but of another strain, gives vigour and fertility to the offspring; and on the other hand, that close interbreeding diminishes vigour and organic being self-fertilises itself for an eternity of generations; but that a cross with another individual is occasionally - perhaps at very long intervals - indispensable. is necessary for improved vigour in a species...and what happened before species that had sexual reproduction? Or indeed with species that do not reproduce sexually now? Do amoeba not just split? How is it that they continue to have "vigour" and "fertility"?

    Further on Darwin mentions that he has not found one land animal that is perfectly hermaphroditic, and that although some marine animals are, that water currents can provide the means by which the occasional cross-fertilisation can take place. He mentions one species that he had initially had problems with - Cirripedes - but he found evidence that it, too, sometimes crosses.

    I am still not sure about amoeba and the like - is there any chance by which they can cross-fertilise?

    A final quote from Darwin on this:

    Finally, then, we may conclude that in many organic beings, a cross between two individuals is an obvious necessity for each birth; in many others it occurs perhaps only at long intervals; but in none, as I suspect, can self-fertilisation go on for perpetuity.

    Information theory and how it pertains to micro/macro evolution

    From Answers in Genesis, on their 'arguments creationists should not use' page

    “Creationists believe in microevolution but not macroevolution.”

    These terms, which focus on “small” vs. “large” changes, distract from the key issue of information. That is, particles-to-people evolution requires changes that increase genetic information, but all we observe is sorting and loss of information. We have yet to see even a “micro” increase in information, although such changes should be frequent if evolution were true. Conversely, we do observe quite “macro” changes that involve no new information, e.g., when a control gene is switched on or off.

    (This is listed under the heading "What arguments are doubtful, hence, inadvisable to use?")

    The question of information is addressed - at least according to one model* of information theory - here. Now I just need to find some examples of where these principles are demonstrated in nature.... Or is that just doing science backwards? :)

    *) I need to have a look and see what that particular model is, and how it differs from other models of information theory...

    Friday, 9 January 2009

    List of references in AronRa's latest YT video (pt 1)

    AronRa's "The 14th foundational falsehood of christianity" takes a look at, among other things, some of the things professed by Ray Comfort and __ when they tried to prove god existed without reference to faith. Comfort is shown in the video explaining why god is good. Here are several of Comfort's quotes, with AronRa's commentary and citations, along with a few relevant summarisations from across the web.

    Comfort: "God is [...] good, he's just."
    In response, AronRa writes: "God describes himself as being as much evil as he is good; and that he created evil - not as the absence of good, but proud of that creation" and cites Isaiah 45:5-7

    I have pulled the relevant passage from The Skeptics Annotated Bible
    45:5 I am the LORD, and there is none else, there is no God beside me: I girded thee, though thou hast not known me
    45:6 That they may know from the rising of the sun, and from the west, that there is none beside me. I am the LORD, and there is none else.
    45:7 I form the light, and create darkness: I make peace, and create evil: I the LORD do all these things.
    There is a commentary on 45:7 which also references a couple of other places that say much the same, and one that it feels contradicts the statement:
    2 Kings 6:33
    6:33 And while he yet talked with them, behold, the messenger came down unto him: and he said, Behold, this evil is of the LORD; what should I wait for the LORD any longer?
    Amos 3:6
    3:6 Shall a trumpet be blown in the city, and the people not be afraid? shall there be evil in a city, and the LORD hath not done it?
    1 John 4:8
    4:8 He that loveth not knoweth not God; for God is love. suggests that 'evil' here should be better translated from the Hebrew as 'adversity, affliction, bad, calamity' rather than 'evil', and points out that the texts are supposedly directed at peoples whom God was attempting to chide back into the "path of righteousness" (and therefore concludes that there is no contradiction between 1John4:8 and the other two passages).

    I'm not sure that this shows God being good or just, even in that light. It sounds then, that he is threatening to cause adversity and calamity if people don't do what he says. To me, that sounds more like a parent who feels unable to control their children...but then since he made them what they are (unlike, or at least in a more direct sense than, human parents), surely he should know how to control them - if that's what he's trying to do. And if he's not trying to control them, why threaten anything? also argues along similar lines about the misinterpretation of the word, although they do say that '`ra' is used in places to mean moral evil. They point at the literary parallel - light/darkness - shalom/`ra... where shalom is generally translated peace, and is never moral goodness. So we have peace/war? peace/conflict? Again while this avoids the verse implying what it appears to in English, it still does not show a 'just' god, really, does it?

    It all reminds me of the first verse of the Tao Te Ching - without dark there cannot be light/without tall there cannot be short/without good there cannot be bad (paraphrased, but I think those three lines are pretty close). In this light, it would seem that perhaps god has caused there to be peace such that humans could enjoy it, but in doing so he had to cause the antithesis of peace and cause humans to kill each other...

    OK - this is a lot longer than I had anticipated. I will post the other commentaries by AronRa in another entry at another time...

    On reading The Origin of Species (ch4)

    ...but in all cases natural selection will ensure that modifications consequent on other modifications at a different period of life, shall not be in the least degree injurious: for if they became so, they would cause the extinction of the species.

    From other sources I know of the way that some genes can piggyback on the success of others just by being close to them on the genome(?). Now, I know that what Darwin said is generally correct, but I cannot see where he would have got that statistic without also noticing that there are also deleterious inherited effects.

    Natural selection obviously selects for the benefit of the beneficial gene, and not for the piggybacker's deleterious effect. And should the deleterious effect be worse than the beneficial effect, presumably it would be selected against. And of course it is all relative. When the environment provides a niche that selects for a particular benefit the piggybacker's effects are perhaps neutral....until such time as the environmental forces start selecting over the remit of that sort of effect.

    So what am I saying? Just that Darwin wasn't aware of genes and how his theory would get reworded once we understood more about how selection works on genes?

    I'm not sure! I'm just dumping my thoughts onto a post; there is no direction to them (yet?). I would like at some point to summarise everything I've written into a post that is more comprehensive, and perhaps actually has a point to make. For now, bear with the ramblings of my mind.

    Thursday, 8 January 2009

    Noah's daughters

    Let's say that all eight people on the Ark were unrelated. That means that each of them could have carried 2 different alleles for each gene or a total of 16 alleles for the entire population. Since the human genome encompasses up to 59 different alleles for some genes, where did the other 43 alleles come from?

    We have three choices:

    1) There were more than 30 people on the Ark (and therefore the bible is fallible)

    2) The flood didn't cover the entire world and at least 22 other humans survived (and therefore, again, the bible is fallible)

    3) 43 different alleles evolved after the flood.

    (very slightly paraphrased from

    Tuesday, 6 January 2009

    On reading The Origin of Species (p 126)

    The dependency of one organic being on another, as of a parasite on its prey, lies generally between beings remote in the scale of nature. This is often the case with those which may strictly be said to struggle with each other for existence [...] But the struggle almost invariably will be most severe between the individuals of the same species, for they frequent the same districts, require the same food, and are exposed to the same dangers.
    This is the start of the central point of chapter 3 - The Struggle for Existence. He goes on to point out that the struggle between varieties will be almost as severe, and (I am guessing, now, as I have not read much further yet) so decreases as you move further away on the 'tree of life'.

    The struggle for existence has previously in the chapter been demonstrated to be the major check on population; different species competing for the same resources, and particularly how different species which were previously deprived of a share of the resources available by a more successful organism, when that organism is removed, begin to thrive.

    Saturday, 3 January 2009

    Changing from 'school' to 'place for learning'?!

    School title decision questioned

    So they want to call their "school" a "place for learning", because of a "new approach to learning"... My only question is: In what way is a school *not* a "place for learning"?

    On reading The Origin of Species

    p. 110

    Where many species of a genus have been formed through variation, circumstances have been favourable for variation; and hence we might expect that the circumstances would generally be still favourable to variation. On the other hand, if we look at each species as a special act of creation, there is no apparent reason why more varieties should occur in a group haveing many species, than in one having few.
    In other words, and turning the statement on its head somewhat, where the environment (and/or other factors) have allowed an organism to diversify and we find many different varieties, we are more likely to find a greater variety of allied species of the organism than in the opposite case where the environmental factors have not been favourable to the diversification.

    Darwin goes on to make the case for this statement with real-world examples.

    On reading The Origin of Species

    It looks like Darwin was driving at exactly the idea I had had - presumably because I am actually understanding what he's saying!

    From these remarks it will be seen tht I look at the term species, as one arbitrarily given for the sake of convenience to a set of individuals closely resembling each other, and that it does not essentially differ from the term variety, which is given to less distinct and more fluctuating forms. The term variety, again, in comparison with mere individual differences, is also applied arbitrarily, and for mere convenience sake.
    I still have to look up what the advantages of continuing to use this dichotomy (or, as Darwin points out, trichotomy - individual difference, variety, species) is. Convenience is an obvious candidate, as is custom - "we've always done it like this"

    Thursday, 1 January 2009

    Exploring Our Matrix: Keith Ward, Big Questions in Science and Religion 9: Has Science Made Belief in God Obsolete?

    Exploring Our Matrix: Keith Ward, Big Questions in Science and Religion 9: Has Science Made Belief in God Obsolete?

    Some interesting comments on the relationship between science and religion - especially from the book's author, but also by Mr McGrath.

    A couple of excerpts:
    Ward rightly criticizes the explanation of religion in terms of memes, which he calls a "pseudoscience" (p.221). While it may be that ideas are transmitted in a fashion that parallels genetic evolution, it may well be that (as in the case of our vision and our mathematics) our ideas provided survival value because they were correct, beneficial or otherwise useful.
    I don't necessarily disagree that memetics is a pseudo-science, but the comment that the ideas survive because they are beneficial....isn't that precisely what memetics would have to say about them? We select them because they are beneficial or useful - and, like with genetics, take along with them whatever extra baggage might be piggybacking along for the ride?

    ...(2) if the choice is between "a huge number of universes, all of which exist for no particular reason" and a "Supreme Intelligence", one may perhaps be excused for concluding that the latter is "the simpler and more rational hypothesis" (p.235).
    I would perhaps have phrased that as: 'one may perhaps be excused for concluding, or at least wishing that the latter is "the simpler and more rational hypothesis".

    (Not having read Ward's book myself (yet), I'm not sure here whether - particularly in the second excerpt - I'm commenting on Keith Ward's statements, or on James McGrath's interpretation of Ward's statements... So I hope the respective authors will take my comments with that in mind!)

    Is the creationist attack on evolution useful?

    Does it make scientists more careful in what they study?
    Does it highlight the places where the theory could be studied further?
    Or is it just fleabites, annoyances that are nibbling while the scientists are trying to get on with their work?

    On reading The Origin of Species

    Is the distinction between 'species' and 'variety' useful? Does it fuel the macro/micro duality?

    If we formally regard all organisms as 'varieties', then perhaps the macro/micro misunderstanding would be cleared up.

    Darwin notes on p. 105:
    A wide distance between the homes of two doubtful forms leads many naturalists to rank both as distinct species; but what distance, it has been well asked, will suffice? if that between America and Europe is ample, will that between the Continent and the Azores, or Madeira, or the Canaries, or Ireland, be sufficient? It must be admitted that many forms, considered by other highly competent judges as varieties, have so perfectly the character of species that they are ranked by other highly-competent judges as good and true species. But to discuss whether they are rightly called species or varieties, before any definition of these terms has been generally accepted, is vainly to beat the air.

    What are the advantages of the distinction? Of classifying organisms according to genera, phyla, etc? The question perhaps sounds rather vacuous - of course labelling has utility. It allows communication. But what if the act of labelling things is actually causing a perceived either/or duality where none actually exists? What are the alternatives?

    On reading The Origin of Species


    But cases of great difficulty, which I will not here enumerate, sometimesoccur in deciding whether or not to rank one form as a variety of another, even when they are closely connected by intermediate links; nor will the commonly-assumed hybrid nature of the intermediate links always remove the difficulty. In very many cases, however, one form is ranked as a variety of another, not because the intermediate links have actually been found, but because analogy leads the observer to suppose either that they do now somewhere exist, or may formerly have existed; and here a wide door for the entry of doubt and conjecture is opened.

    Darwin seems to have hit the nail on the head, here - this is where much creationist attack appears to stem from. They see all the evidence, but then say "but you're just guessing at the intermediate forms". Of course, we can nowadays compare DNA and the like, which (again) Darwin would have been most glad to have had. However, he goes on, in an effort to allay the problem raised by his last sentence:

    Hence, in determining whether a form should be ranked as a species or a variety, the opinion of naturalists having sound judgement and wide experience seems the only guide to follow. We must, however, in many cases, decide y a majority of naturalists, for few well-marked and well-known varieties can be named which have not been ranked as species by at least some competent judges.

    So...let's have a vote? Perhaps before the advent of being able to use DNA to place an organism on the tree of life by comparing its sequences to others already catalogued, this was indeed the best way. I suppose, in a way, the current strategy is also a majority vote - the majority of biologists agree that this method works as well as, or, in fact, better than, a rather subjective appraisal by a committee of naturalists.